Start j2c fresh on 101006 following instructions in
http://www-d0.fnal.gov/Run2Physics/ckm/d0_private/bgv/aa/stand_alone_root.htm
-----------------------------------------------------------------------------

mkdir Jpsi_phi
cd Jpsi_phi
setup D0RunII p16.05.02
kinit -f

do only once:

setup d0cvs
cvs co AATrack              # always use the head version from CVS!
ln -fs /d0dist/dist/packages/CLHEP/R-04-09-15 AA/CLHEP #new step
AATrack/script/init.sh      # puts all stand alone AA code in Jpsi_phi

Jpsi_phi/j2c.cpp is my driving program for the root analysis

To put my code in Jpsi_phi:
tar xvf j2c_111006.tar     # or whatever the latest date is

To compile the program, do:

setup D0RunII p16.05.02         (Obviously, it needs to be done only once per session)
touch j2c.cpp     (so compiler thinks it has to be recompiled)
AATrack/script/makeSelf.sh j2c (Should be done each time when you modify your program)

#this example creates the list of files to process and then runs:

ls /prj_root/1008/ckm_write/bgv/data/muinc/f14.03.00_03010131/* > files
AA/exe/j2c files

To process events using event lists:

#This example uses the event list of B->mu D* X events
cp /prj_root/1008/ckm_write/bgv/evt/muDstar-std/f14.03-1 elist
AA/exe/j2c elist

To submit:

cluesow -l cput=35:00:00 -l mem=500M rsubmit.sh 

IT ALL WORKED!

To make a tar file of everything I use for the B^0_s -> Jpsi phi analysis:

tar cvf j2c_111006.tar README.txt Makefile rsubmit.sh j2c.cpp BH_*.cpp BH_*.hpp\
 LOG_jpsi_phi_131006.txt


**************************************************************************
Muon variables: AA/src/Muo.hpp
Track variables: AA/src/Ptl.hpp
Example of looping through muons: AA/phy/selectMuo.cpp
Information on bana: http://www-d0.fnal.gov/Run2Physics/ckm/d0_private/bgv/aa/links.htm
Accessing solpol and torpol: see AA/src/Field.cpp
Example of looping through muons: AA/phy/selectMuo.cpp
How to access primary vertex: Ptl.hpp, Ptl.cpp

**************************************************************************
      myMuonCand1.pt = ptl1->pt();
      myMuonCand1.phi = 0.0;
      myMuonCand1.eta = ptl1->eta();
      myMuonCand1.ptot = ptl1->ptot();
      myMuonCand1.q = ptl1->q();
      myMuonCand1.ip1 = ptl1->imp(1);
      myMuonCand1.ip2 = ptl1->imp(2);
      myMuonCand1.nCFT = ptl1->nCFT();
      myMuonCand1.nSMT = ptl1->nSMT();
      myMuonCand1.vip1 = ptl1->vimp(1,1);
      myMuonCand1.vip2 = ptl1->vimp(2,2);
      myMuonCand1.nseg = pmu1->nseg();
AA.cpp:   if(fabs(imp(1))>0.2) ok = false;
AA.cpp:   if(fabs(imp(1))>0.2) ok = false;
AA.cpp:   if(fabs(imp(2)-xv(3)) < 0.1 && countPV > 0) ok = false;
So it apears that imp(1) is the impact parameter of the track with respect
to the beam in cm, while imp(2) is the z of closest aproach to the beam. (?)
********************************************************
In main:

bookHist()

calls bookHistROOT()

defines bFile j2c.root
and bTree bTree.

selectJ2c()

loops over Jpsi, if(mjpsi<2.80 || mjpsi>3.35) continue,
ptl1 and ptl2 are the two muons,
loops over pairs of tracks (excluding the two muons)
(all have pT > 0.4, > 2 SMT hits, opposite charge, 
all 4 tracks from same vertex vrt,  
find primary vertex pv,
combine ptl3 and ptl4 into one particle jkst,
obtain mass asuming mjkpi1, mjkpi2, mjkk, mjpipi,
isolation: pT of other particles with dR < 0.5 = sum,
iso = jkst.ptot()/(jkst.ptot() + sum),
particles from B: lstTag = ptl1, ptl2, ptl3, ptl4
tag returns d: 
  sign of d gives the sign of flavor
  larger |d| correspond to a better flavor tag
selection of Bs->J/psi phi.

*************************
Includes:

BH_functions.cpp // in j2c.cpp: defines functions used by BH
BH_instantiate_histos.hpp // instantiates histos and counters
BH_initialize_histos.cpp // in main before loop: initializes histos and counters
BH_fill_histos.cpp // in selectJ2c: fills histos and updates counters
BH_write_histos.cpp // in saveHist: writes histos and counters