--- MITgcm/doc/tag-index	2001/07/30 20:47:52	1.43
+++ MITgcm/doc/tag-index	2002/12/02 13:28:30	1.107
@@ -1,8 +1,507 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.43 2001/07/30 20:47:52 heimbach Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.107 2002/12/02 13:28:30 cheisey Exp $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+checkpoint47a_post
+o new pkg: aim_v23 
+ = F. Molteni atmos.physics (SPEEDY, ver23) adapted to MITgcm. 
+   for now, keep the same surface forcing as before.
+ - Part-Cell implemented into AIM; check that Heat & Water are conserved
+ - aim.5l_cs: use new aim pkg (run 10yr & get better results than before)
+ - aim.5l_LatLon & aim.5l_Equatorial_Channel are still using old aim pkg
+o add diagnostic of surface correction term in monitor output
+
+o bulk_force and therm_seaice 
+- Two packages:  bulk_force (Bulk forcing)
+  and therm_seaice (thermodynamic_seaice) - adopted from LANL CICE.v2.0.2
+- Earlier integration from Stephaine Dutkiewicz
+  and Patrick Heimbach.
+- Two ifdef statements for compile time,
+   ALLOW_THERM_SEAICE and ALLOW_BULK_FORCE
+
+checkpoint47
+differentiable version of checkpoint46n_post
+o bug fix in quasihydrostaticterms
+o * "clean" adjoint code (in terms of extensive recomputations)
+    can now be obtained for all GMREDI options (i.e. for 
+    - GM_VISBECK_VARIABLE_K
+    - GM_NON_UNITY_DIAGONAL
+    - GM_EXTRA_DIAGONAL
+    - GM_BOLUS_ADVEC )
+  * However, wrong gradient check problem remains unsolved.
+  * New CPP options have been introduced for different
+    tapering schemes
+o external_fields_load now part of differentiation list
+o pressure needs multiple storing;
+  would be nice to have store_pressure at beginning or
+  end of forward_step, e.g. by having phiHyd global (5-dim.)
+  (NB: pressure is needed for certain cases in find_rho,
+  which is also invoked through convective_adjustment).
+o recomputations in find_rho for cases 
+ 'JMD95'/'UNESCO' or 'MDJWF' are OK.
+o #define ATMOSPHERIC_LOADING should be differentiable
+o ini_forcing shifted to begining of initialise_varia
+o Incorporating QNVS line search routines into MITgcm
+  (this is separate code, and therefore not under pkg)
+  lsopt/, optim/
+o Updated verification/carbon/
+  - #define GM_VISBECK_VARIABLE_K
+  - GM_taper_scheme    = 'ldd97'    
+
+checkpoint46n_post
+Merging from 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
+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).
+
+checkpoint46m_post
+o modified testscript to return -- when there are no lines of "%MON" output 
+o added new flag "quasiHydrostatic" for QH mode
+  and new routine quasihydrostaticterms()
+o added 2*Omega*Cos(phi)*W to u equations (non-hydrostatic Coriolis term)
+  New routine: mom_u_coriolis_nh()
+o fixed sign of non-hydrostatic metric terms in u and v equations.
+  Depend on correct sign of gravitySign.
+o added work.pc* to .cvsignore in aim directories using ifc
+o introduced flag for controllin non-hydrostatic metric terms
+o removed gravitySign from PARM04
+o switched to g77/ifc from pgf77 in aim experiments
+
+checkpoint46l_post
+o made convective adjustment work with pressure coordinates:
+ - changed the direction of k-loop in convective_adjustment.F for the
+   case of pressure coordinates (OCEANICP,ATMOSPHERIC buoyancyRelation)
+ - adjusted the reference pressure k-index in convective_adjustment.F
+ - adjusted the convection condition in convect.F (in analogy to
+   calc_ivdc.F)
+ - convective_adjustment no longer computes anything on the halos
+ - removed the warnings about negative salinity from find_rho.F and
+   find_alpha.F; instead the new routine look_for_neg_salinity, called
+   at the beginning of find_rho, find_alpha, and find_beta, does a 
+   check of the entire slice, if CPP-option 
+   CHECK_SALINITY_FOR_NEGATIVE_VALUES is defined
+checkpoint46l_pre
+
+checkpoint46k_post
+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: JMD95P or MDJWF)
+ - fixed several errors and redundancies in the data file
+ - experiment uses looped cells
+ - added matlab directory with diagnostic scripts for plotting of output
+
+o S/R aim_initialise.F replace S/R aim_init from file aim_do_inphys.F:
+ - read AIM physics parameters from a file (data.aimphys)
+ - set defaults values = F.Molteni paper (Clim.Dyn., 2002)
+
+checkpoint46j_post
+o split calc_exact_eta in 2 S/R : integr_continuity & update_etaH
+o move wVel computation at the end of the time step, in S/R integr_continuity
+o create specific S/R to exchange T,S before DYNAMICS (for stagger time step)
+o update timeave pkg for wVel diagnostic.
+checkpoint46j_pre
+
+checkpoint46i_post
+o Clean up AIM package (and keep the results unchanged):
+  include CPP_OPTION and use IMPLICT NONE in all routines ; 
+  declare all the variables _RL ; use _d 0 for all numerical constants.
+  use ifdef ALLOW_AIM everywhere. And now AIM can be used with g77 !
+
+checkpoint46h_post
+o cleaned up the use of rhoNil and rhoConst. 
+  - rhoNil should only appear in the LINEAR equation of state, everywhere 
+    else rhoNil is replaced by rhoConst, e.g. find_rho computes rho-rhoConst
+    and the dynamical equations are all divided by rhoConst
+o introduced new parameter rhoConstFresh, a reference density of fresh 
+  water, to remove the fresh water flux's dependence on rhoNil. The default
+  value is 999.8 kg/m^3
+o cleanup up external_forcing.F and external_forcing_surf.F
+  - can now be used by both OCEANIC and OCEANICP
+checkpoint46h_pre
+
+ Added code to convert surface volume flux (fresh water) into
+ a mass flux when using P coordinates in the ocean (OCEANICP).
+ Note: It assumes you have set rho0=rhoConst=density of fresh water.
+
+checkpoint46g_post
+o Include a new diagnostic variable phiHydLow for the ocean model
+  - in z-coordinates, it is the bottom pressure anomaly
+  - in p-coordinates, it is the sea surface elevation
+  - in both cases, these variable have global drift, reflecting the mass
+    drift in z-coordinates and the volume drift in p-coordinates
+  - included time averaging for phiHydLow, be aware of the drift!
+o depth-dependent computation of Bo_surf for pressure coordinates 
+  in the ocean (buoyancyRelation='OCEANICP')
+  - requires a new routine (FIND_RHO_SCALAR) to compute density with only 
+    Theta, Salinity, and Pressure in the parameter list. This routine is 
+    presently contained in find_rho.F. This routine does not give the
+    correct density for 'POLY3', which would be a z-dependent reference
+    density.
+o cleaned up find_rho
+  - removed obsolete 'eqn' from the parameter list.
+o added two new verification experiments: gop and goz
+  (4x4 degree global ocean, 15 layers in pressure and height coordinates)
+checkpoint46g_pre
+
+checkpoint46f_post
+o Enable tangent linear (forward mode) gradient checks:
+  - extended active file handling to g_... files
+  - added TANGENT_SIMULATION to theSimulationMode
+  - extended grdchk package accordingly
+o added tangent linear setup in verification/carbon/code_ftl
+o added adjoint setup in verification/front_relax/code_ad
+
+checkpoint46e_post
+o Added new equation of state -> MDJWF
+  - EOS of McDougall et al., 2002, JAOT, submitted
+  - caveat: the equation of state is only valid for a smaller (more
+    realistic?) range of values than JMD95P/Z and UNESCO
+  - added masks to the calculation of pressure in store_pressure
+  - added more check values for density in check_eos (ini_eos.F), some of 
+    the old check values are out of the range of the MDJWF-eos, so don't
+    expect perfect matches for those 
+checkpoint46e_pre
+
+checkpoint46d_post
+o fixed store_pressure to work with both buoyancy relation = 'OCEANIC' and
+  'OCEANICP', also initialised field pressure correctly in ini_eos in the 
+  case of pressure coordinates. eosType='JMD95Z' in 
+  combination with buoyancyRelation='OCEANICP' now causes an error.
+o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
+  in find_alpha/beta.
+checkpoint46d_pre
+
+o Changed p = pressure(i,j,k,bi,bj)  to  p = pressure(i,j,kRef,bi,bj)
+  so that JMD95Z and JMD95P give approptiate static stability in find_rho. 
+
+checkpoint46c_post
+o Changes necessary for ocean in p-coordinates
+ -  Added new buoyancy relation = 'OCEANICP'
+ -  Added new parameters = gravitySign (this used to be contained inside
+    the factor dRdZ which I added when we first switched to R coordinates).
+ X GM/Redi is not compatible (yet)
+ X bottom drag and no-slip need to be debugged.
+checkpoint46c_pre
+
+checkpoint46b_post
+o Added new equation of state -> JMD95Z and JMD95P
+  - EOS of Jackett and McDougall, 1995, JAOT
+  - moved all EOS parameters into EOS.h
+  - new routines ini_eos.F, store_pressure.F
+o Added UNESCO EOS, but not recommended because it requires 
+  in-situ temperature (see JMD95)
+o Modified formatting for knudsen2.f in utils/knudsen2 and added
+  unesco.f to be used with POLY3
+checkpoint46b_pre
+
+checkpoint46a_post
+o Added (atmospheric) pressure loading
+  - new field in FFIELDS.h, etc...
+  - new cpp flag ATMOSPHERIC_LOADING
+o Changed hFacC to _hFacC in calc_phi_hyd.F
+o Added SHORTWAVE_HEATING to some files for consistency
+checkpoint46a_pre
+
+checkpoint46
+further merges from release1_p5
+o new ctrl package
+  - adopted from ECCO environment to enable optimization
+  - added Eliassen Palm fluxes to controls
+o added Eliassen Palm flux controls to gradient check package
+o cost package
+  - Compatible with new ctrl package
+  - added Eliassen Palm cost hooks
+  - modif's of existing cost functions
+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 autodiff package
+  - flow directives:
+    + new for S/R do_the_model_io
+    + enhanced for S/R checkpoint
+    + new gmredi.flow
+  - Introduced CPP option ALLOW_AUTODIFF_MONITOR to
+    disable adcommon.h/g_common.h by default.
+  - fixed problem for adjoint of global_max
+o modified verification/carbon/
+o New setup for adjoint of global_ocean
+o added hooks for Eliassen Palm fluxes (dynamics.F, ini_fields.F)
+o cleaned TAF keys iikey, idkey (dynamics.F, thermodynamics.F)
+o incorporated hooks for sponge layer code (external_forcing.F)
+
+checkpoint45d_post
+o import 2 fixes from release1_p5 (CG2D.h & packages_readparms.F)
+o use recip_dx*,recip_dy* instead of /dx*,/dy* in orlanski_E,W,N,S
+  (affects plume_on_slope "cg2d" output)
+o add new parameter deltaTfreesurf for free-surface time stepping
+o exchange gT,gS when using staggerTimeStep & GM & Oly<4 
+o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
+o change phiMin in exp1 (to agree with documentation)
+o add new flags: 
+ - T,S forcing inside/outside Adams-Bashforth
+ - turn off temp,salt advection and/or forcing
+ - for each tracer, define internal flag for multiDimAdvection & A-B
+o monitor: change definition of KE to check conservation of Energy
+
+checkpoint45c_post
+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
+
+checkpoint45b_post
+o cleaned exchange calls in cg2d
+o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
+o included CPP option SINGLE_LAYER_MODE in thermodynamics
+  to configure barotropic setup (Martin Losch)
+o moved some initialisations within bi,bj loop in dynamics
+  (TAF flow dependency)
+o in initialise_varia, moved call packages_init_variables
+  before convective_adjustment_init
+  (corresponding adjustment of TAF tape initialisation).
+o in calc_diffusivity/calc_viscosity extended domain to full overlap.
+
+checkpoint45a_post
+o compute Rho over the whole domain (extend iMin,jMin indices)
+o specific exchange for X-slice domain (case Ny=1)
+o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
+o solve_for_pressure : set cg2d_x to zero where OBCS are applied
+
+checkpoint44h_post = checkpoint45
+o Fix to restore differentiability:
+  place at which packages_init_variables is called in
+  initialise_varia is crucial for reverse control flow.
+o modifications in GMRedi to enable stable adjoint
+  (corresponding modif's in thermodynamics, dynamics)
+o added missing hook for sponge layer code in external_forcing
+o modified test cost functions
+o storing in gad_advection (plus removal of write(0,*)!
+o missing headers TR1.h added in convective_adjustment routines
+o errorMessageUnit set non-equal zero in eeboot
+  (conflict on some platforms, e.g. IBM SP3)
+o modified carbon verif.
+
+checkpoint44h_pre
+o vertical grid option: allow to put the Interface at the middle between
+  2 cell-centers ; replace delZ in pkg/kpp by drF.
+o GM Advective form: Tracers are advected using the residual transport (=
+  Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
+
+checkpoint44g_post
+o fix surface correction term in multiDimAdvection (affects plume_on_slope 
+  results) ; ifdef missing in thermodynamics.F
+
+checkpoint44f_pre,checkpoint44f_post
+o added PTRACERS package
+  This allows an arbitrary number of passive tracers to be integrated
+  forward simultaneously with the dynamicaly model.
+  + Implemented so far:
+    - basic forward algorithm (time-stepping, advection, diffusion, convection)
+    - I/O and checkpointing
+    - GM/Redi  *but*  using the GM/Redi coefficient of Salt
+  + Not implemented so far:
+    - KPP
+    - OBCS
+  + No specific example supplied (yet) but global_ocean.90x40x15 has the
+    necessary data.ptracer file. Simply use -enable=ptracers and uncomment
+    line in data.pkg.
+  + This package is disabled by default since it increases storage.
+
+
+o testscript: added -cleanup option
+o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
+             b) enable to filter 2D fields.
+
+checkpoint44e_pre,post
+o re-wrote convective adjustment to use pre-calculated weights
+  Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
+  Adds:    model/src/convective_weights.F, convectively_mixtracer.F
+  Original calls to convect() still in place.
+
+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
+!!! I forgot to create tag chkpt44d_pre !!!
+!!! But chkpt44d_pre = chkpt44c_post    !!!
+
+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.