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-revision 1.53.2.40 by dimitri,
Fri May 23 17:51:21 2003 UTC
+revision 1.53.4.26 by dimitri,
Fri Feb 28 03:34:29 2003 UTC
 Line 3 
 $Header$
      Notes on tags used in MITgcmUV
      ==============================
- o adjoint-friendly modifications to pkg/seaice
+ o Added cost_ice for sea-ice volume sensitivity experiment.
+ o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
- release1_p17
- o added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
- release1_p16
+ icebear3
- o fixed gather/scatter inital MPI dialogue in ini_procs.F
+ o Removed spurious iikey and idkey
- o pkg/seaice/lsr.F has been moved to SouthWest B-grid location
+ o pkg/exf
-   and has been made the default dynamic solver because of its
+   - bug fix in treatment of downward radiation
-   fast convergence properties relative to adi.F solver.
+ o pkg/seaice
+   - added initial sea-ice thickness parameter SEAICE_initialHEFF
- release1_p15
+ o updated verification/natl_box_adjoint
- o Added CFC-11 diagnostics, see
-   verification/global_with_CFC11/README
- release1_p14
- o Added interpolation routine pkg/exf/new_interp.F for on-the-fly
-   interpolation.  Enable with USE_EXF_INTERPOLATION and specify
-   input grids in data.exf
- o Added direct pressure solver pkg/solver.
-   See pkg/solver/README.directSolver for instructions.
- release1_p13
- o bug fix for pkg/seaice/adi.F dynamic solver
- release1_p13_pre
- o Added net flux to downward flux conversion to pkg/exf/exf_getffields.F
- o Added SEAICE_initialHEFF to pkg/seaice
- o the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
- o Updated pkg/seaice and pkg/exf with adjoint modifications from icebear4
- release1_p12
+ icebear2
  o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
-   kpp_transport_t.F, forward_step.F, and the_main_loop.F
+   kpp_transport_t.F,and ecco_the_main_loop.F
- o pkg/seaice:
+ o adjoint-friendly modifications to pkg/seaice
-   - adjoint-friendly modifications
+ o added verification/lab_sea as per release1_p12_pre
-   - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
- release1_p12_pre
- 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
- release1_p11
- 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).
- 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
+ ecco_c44_e26
- o pkg/seaice
+ o Merging pkg/exf and pkg/seaice from cvs tag ecco_ice2
-   - removed GOTO's and added taf directives
+ o exf: Modifications to correctly handle evap field for adjoint
-   - double precision constants to reduce the g77 (Linux)
+ o grdchk:
-     to F77 (SGI) differences reported in release1_p8
+   Added code to perform gradient checks for bulk formulae/atmos. state
- o tools/genmake
+   (atemp, aqh, uwind, vwind).
-   - added SGI options
+   NOTE:
- o verification/testscript
+   This package is out of synch with c48 package.
-   - updated to that of checkpoint47a_post
+   The latter also has the tangent linear gradient checks.
- o verification/global_ocean.90x40x15/input/eedata
+   Need to be merged.
-   - modified for SGI f77 compatibility
+ o verification/natl_box_adjoint:
- o verification/lab_sea
+   * added new setup: code_bulk/, input_bulk, results_bulk
-   - added description of sea-ice model
+     (Experiment 2, described in README)
-   - added missing matlab routines
+     uses bulk formulae and atmos. state as control instead of
-   - added test of thermodynamics parallelization
+     air-sea fluxes.
+     Performs gradient checks for first 4 elements of atemp control.
- release1_p8
+   * changed standard verification to perform
- o verification/natl_box:
+     gradient checks on first 4 elements on hflux control.
-   updating new external_fields_load routine
+   * gmredi switched off (will come after merge with c48).
- o New package: pkg/seaice
-   Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle).
+ ecco_c44_e25
-   The sea-ice code is based on Hibler (1979-1980).
+ o Merging some GM changes from main trunk (c47) to ecco-branch.
-   Two sea-ice dynamic solvers, ADI and LSR, are included.
+ o Updating verif. natl_box_adjoint with GMRedi.
-   In addition to computing prognostic sea-ice variables and diagnosing
+ o Adding setup with explicit differentiaton of pressure solver.
-   the forcing/external data fields that drive the ocean model,
+ o Bug fix: missing OBCS_OPTIONS.h for sponge layer code.
-   SEAICE_MODEL also sets theta to the freezing point under sea-ice.
+ o (Re-?) Commiting old bug fixes in kpp to ecco-branch
-   The implied surface heat flux is then stored in variable
+   (kpp_calc.F, kpp_routines.F)
-   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
+   - cleaned old exfa stuff
+   - bug fixes
      (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
+ ecco_c44_e24
-   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
+ o bug fix for nwettile contents
+   so far assumed global sum  in first entry (1,1,k),
+   needed for global control vector
+   -> introduced new variable nwet[c/w/s]global(nr)
+ o shifts of calls to cal/exf package to be accessible
+   in MITgcm stand-alone
+ o shifted packages_init_variables before convective_adjustment_ini
+   (corresponding update of TAF tape initialisation).
+ o removed auxiliary field in impldiff
+   (caused numerical differences for GMRedi cases)
+ o updated obcs control part (G. Gebbie)
+ o removed some f90 comments ("!")
+ o Bug fixes and updates in cost package
+  * cost_final: correct multiplier mult_tauv, mult_sflux
+  * cost_hyd: added call cost_ssh
+  * cost_init_barfiles.F: replaced arrays by tmpfld's
+  * cost_readtopexmean.F: ersmask -> tpmeanmask
+  * cost_weights.F: corrected wtheta[2], wsalt[2]
+ o cleaned exchanges in cg2d.F
- release1_p3
+ ecco_c44_e23
- o added tangent linear setup to verification/carbon/
+ merged patches between release1_p1 and release1_p2:
- 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_...
-Line 215 
 o fixed recomputation in thermodynamics
+Line 90 
 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
+ Bug fix in ctrl_mask_set_yz (spotted by G. Gebbie)
+ ecco_c44_e22
+ o Finally, the merges with the Scripps cost function terms:
+   Various additions, modifications, quality checks.
+ o Plus: Included switch ALLOW_AUTODIFF_MONITOR to handle
+   monitoring of adjoint state.
+ o Plus: removed comm_stats, ini_communication_patterns from diff. list
+   (no more need to "keep" MPI headers for adjoint generation)
+ o Plus: exf changes:
+   o added run-off routine
+   o additional storing needed for ustress,vstess
+     because of state-dependent quality check
+   o added missing initialisations
+ o Plus: genmake with MAKEDEPEND variable was still missing in ecco-branch
+ NB: - verification/natl_box_adjoint/ 240 steps run
+       * looks ok under Linux (twain.lcs.mit.edu)
+       * looks ok on MIT SUN's (fjord.mit.edu)
+       * NaN in reverse mode on Scripps SUN's at iter=214
+       * NaN in reverse mode on IBM SP3 (BlueHorizon) at iter=204
+     - 1 year forward int. global 2x2 deg. produces similar cost functions
+       * all cost terms of new code are slightly smaller (0.5 to 3%).
+ ecco_c44_e21
+ o reversed order of ctrl/cost initialisation
+ o gmredi_slope_psi.F: Inconsistent types in MIN/MAX expressions
+ o modified to enable ctrl field swapping
+ o bug fix for global sum of ncvarlength in ctrl_init
+ o no more call to ctrl_unpack from ctrl_init
+ o no more write of ctrl vector in ctrl_pack
+   however, init. of control vector from ctrl_unpack
+ o various bug fixes & consistent nobcs handling in
+   ctrl_pack/unpack routines (by G. Gebbie)
+ o optim package: Added obcs control part for lsopt I/O
+   (by G. Gebbie)
+ o missing call to obcs_diags
+ o moved calls in packages_init_fixed to packages_readparms
+   because some quantities are needed earlier.
+ ecco_c44_e20
+ o before major merges from the Scripps setup
+   here are two small updates:
+   - field swapping for surface flux controls enabled
+     (remains t.b.d. for atmos. state plus obcs)
+   - bug fix in active_file.F for xz-/yz- routines
+   - added missing xz-/yz- routines to active_file_ad.F
- release1_p1
+ ecco_c44_e19
  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.
+   - included GMREDI, EXACT_CONSERV to natl_box_adjoint verif.
- release1_chkpt44d_post = chkpt44d_post
- chkpt44d_pre,post
+ ecco_c44_e18
- o added missing EXCLUDE_MONITOR flags
+ o sponge layer code for obcs was missing
- o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
+   - added hook in external_forcing.F
-   (incompatible typ in MIN/MAX expressions caused problems
+   - added storing for TAF
-   on IBM SP3)
+ o new routine cost_init_barfiles to initialise
- o in genmake added variable MAKEDEPEND
+   adjoint fields adtbar, adsbar, adpsbar
-   plus resetting for case SunOS
+   (needed in conjunction with corrected ladinit for active I/O)
- o added timer_stats.c routine for IBM SP3
+ o cleaned up and corrected order in packages_readparms, ecco_readparms
- o removed variables in dynamics
+ o corrected and simplified weights for obcs controls
+   - weight fields simplified
- o real fresh water flux implemented with non-linear free-surface.
+   - bug fix in ctrl_pack
+   - no more write of control vector in ctrl_pack
- chkpt44c_pre,post
+ o i/j index bug fixes in cost_ssh_mean
- o few fix (mask in shap_s2, EmPmR in external_field_load,
-   USE_NATURAL_BCS in solve_for_P);
+ ecco_c44_e17
- o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
+ o bug fixes in cost package
+   * wrong identifier for active I/O of monthly mean psbar
- checkpoint44b_pre/_post
+     (cost_averagesfields, cost_ssh) xx_psbar_dummy
- o merge of relevant stuff from the ecco-branch:
+   * cleaned all identifier for active I/O of monthly fields
+   * wrong ladinit in various cost routines
+ o merge with interval (chkpt44c_post - chkpt44d_post)
+   * added missing EXCLUDE_MONITOR flags
+   * changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
+     (incompatible typ in MIN/MAX expressions caused problems
+     on IBM SP3)
+   * in genmake added variable MAKEDEPEND
+     plus resetting for case SunOS
+     added timer_stats.c routine for IBM SP3
+   * removed variables in dynamics
+ ecco_c44_e16
+ o new ECCO checkpoint, the first since ecco_c43_e15
+   which is branched from MITgcm.
+   All changes were merged in between (see ecco-branch-mod? tags).
+ o last changes:
+   * assuming path for TAF and TAMC are known (e.g. in $path)
+   * genmake:
+     - added tools/xmakedepend to circumvene shortcoming of
+       SUN's makedepend (size too small)
+     - invoking ../tools/xmakedepend instead of makedepend
+     - changed compiler flags for case SunOS
+ ecco-branch-mod5
+ o mod's to reproduce open boundary run
+ o enable field swapping for OB's and climatology
+ o update store directives for OB control
+ o added option ALLOW_OBCS_PRESCRIBE
+ o call of getobcs now out of obcs_calc (param. list modified)
+ ecco-branch-mod4
+ o this is the second part of changes necessary to reconcile
+   the natl_box_adjoint verification (with and without grdchk).
+   >>>!!! CHANGES BETWEEN THE TAGS ecco-branch-mod3 !!!<<<
+   >>>!!!                      AND ecco-branch-mod4 !!!<<<
+   >>>!!! SHOULD BE MERGED INTO THE MAIN TRUNK      !!!<<<
    - 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
-Line 252 
 o merge of relevant stuff from the ecco-
+Line 207 
 o merge of relevant stuff from the ecco-
    - 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)
+ ecco-branch-mod3
- o OBC and NonLin_FrSurf.
+ o this is the first part of changes necessary to reconcile
+   natl_box_adjoint verification (with and without grdchk).
+   This set of changes is relevant for ECCO only.
+   The next set/tag of changes (ecco-branch-mod4)
+   should be merged into the main trunk.
+   - update some options
+   - parameter lists of ecco_the_model_main and ecco_the_main_loop
+     differed from those of the MITgcm counterparts.
+ ecco-branch-mod2
+ o update ecco-branch-mod1 to checkpoint44
+ o exclude from updates:
+   - verification/
+   - adjoint/
+   - pkg/cost
+   - pkg/ctrl
+   - pkg/ecco
+   - pkg/obcs
+   - model/src/the_model_main.F
+   - model/src/the_main_loop.F
  checkpoint44
+ o apply Shapiro filter on T&S before calc_PhiHyd (stagger time stepping)
  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
+ ecco-branch-mod1
+ o based on c43
+ o replaced packages cost, ctrl, ecco, obcs
+ o removed MITgcm verif.'s, added ECCO verif.'s
+ o added lsopt, optim for line search optimization.
  checkpoint43
  o added two new advection tests
  o added global 4x4 degree ocean test

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