--- MITgcm/doc/tag-index	1998/10/28 03:23:17	1.15
+++ MITgcm/doc/tag-index	2003/01/12 08:20:09	1.53.2.18
@@ -1,8 +1,529 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.15 1998/10/28 03:23:17 cnh Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.53.2.18 2003/01/12 08:20:09 dimitri Exp $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+release1_??? (not taged yet)
+o modifications for using pkg/exf with pkg/seaice
+  - improved description of the various forcing configurations
+  - added basic radiation bulk formulae to pkg/exf
+
+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
+
+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
+
+release1_p8
+o verification/natl_box:
+  updating new external_fields_load routine
+o New package: pkg/seaice
+  Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
+  The sea-ice code is based on Hibler (1979-1980).
+  Two sea-ice dynamic solvers, ADI and LSR, are included.
+  In addition to computing prognostic sea-ice variables and diagnosing 
+  the forcing/external data fields that drive the ocean model, 
+  SEAICE_MODEL also sets theta to the freezing point under sea-ice.
+  The implied surface heat flux is then stored in variable 
+  surfaceTendencyTice, which is needed by KPP package (kpp_calc.F and 
+  kpp_transport_t.F) to diagnose surface buoyancy fluxes and for the 
+  non-local transport term.  Because this call precedes model 
+  thermodynamics, temperature under sea-ice may not be "exactly" at 
+  the freezing point by the time theta is dumped or time-averaged.
+  N.B.: fairly large differences in accuracy occur across
+        different platforms/compilers; comparison between
+        g77 (Linux) and F77 (SGI Origin 2000/MIPSpro) 
+        generated output gives:
+   T           S           U           V
+  C D M    c        m  s        m  s        m  s        m  s
+  n p a R  g  m  m  e  .  m  m  e  .  m  m  e  .  m  m  e  .
+  f n k u  2  i  a  a  d  i  a  a  d  i  a  a  d  i  a  a  d
+  g d e n  d  n  x  n  .  n  x  n  .  n  x  n  .  n  x  n  .
+
+  Y Y Y Y  5  5  7  7  7  8 10  9  6  6  6  6  7  5  7  5  7 FAIL  lab_sea
+
+
+release1_p7
+o GAD: 
+  - generated new common blocks to account for call of
+    same gad routines with differing traceridentities
+    (needed to modify tracerIdentity indices in GAD.h)
+  - generated separate common blocks for case useCubedSphereExchange
+    (Department of Futurology)
+  - parameter lists to gmredi_?transport: added tracerIdentity
+  - added new key indices to tamc.h
+o external_fields_load:
+  - added this routine to TAF list
+  - needed to make some common blocks global and additional storing
+    along the same lines as exf package (checkpoint_lev?_directives.h)
+o exf:
+  updated external forcing package
+  - bug fixes carried over from ecco-branch
+    (missing OBCS_OPTIONS.h in two routines)
+  - enable easy to use "no forcing".
+  - added exf I/O for atmospheric loading
+  - added exf I/O for runoff data
+  - transfered scaling between exf <-> MITgcm to exf namelist
+o Adding new verification experiment global_with_exf.
+  This verification experiment is almost identical to the
+  global_ocean.90x40x15 experiment, except that it uses
+  the exf (and cal) package instead of the
+  external_fields_load routine (cf README file).
+
+release1_p6
+o fixed the verification/global_ocean.90x40x15 experiment:
+ - new bathymetry (the world according to A., JMC, and M.)
+ - new initial fields and forcing fields (*.bin files)
+ - new POLY3.COEFFS (for the next release one should switch to a full
+   equation of state)
+ - fixed several errors and redundancies in the data file
+ - experiment uses looped cells
+ - added matlab directory with diagnostic scripts for plotting of output
+
+release1_p5
+o import recent fix from MAIN branch:
+  - use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
+  - change phiMin in exp1 (to agree with documentation)
+ from checkpoint45 to checkpoint45a_post:
+  - specific exchange for X-slice domain (case Ny=1)
+  - argument futureIter of S/R obcs_calc missing in 
+    exp4 & internal_wave /code
+  - solve_for_pressure : set cg2d_x to zero where OBCS are applied
+ from checkpoint44f_post to checkpoint44g_post:
+  - fix surface correction term in multiDimAdvection
+    (affects plume_on_slope results
+o bug fix in packages_readparms (missing ALLOW_CALENDAR)
+o bug fix in CG2D.h (correct array size for LETS_MAKE_JAM
+o Adjoint-related bug fixes in kpp:
+  - kpp_calc: sore of kpphbl avoids recomputation/call to S/R kppmix
+  - kpp_routines: store of Rib avoids partial recomputation bug of TAF.
+o added Eliassen-Palm flux hooks (dynamics,ini_fields)
+o removed unused TAF keys iikey, idkey (dynamics,thermodynamics)
+o flow directives:
+  - new for S/R do_the_model_io
+  - enhanced for S/R checkpoint
+o added Eliassen Palm flux controls to gradient check package
+o new ctrl package
+  - adopted from ECCO environment to enable optimization
+  - added Eliassen Palm fluxes to controls
+  - adjusted global_ocean.90x40x15/ and carbon/ accordingly
+
+release1_p4
+o Removed f90 comments ("!")
+o Modified initialisations to enable exf package for MITgcm
+  (without invoking ECCO_PACKAGE).
+o modifications to gradient check package (Martin Losch)
+  - enable centered differences
+  - modified format of standard output
+
+release1_p3
+o added tangent linear setup to verification/carbon/
+o added adjoint sensitivity setup to verification/global_ocean...
+o moved packages_init_variables before convective_adjustment
+o output of verif. which use GMRedi brought up-to-date with
+  MAIN trunk (those were re-created after changes in GMRedi)
+o included CPP option SINGLE_LAYER_MODE
+  to configure barotropic setup (Martin Losch).
+o Removed auxiliary variable in impldiff
+  (caused numerical differences with MAIN trunk routine).
+o Introduced CPP option ALLOW_AUTODIFF_MONITOR to
+  disable adcommon.h/g_common.h by default.
+o Cleaned exchange calls in cg2d.
+
+release1_p2
+o fixed array boundary problem for adjoint
+  (related to partial recomputation within subroutine
+  related to dynamics -> calc_viscosity -> mom_...
+o fixed recomputation in thermodynamics
+o prepare (but not complete) recomputation problem in impldiff
+o fixed problem for adjoint of global_max
+o switched off sponge layer code in external_forcing
+
+release1_p1
+o merged necessary patches:
+  - AD-related changes for GMRedi
+  - fixes i KPP (delZ -> drF)
+  - hook to OBCS songe layer code in external_forcing
+  - errorMessageUnit non-zero in eeboot.F
+  - modified test cost function and carbon verif.
+
+release1_chkpt44d_post = chkpt44d_post 
+
+chkpt44d_pre,post
+o added missing EXCLUDE_MONITOR flags
+o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
+  (incompatible typ in MIN/MAX expressions caused problems
+  on IBM SP3)
+o in genmake added variable MAKEDEPEND
+  plus resetting for case SunOS
+o added timer_stats.c routine for IBM SP3
+o removed variables in dynamics
+
+o real fresh water flux implemented with non-linear free-surface.
+
+chkpt44c_pre,post
+o few fix (mask in shap_s2, EmPmR in external_field_load, 
+  USE_NATURAL_BCS in solve_for_P); 
+o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
+
+checkpoint44b_pre/_post
+o merge of relevant stuff from the ecco-branch:
+  - genmake: removed $S64 overwrite for case SunOS
+  - pkg/exf: update and corrections for field swapping and obcs
+  - pkg/ecco: parameter lists for the_model_main, the_main_loop
+              harmonized between ECCO and MITgcm
+  - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
+                  updated checkpointing_lev... lists for obcs
+  - model/src: minor changes in forward_step, plot_field
+               added directive for divided adjoint in the_main_loop
+  - pkg/mdsio: added mdsio_gl_slice
+
+o check parameters & config (chkpt44a_pre,post)
+o OBC and NonLin_FrSurf.
+
+checkpoint44
+o fix bug in mom_vi_del2uv
+o select when filters are applied ; add options to zonal_filter (data.zonfilt)
+o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
+o update AIM experiments (NCEP input files)
+o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
+o added some stuff for AD
+
+checkpoint43
+o added two new advection tests
+o added global 4x4 degree ocean test
+o added test of H&S94 with free surface on cube
+o some final mods for gradient check, adjoint,...
+
+checkpoint42
+  Fixed AD-related problems:
+o Store directives up-to-date with re-arranged Adams-Bashforth
+  (mainly thermodynamics.F)
+o New store directives for multi-dim. advection schemes
+  * new CPP flag ALLOW_MULTI_DIM_ADVECTION
+  * new common block and key passkey
+  (mainly gad_advection.F)
+o Modified store directives for split of dynamics/thermodynamics
+  for the case ALLOW_KPP
+o Cleaned argument list for timestep_tracer.F
+
+checkpoint41
+o re-formatted/added comments in prologues of key subroutines
+  to work with protex
+
+checkpoint40
+o moved calc_gs, calc_gt and calc_tr1 back to model/src
+o added FLT (floats) package from Arne along with demo. experiment
+o re-arranged Adams-Bashforth scheme for tracers to allow easier
+  implementation of forward-in-time forcing terms
+o more mods for non-linear free-surface including new variable
+o modified multi-dim method to work on cube
+o bug fix in KPP (from DM)
+
+checkpoint40pre9
+o added DST advection schemes
+o fix MPI bug on SGI's
+o modifications for non-linear free-surface
+o fixed conditionals for fixed flow/passive tracer only mode
+o added tension/strain form of stress tensor
+o changes to commenting of arguments for TAF/TAMC
+o added/updated many matlab scripts
+o added multi-dimensional advection method for tracers
+  
+checkpoint40pre8
+o new package rw/
+  Added method for dumping intermediate local arrays:
+  mdsio_writetile - same as mdsio_writefield except works from inside
+                    bi,bj loop
+  mdsio_writelocal - same as mdsio_writetile except works for local
+                     arrays
+  write_local_r? - higher-level wrapper for mdsio_writelocal
+  Controlled by diagFreq. Defaults to zero (ie. no dumps)
+  Example given at end of mom_vecinv.F that dumps some local arrays.
+o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
+  control flux-form versus vector invariant code.
+  Switch is runtime flag vectorInvariantMomentum (defaults to false)
+  or genmake -DISABLE ...
+o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
+  (additional storing is now needed for case vecinv;
+  currently nothing implemented to switch this storing off
+  in case fluxform is used since no CPP flag available).
+
+checkpoint40pre7
+o bug fix in dynamics.F
+  calc_viscosity called before k=1,Nr loop.
+o added some #ifdef's ALLOW_PASSIVE_TRACER
+o cleaned initialisations in ctrl_map_ini
+  related to TAF
+
+checkpoint40pre6
+o split dynamics into thermodynamics & dynamics
+o corresponding split of calc_diffusivity into
+  calc_diffusivity, calc_viscosity
+  (kpp_calc_diff, kpp_calc_visc).
+o Added diffkr, kapgm to control variables
+o bug fix in gmredi_slope_limit for ldd97
+
+checkpoint40pre5
+o proper initialization of Adams-Bashforth time stepping
+  + uses forward step for very first step of model (iter=0)
+o re-generated *all* output since almost all output is modified by this
+  change (sorry but we've been putting this one off for about 2 years)
+  + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
+    *not* regenerated since they are already out of date and I don't
+    want to create the impression that they are suddenly working.
+o removed KAP stuff for DEC's
+o modified/added many .cvsignore files in */code and */input
+o added new expt "solid-body.cs-32x32x1"
+  + this uses an alternative form of ini_curvilinear_grid.F which
+    is not necessarily any better than the current one...
+
+checkpoint40pre4
+o added re-initialisations of utrans,vtrans,rtrans in
+  calc_common_factors which are crucial for TAF.
+o extended iMin,jMin range for calc_common_factors,
+  calc_diffusivity
+o added option ALLOW_PASSIVE_TRACER
+o a few minor updates and fixes
+
+checkpoint40pre3
+o created calc_gtr1.F for gad package
+o split the_main_loop and re-introduced forward_step
+o some recomputations of nIter0 for TAMC
+
+checkpoint40pre2
+o Updated to latest branch of AJA, JMC
+o Added gradient check package
+o Added routines for passive tracer handling
+o Added carbon sequestration sensitivity experiment
+
+checkpoint39
+ o Modifications and fixes to support TAMC
+   (mainly missing or wrong directives)
+ o Corrected common blocks when fooling TAMC to produce adjoint I/O
+   in addummy_in_stepping
+ o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
+ o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
+ o Included following packages:
+   cal: calendar
+   exf: external forcing
+   ecco: essential routines to control use of cal, exf
+         (NB: this is not the full ECCO environment)
+ o disabled some packages by default in genmake
+
+checkpoint38
+ o see notes_c37_adj.txt
+ o corrected wrong layer index in external_forcing_t
+ o replaced the_main_loop/forward_step by the_main_loop
+ o removed forceoutput from write_state
+   (replaced criteria for initial/final state)
+ o added runtime flag for pre-C35 pickups: usePickupBeforeC35
+
+checkpoint37
+ o mdsio.F routine split and packaged in pkg/mdsio
+   (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
+    used unless genmake -disable=mdsio)
+ o allow a more precise surface-geopotential gradient for the atmosphere
+   taking into account the change in space of Alpha (=1/rho) at the surface.
+ o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
+   (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
+ o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
+   Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
+   [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
+ o Time-Average diagnostics defined as a pseudo package "timeave".
+ o pickup files : old pickup (before c35) did not work with new code (c35
+   and after) unless activating 2 commented lines in initialise-varia.
+ o Non-Hydrostatic pickup file Pb fixed.
+ o bug with Rigid-lid version (since c35) fixed.  
+
+checkpoint36
+ o implement Crank-Nickelson barotropic time-stepping
+ o recover Time-Average diagnostics
+ o fix Pb in checkpoint (PR#19) 
+ o AIM become a standard package ; clean unused CPP_kees
+
+checkpoint35
+ o subtantial rewrite of dynamics.f
+ o allows staggered time-stepping
+ o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
+ o added bottom drag (linear + quadratic)
+
+checkpoint34
+ o Modified exchange routines for correct reverse simulation.
+ o Added verification output to comply with bug fix in impldiff.F
+   as of c33 (exp2, natl_box).
+ o Corrected store directives in dynamics.F
+ o Corrected array boundaries in impldiff.F
+ o Corrected array dimensions in gmredi.
+   Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
+ o Added routine GLOBAL_SUM_INT to global_sum.F
+ o Added mdsio_gl.F for ECCO purposes.
+
+checkpoint33
+ o Fixed bug in lower BC in impldiff.F
+ o Fixed confusion about units of forcing arrays in FFIELDS.h
+   namely Fu,Fv,Qnet,Qsw,EmPmR:
+   - Removed verification/natl_box/code/external_fields_scale.F
+     (did not differ from that in model/src)
+   - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
+     (see FFIELDS.h for description)
+   - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
+     kpp_calc.F and kpp_transport_t.F
+   - Removed model/src/external_fields_scale.F and calls to it
+   - verification/natl_box uses flux data with "atmospheric" sign so
+     a special version of external_fields_load.F is used to
+     change the data as it's read in. This way, the arrays
+     have the right units and signs at all times tha a user could
+     possibly use them.
+ o Corrected genmake to delete a temporary file during configuration
+
+checkpoint32
+ o Scaling of forcing fields moved from external_forcing.F to
+   external_fields_scale.F, called directly after loading fields.
+ o Surface relaxation terms added to surface tendency fields in
+   extra subroutine.
+ o impldiff.F changed to avoid storing by TAMC of huge intermediate
+   fields.
+ o Changes in GMRedi to comply with packaging structure.
+ o Modifications and bug fixes in KPP package.
+ o Verification experiment for KPP added (verification/nat_box/)
+
+checkpoint31
+ o Packages interface brought in line with defined standard
+   -> new routines packages_...F
+   -> changes in initialise_fixed.F, initialise_varia.F
+   -> enables initialisation interface for ECCO package
+ o Rescaling of external forcing fields immediately after read
+   (removed from external_forcing.F) 
+   -> new: surface_fields_scale.F
+   -> affects ini_foorcing.F, external_fields_load.F
+ o Computation of surface tendencies before tendency updates.
+   -> new: external_forcing_surf.F
+ o Change of variable names useGMRedi, useKPP, useECCO
+ o Further changes in dynamics.F, impldiff.F for TAMC
+ o Tested for experiments 0, 2, 4.
+   - not yet tested for GMRedi.
+   - not yet tested for KPP.
+
+checkpoint30
+ o Updates for OBCs
+ o New experiment for test OBCs (internal_wave)
+ o New output.txt in verification/exp4/results/
+ o Updates for KPP: calculation of viscosity corrected, new variables
+   kpp_dumpFreq and kpp_taveFreq
+ o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
+   and entry for T90 in genmake
+
+checkpoint29
+ o packaged KPP and GM/Redi
+
+checkpoint28
+ o Corrected initialization of hFacMin for difference vertical coordinates
+ o Modified calculation of partial cell thickness to more robust algorithm
+ o config_summary.F: replaced write_1D_... by write_0D_...
+   read_write.F: added subroutines write_0D_...
+ o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
+   included some initialisations required for TAMC.
+ o routine calc_isoslopes: modified sqrt computation to make it 
+   differentiable for zero argument.
+ o routines dynamics, impldiff:
+   included store directives and tape key computations required for TAMC.
+ o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
+
+checkpoint27
+ o fixed calc_isoslopes() to so that cancellation of terms in tensor
+   formulation works properly with variable resolution.
+ o restructured the calling tree between the_model_main() and dynamics()
+ o split initialise() into initialise_fixed() and initialise_varia()
+ o introduced initialization file pSurfInitFile for free surface (cg2d_x)
+   in new routine ini_psurf()
+
+checkpoint26
+ o moved some #ifdef in optional routines to encompass everything
+   except the argument declarations. This was using up some memory.
+ o fixed macros like _ADT to work with both versions of Linux cpp
+ o cleaned up some unused and uninitialized variables
+   (helps when debugging with strict compile options)
+ o split up CPP_EEOPTIONS.h into options and macros
+   (macros are now in eesupp/inc/CPP_EEMACROS.h)
+ o patch for 2 processor JAM mode
+
+checkpoint25
+ o updates for OBCs and NH
+ o dramatically reduced memory usage
+ o added "JAM" routines for use on Artic network
+ o parameterization of convection by implicit vertical diffusion
+ o added a diagnostic of convective index
+ o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
+   (this is was partly for OBCs and NH but also in anticipation of
+    an explicit free-surface option)
+ o initial state input files for U and V
+
+checkpoint24
+ o Removed some spurious "REAL"s
+ o Updated KPP to latest version from JPL
+ o Added a COS(latitude) in horizontal viscosity
+
+checkpoint23
+ o Added del^4 diffusion for salt and temperature
+ o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
+
+checkpoint22
+ o Made many small changes: implicit none, format(i5), etc...
+ o Introduced KPP mixing scheme (compiles and runs but *not* tested)
+
+checkpoint21
+ o Introduced new I/O package that supports direct-access records (mdsio.F)
+ o Split-up mid-level I/O routines
+ o Updated input data for experiments 0,1,2,4 and 5
+ o Finally removed the genmake.* scripts (everyone seems happy with genmake)
+
+checkpoint20
+ o Tidied up open-boundaries some more
+ o Added non-hydrostatic code
+ o Fixed some input data
+ o Modified MPI start-up to work in "coupled" context.
+
+checkpoint19
+ o Tidied up directory structure for verification experiments.
+ o Added new code for open boundaries.
+ o Corrected advective terms near boundaries.
+ o Added CPP flag for "old UV" geometry and corrected spherical geometry.
+ o Implemented free-slip/no-slip BCs and del^4 dissipation.
+ o Split default parameters out of ini_parms.F into set_defaults.F.
+
+checkpoint18
+ o Further changes for optional code generation with 
+   CPP - ugh!
+
+checkpoint17
+ o Beginning to incorporating modularity
+   for supporting atmos. and ocean configs.
+ o Small changes for TAMC complinace
+ o New ultra simple test case. Barotropic box
+   configuration "exp0".
+
 checkpoint16
  o Minor changes to exchange routines to support 
    accumulation in reverse mode. Adjoint of an