--- MITgcm/doc/tag-index	2003/02/26 03:29:08	1.137
+++ MITgcm/doc/tag-index	2003/08/04 22:53:41	1.175
@@ -1,12 +1,239 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.137 2003/02/26 03:29:08 jmc Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.175 2003/08/04 22:53:41 dimitri Exp $
 
     Notes on tags used in MITgcmUV
     ==============================
 
-untagged
+checkpoint51f_post
+o Added on-the-fly spatial interpolation capability
+    "USE_EXF_INTERPOLATION" to pkg/exf.
+    This is a temporary Cartesian-grid hack until
+    the super-duper ESMF coupler becomes available.
+    Usage example is in verification/global_with_exf.
+o Bug fix to pkg/ptracers, pkg/generic_advdiff/gad_calc_rhs.F,
+    and pkg/kpp/kpp_transport_ptr.F for dealing with tracer
+    non-local transport term.
+
+checkpoint51e_post
+o pkg/mom_vecinv: 
+  - changes related to hFac: use S/R from aim.5l_cs/code (coriolis & vort.advec)
+  - add time-ave diagnostic of vorticity advection.
+o add diagnostic (instantaneous) of Shapiro Filter effect for T,S & UV.
+o atmospheric geopotential: - include water vapor effect; 
+                            - use p^kappa in p* scaling.
+o land pkg: read initial state from files.
+o AIM : add stratospheric drag in the upper level
+
+checkpoint51d_post
+o change function ILNBLNK (=> last non-blank char.) to return zero
+  (instead of the string length) when the string. char is empty
+o fix bug in dxV,dyU definition of cubed-sphere grid (ini_curvilinear_grid)
+o modif's to restore TAMC compatibility
+  - avoid "_d" constructs in PARAMETER declarations
+  - avoid interrupting lines by comment lines
+o Use cluster local disks for purely local I/O
+  vs. globally visible disks needed for ctrl stuff
+  (merged from ecco-branch)
+  - new active_file_loc... and mdsio_..._loc routines
+  - affected packages: autodiff, ctrl, grdchk, mdsio
+
+checkpoint51c_post
+o introducing integer flag debugLevel
+  - debLevZero: suppress all output
+  - debLevA: standard
+  - debLevB: equivalent to current debugMode=.TRUE.
+o introducing pathname variable mdsioLocalDir for mdsio
+  that can be specified at runtime
+  (relevant for cluster I/O to local disk)
+`
+>>>checkpoint51b_post
+adjoint of ptracers
+o disentangled ALLOW_PTRACERS using new ALLOW_GCHEM
+o extended state in checkpoint_lev?, etc.
+o alternative ctrl/cost with tr1 or ptracer
+o new comlev1_bibj_ptracers
+o new ptracers.flow
+o made ptracers_forcing same as external_forcing_s
+o added verification for adjoint with ptracers
+  - adm. grdchk fail so far
+  - tlm. grdchk OK
+  - checked tapelev/comlev recomputations: OK
+<<<checkpoint51b_pre
+
+checkpoint51a_post
+o added code for biogeochemistry package
+  - new pkgs: dic, gchem
+  - new subroutine in ptracers
+o modify code for biogeo packages
+  - in model/src and pkg/ptracers
+
+checkpoint51
+o merged improved packages from ecco-branch (ecco_c51_e34) to MAIN
+  - autodiff, ctrl, exf, grdchk, seaice
+  kept separate packages
+  - cost, ecco, obcs
+o updating verification/internal_wave, verification/lab_sea
+  (all verif's pass on faulks.lcs.mit.edu RH7.3, g77)
+
+checkpoint50i_post
+o Preparing next differentiable checkpoint and sync
+  of MAIN vs. ecco-branch
+  - 1st step: this one is differentiable
+  - 2nd step: next(! not this) checkpoint will have updated packages 
+              from ecco-branch)
+
+checkpoint50h_post
+o new package "land": provide surface BC for AIM.
+o pkg/ptracers: apply exchange to all tracers after reading a pickup.
+o AIM: use true log-P extrapolation for near surface temp (= as in 
+    F.Molteni paper) ; update aim.5l_cs output.
+o New variable in PARM03 for more flexible pickups
+o somewhat cleaned package initialisation sequence for
+  ctrl/ cost/ ecco/ in packages_... routines
+
+checkpoint50g_post
+o merged with release1_p17 (pkg/seaice and verification/lab_sea)
+  - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
+  - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
+    made the default because of faster convergence than ADI
+
+checkpoint50f_post
+o exf totally restructured
+  - replaced all exf_set_ routines by one generic exf_set_gen.F
+    and made sure it's still differentiable
+  - split exf_getffields.F into new exf_bulkformulae.F
+  - exf_inscal_/exf_outscal_ suffixes consistent with field names
+  - updated adjoint/makefile and relevant verif. accordingly
+
+checkpoint50f_pre
+ o AIM: near surface temp evaluated from Pot.Temp: fixed for Part Cell ;
+      + change Evap over land. (update aim.5l_cs output)
+ o added missing .cvsignores and made uniform across expts
+ o changed configuration of tidal_basin_2d expt
+ o added pkg/debug functions for tracing code in fatal crashes
+ o tidied pkg/monitor to use MONITOR_OPTIONS.h
+ o new fn in pkg/monitor to stop model if solution grows too big
+ o removed lots of single quotes from comments
+
+checkpoint50e_post
+o make KPP work with PTRACERS
+ - fix gad_calc_rhs to call new routine kpp_transport_ptr, which is
+   nearly a copy of kpp_transport_s
+ - there is no analogue to SurfaceTendencyS, so I have to use 
+   gPtr(of the surface layer) instead
+o add a new platform SunFire+mpi (SunFire 15000) to genmake
+checkpoint50e_pre
+
+checkpoint50d_post
+o change kpp output from multiple-record state files to single-record state 
+  files analogous to write_state.F
+o reduce the output frequency of cg3d-related stuff to the monitor frequency, 
+  analogous to the cg2d-related output. 
+o fix small problem with in ptracers_write_checkpoint.F: len(suff)=512, 
+  so that writing to internal file fn (with length 512) fails.
+checkpoint50d_pre
+
+checkpoint50c_post
+o fix problem in ini_procs.F when using MPI (was there since checkpoint48f)
+o add monitor diagnostic of vorticity (mon_vort3.F) and potential energy.
+o add time-average diagnostic of U*V and vertical diffusive flux for theta.
+o bug fixed in convective adjustment diagnostic (multi-tile set-up).
+o 4th Order Adv scheme: return to previous (c40pre7) masking near boundaries.
+
+checkpoint50c_pre
+Merging from release1_p13:
+o bug fix for pkg/seaice dynamic solver
+o Added SEAICE_initialHEFF to pkg/seaice
+
+checkpoint50b_post
+o store u*,v* in gU,V instead of in guNm1,gvNm1
+o in order to put the momForcing out of the Adams-Bashforth:
+  move forcing & CD-scheme calls from mom_fluxform & mom_vecinv
+  to timestep.F
+o new flag "useCDscheme" (default=F); replace guCD,gvCD by local arrays
+o re-generate output for highly sensitive test-exp:
+   global_ocean_pressure, ideal_2D_oce, lab_sea, natl_box
+
+checkpoint50b_pre
+o restore the use of momAdvection & useCoriolis flags (mom_vecinv)
+o corrected CPP option mismatch in exf_Bulk... functions for case 
+  #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
+
+checkpoint50a_post
+o Bug fix for merging between c50 and KPP.
+  ikey was passed from thermodynamics to kpp_calc via
+  common block rather than being recomputed in kpp_calc,
+  in contradiction with new key itdkey.
+  New key ikppkey created, and tamc.h headers updated.
+
+checkpoint50
+- 2nd step of merge with ecco-branch:
+  merge changes in ecco-branch back into main trunk
+- bug fix in find_alpha
+- more storing in gmredi_calc_tensor.F, kpp_routines.F
+- avoid iterative loop in ini_pressure for ALLOW_AUTODIFF_TAMC
+- merged some sliced AD support routines
+
+checkpoint49
+merged from ecco-branch:
+o exf:
+  - Enable initialisation of forcing fields to constant 
+    (runtime) values.
+  - in exf_getffields.F
+    Reduce i-/j-loop to interior domain, discarding overlaps.
+    That also fixes wrong TAF-key computations for key_1, key_2
+    with bulf formulae.
+  - exf_init.F modify #ifdef for exf_init_evap
+  - exf_getffieldrec.F, ctrl_getrec.F
+    The following INT-usages are not safe:
+      fldsecs  = int(fldsecs/fldperiod)*fldperiod
+      fldcount = int(fldsecs/fldperiod) + 1
+    and were modified.
+o autodiff: checkpoint_lev...
+  - updated storing for bulk formulae (some arrays were missing)
+  - added state for seaice package
+  - synchronized with main branch
+o DIVA:
+  Modif.s in
+  - the_main_loop.F
+  - the_model_main.F
+  and added cost_final_restore.F cost_final_store.F
+  o With these changes, it is possible to fully separate
+    the first forward run to compute the cost function (mdthe_main_loop)
+    and adjoint runs over individual DIVA intervals (adthe_main_loop)
+    into separate model executions.
+    This enables better tuning of DIVA to given queue sizes.
+  o Loss of cost function value in consecutive DIVA runs is
+    fixed by storing to 'costfinal' file.
+  o Appropriate call of ctrl_unpack/_pack,grdchk_main at 
+    beginning/end of adjoint integration is accounted for.
+  The current changes apply to TAF-1.4.26.
+  TAF has one remaining bug, requiring one manual change
+  (see MITgcm manual).
+o cal: synchronized between MAIN and ecco-branch
+
+checkpoint48i_post
+o Changes to restore differentiability of code w.r.t. previous tag
+  (mostly adding new routines to make list and replacing
+  pressure by totPhiHyd).
+o Updated and merged grdchk package
+  - has both ADM and TLM checks
+  - works for single- and multi-proc.
+  - output cleaned
+  - worked successfully for parallel DIVA
+o genmake:
+  - Adding -platform=SP4
+  - Modif. for DEC Alpha (many don't have makedepend; use mkdep instead).
+o Modif. for DIVA:
+  ctrl_unpack should not be called in intermediate DIVA interval.
+  (similar thing would apply for active files such as
+  tbar, sbar, psbar, which should not be reinitialised;
+  only relevant for ecco-branch)
+
+checkpoint48h_post
 o improve "ini_p_ground" when using finite difference form for calc_phi_hyd
 o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
 o Added SEAICE_initialHEFF to pkg/seaice
+o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
 
 checkpoint48g_post
 --- EOS: