--- MITgcm/doc/tag-index	2002/12/02 13:28:30	1.107
+++ MITgcm/doc/tag-index	2003/10/09 04:19:17	1.184
@@ -1,8 +1,478 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.107 2002/12/02 13:28:30 cheisey Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.184 2003/10/09 04:19:17 edhill Exp $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+checkpoint51i_post
+o merge of the branch-genmake2
+  - knowingly breaks the older genmake
+  - automatic generation of all ALLOW_${PKG_NAME} defines
+  - new testreport supersedes older testscript
+o large number of package inclusion and header cleanups
+checkpoint51i_pre
+
+o new output for adjoin of global ocean vector invariant
+o fix for checkpoint of thermodynamic seaice and bulk_force
+o Steph gchem various cleanups
+
+checkpoint 51h_pre
+o fixed some single quotes
+o modify gchem pkg to be more versatile
+o modifications to clean up dic pkg
+o add pkg/cfc
+
+checkpoint51g_post
+o provide links for ARPACK and ADM*TLM
+o start removing verification/vero/
+o update AD-related stuff
+  (in particular some IF-statements in model/src/ routines)
+o adding to verification/global_ocean.90x40x15/ adjoint of
+  vector invariant setup
+
+checkpoint51f_post
+o update advect_xz/output.txt (left from chekpoint50f_pre, ini_vel modif)
+o Mods and bug fixes to pkg/cal, pkg/exf, etc., needed for computation
+  of tracer Green's fucntions for ocean inversion project.
+
+checkpoint51f_pre
+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.
+  - See verification/global_with_exf/README for usage example.
+  - Removed obsolete EXFwindOnBgrid and SEAICEwindOnCgrid
+    flags and modified pkg/seaice accordingly.
+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:
+o compute locally the pressure for use in EOS: UNESCO, JMD95P, MDJWF
+  store total Potential in totPhyHyd for diagnostics & EOS.
+o fix restart and overlap Pb when using Z-coord and EOS funct. of P
+--- Pressure/geopotential gradient:
+o use Ro_surf & R_low instead of hFac in cal_phi_hyd:
+o NLFS + p-coord.: eta*Alpha' is not longer lagging 1.time-step behind
+  ( changes results of global_ocean_pressure )
+o NLFS + z-coord.: add eta*Rho' contribution.
+o accurate phiHyd when using interface-W at the middle between 2 centers
+ ( changes results of ideal_2D_oce )
+o includes r* 2nd term in potential gradient.
+
+checkpoint48f_post
+Merging from release1_p12:
+o Modifications for using pkg/exf with pkg/seaice
+  - improved description of the various forcing configurations
+  - added basic radiation bulk formulae to pkg/exf
+  - units/sign fix for evap computation in exf_getffields.F
+  - updated verification/global_with_exf/results/output.txt
+o Added pkg/sbo for computing IERS Special Bureau for the Oceans
+  (SBO) core products, including oceanic mass, center-of-mass,
+  angular, and bottom pressure (see pkg/sbo/README.sbo).
+o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F
+  to avoid negative values in shallow regions.
+  - updated verification/natl_box/results/output.txt
+  - updated verification/lab_sea/results/output.txt
+o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F
+o Added useSingleCpuIO option (see PARAMS.h).
+o Updated useSingleCpuIO option in mdsio_writefield.F to
+  work with multi-field files, e.g., for single-file pickup.
+o pkg/seaice:
+  - bug fix in growth.F: QNET for no shortwave case
+  - added HeffFile for specifying initial sea-ice thickness
+  - changed SEAICE_EXTERNAL_FLUXES wind stress implementation
+o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
+  kpp_transport_t.F, forward_step.F, and the_main_loop.F
+o pkg/seaice:
+  - adjoint-friendly modifications
+  - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
+
+checkpoint48e_post
+o New S/R for diagnostic of bottom pressure (phi0surf was missing in c48d_post)
+o dynamics: change definition of computational domain & adapt mom_fluxform
+  accordingly ; when viscA4=0, allows to run the dynamics with Olx=Oly=2. 
+o following exp works with Olx=Oly=2 (and pass through checkbounds option):
+    adjust_nlfs.cs-32x32x1 adjustment.128x64x1 adjustment.cs-32x32x1
+    exp0 exp1 exp2 exp4 exp5 hs94.cs-32x32x5 hs94.128x64x5 hs94.1x64x5
+    global_ocean.90x40x15 global_with_exf global_ocean_pressure 
+    inverted_barometer solid-body.cs-32x32x1
+  (high order AdvScheme and/or multiDimAd works with Olx=Oly=2 ? not sure)
+
+checkpoint48d_post
+o in preparation for r*:
+ a) use pre-computed gradient of hydrostatic potential:
+    changes in timestep.F & mom_cdscheme.F affects results of ideal_2D_oce
+ b) move phi0surf from calc_phi_hyd to calc_grad_phi_hyd:
+    => affects results of glob_oce_pressure (different truncation error)  
+  update output.txt of ideal_2D_oce & global_ocean_pressure
+
+checkpoint48d_pre
+o in preparation for r*:
+  new S/R (calc_grad_phi_hyd.F) to compute Hydrostatic potential gradient.
+  pass the 2 comp. of the grad. as arguments to momentum S/R.
+  but for the moment, only used if it does not change the results. 
+o add finite volume form of calc_phi_hyd for buoyancyRelation OCEANIC & OCEANICP
+
+checkpoint48c_post
+Modifications in treatment of initial flux forcing controls
+to avoid extra storing of flux fields.
+
+checkpoint48c_pre
+o Added tidal_basin_2d experiment (currently 1D!)
+o can use r* Coordinate with OBC (but Orlanski Rad. BC not yet implemented) 
+
+checkpoint48b_post
+o r* coordinate added in #ifdef NONLIN_FRSURF block.
+ (modification to pressure gradient not yet implemented)
+o mom_fluxform: new S/R mom_calc_rtrans.F computes vertical transports
+  (for U & V) that are used for vertical advection of momentum.
+
+checkpoint48a_post
+o In preparation for r*, use temp. array to compute vertical transport
+   in flux-form momentum pkg. => change results of few test-exp. 
+  Update output of: exp4, exp5, front_relax, global_ocean_pressure, 
+                    lab_sea, natl_box & plume_on_slope
+
+checkpoint48
+o fix small bug that was causing lot of warning (TIMER_STOP 'UPDATE_CG2D')
+
+checkpoint47j_post
+o add new exp. (ideal_2D_oce) to test "exotic" parameters and options.
+o moved adexch from forward_step to addummy_in_stepping
+o added exch in ctrl_map_...
+o aveFreq.=0. at end of cost_final to avoid overwrite in
+  reverse checkpointing loop
+o Yet more changes in gmredi:
+  * adgmredi_calc_tensor
+    avoiding all recomputation of gmredi_slope_limit
+  * adgmredi_x/y/rtransport
+    added flag for excessive storing to avoid recomp. of
+    u/v/rtans, dTdx/y/z
+    -> this is not really necessary and very memory-consuming
+  * adgmredi_slope_psi:
+    consistency with gmredi_slope_limit in treatment of GM_slopeSqCutoff
+  * gmredi_slope_limit
+    re-activated full calculation of taperfct for case 'ac02'
+o updating verification/ adjoints of carbon, global_ocean.90x40x15
+
+checkpoint47i_post
+o GM_EXCLUDE_() replace GM_TAPER_(): by default, all the code is compiled.
+o add GM_Small_Number & GM_slopeSqCutoff as run-time parameters (data.gmredi)
+  default values = 1.D-12 & 1.D+48 (=> give same results as checkpoint47f_post)
+o cg2dTargetResWunit: define tolerance using deltaTmom (and not deltaTfreesurf) 
+o gmredi: fix few bugs.
+
+checkpoint47h_post (duplicate tag for PH's c48 tag, in order to move c48)
+This will be a good checkpoint to plug into the ecco-branch.
+o few modif.'s to get latest version adjointed
+  (mainly kick out code in ini_linear_phisurf)
+o modif's to run adjoint with exactConserv
+o case GM_BOLUS_ADVEC should be cleaned
+  S/R gmredi_slope_psi should be cleaned
+o verification/carbon now has exactConserv=.TRUE.
+
+checkpoint47g_post
+o time-average AIM output: becomes independent from statvars time-average
+  (can be used with #undef ALLOW_TIMEAVE) ; add new variables (e.g., RH)
+o After TAF bug fix:
+  Tested adjoint of gmredi package.
+  Tests were done with checkpoint47 rather than with latest
+  checkpoint47f_post since the latter is broken for the adjoint
+  verification/carbon/ contains both ADM and TLM gradient checks.
+Here they are, before they get changed/lost/stolen.
+Mostly modif.'s to fix numerical sensitivities.
+Gradient checks OK for
+- GM_taper_scheme:
+  * clipping
+  * ac02
+  * linear
+  * glw91
+  * dm95
+  * ldd97
+- GMREDI_OPTIONS:
+  * GM_VISBECK_VARIABLE_K
+  * GM_NON_UNITY_DIAGONAL
+  * GM_EXTRA_DIAGONAL
+  * GM_BOLUS_ADVEC
+in conjunction with data.gmredi parameters to be checked in
+in a few minutes under verification/carbon/code/
+
+checkpoint47f_post
+Merging from release1_p10:
+o modifications for using pkg/exf with pkg/seaice
+  - pkg/seaice CPP options SEAICE_EXTERNAL_FORCING
+    and SEAICE_EXTERNAL_FLUXES
+  - pkg/exf CPP options EXF_READ_EVAP and
+    EXF_NO_BULK_COMPUTATIONS
+  - usage examples are Experiments 8 and 9 in
+    verification/lab_sea/README
+  - verification/lab_sea default experiment now uses
+    pkg/gmredi, pkg/kpp, pkg/seaice, and pkg/exf
+
+checkpoint47e_post
+o created a tag prior to creating a branch
+
+checkpoint47d_post
+o fixed bug in the oceanic pressure coordinates code: vertical viscosity 
+  at the bottom boundary had an erroneous half slip boundary condition
+o added bottom drag and no slip boundary condition capabilities to 
+  oceanic pressure coordinates code
+o added new verification experiment global_ocean_pressure, this experiment is
+  also described in the tutorial section of the manual
+checkpoint47d_pre
+
+checkpoint47c_post
+o Added a verification experiment for a global cubed-sphere ocean run
+  -  verification/global_ocean.cubed32x32x30
+  -  uses pkg/therm_seaice and pkg/bulk_forcing
+
+o allow to run AIM physics with SPEEDY input files (from Franco Molteni)
+o allow a more accurate definition of Ro_Surf (selectFindRoSurf=1)
+  when using P-coordinate; only implemented for atmospheric config.
+o OCEANICP & realFreshWater: include P-E direct effect on wVel ;
+  NOTES: requires option NONLIN_FRSURF to be "#define".
+o update advect_xz/results/output.txt (left from checkpoint44g_post)
+
+checkpoint47b_post
+Merging from release1_p9:
+o pkg/seaice
+  - removed GOTO's and added taf directives
+  - double precision constants to reduce the g77 (Linux)
+    to F77 (SGI) differences reported in release1_p8
+o tools/genmake
+  - added SGI options
+o verification/testscript
+  - updated to that of checkpoint47a_post
+o verification/global_ocean.90x40x15/input/eedata
+  - modified for SGI f77 compatibility
+o verification/lab_sea
+  - added description of sea-ice model
+  - added missing matlab routines
+  - added test of thermodynamics parallelization
+
 checkpoint47a_post
 o new pkg: aim_v23 
  = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm.