--- MITgcm/doc/tag-index	2011/10/26 09:30:32	1.1522
+++ MITgcm/doc/tag-index	2011/11/29 10:56:03	1.1537
@@ -1,20 +1,113 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1522 2011/10/26 09:30:32 mlosch Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1537 2011/11/29 10:56:03 mlosch Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o pkg/obcs/obcs_calc_stevens.F:
+  - fix a bug in code for northern and southern boundaries.
+o pkg/seaice/seaice_init_varia.F
+  - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and 
+    caused zero ice-velocities for the B-grid code
+o pkg/seaice/seaice_init_fixed.F
+  - fix a bug in the initialisation of the second metric terms 
+    k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
+  - this affects all seaice configurations with useCurviLinearGrid = .true.
+    and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
+    = .true. (default)
+  - the only verification experiment affected is global_ocean.cs32x15:
+    icedyn, seaice, and seaice_dynmix (AD)
+o pkg/thsice/thsice_diagnostics_state.F
+  - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
+    not contain garbage that can lead to surprises in diagstats_calc.F
+o model/src:
+  - move bi,bj loops inside INTEGR_CONTINUITY ;
+  - call INTEGR_CONTINUITY directly from forward_step.F
+    (previously called from momentum_correction_step.F)
+  - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
+    forward_step.F and pkg/ecco/the_main_loop.F
+o model/src/do_oceanic_phys.F:
+  - reset addMass to zero only if useICEFRONT ;
+  - separated k-loop for rhoInSitu calculation ;
+  - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
+    and at constant T,S (= WdRHOdP);
+  NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
+    of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
+    transport of locally-referenced potential density);
+    to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
+o gluemnc:
+  - replace ncrcat with ncks when adding variables to *.glob.nc
+  - change the way variables without record dimensions are handled so that
+    files that have variables with and without record variables can be glued:
+    add a record dimension with a new unique name to be able to differentiate
+    between variable with and without a-prior record dimensions. Remove
+    this record dimension before adding the variable to the *.glob.nc file.
+    This procedure automatically works also for grid.*.nc files that do not
+    have any record dimension.
+o verification/cpl_aim+ocn:
+  - generate new reference output on baudelaire (gfortran, mpich2) (previously
+    from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
+o pkg/obcs/obcs_calc_stevens.F:
+  - add code for northern and southern boundaries.
+  - reorder some loops to save some operations and so that drFBar can be scalar
+o model/src:
+  - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
+    truncation) and add diagnostics for Adams-Bashforth tendency increment.
+  - update test-exp. AD output:
+    1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
+  and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
+    front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
+    global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
+    matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
+    tutorial_global_oce_in_p, tutorial_global_oce_latlon and
+    tutorial_plume_on_slope.
+o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
+  that vectorises. This code uses 3 extra 2D fields, F90 array assignments
+  and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
+  does not even come with an F77 compiler anymore, this should not be
+  a limitation
+
+checkpoint63e (2011/11/06)
+o pkg/seaice adjoint of LSR:
+  - substantially rework STORE dirs.
+  - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
+    this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
+    and only perform SOLV_MAX_FIXED adjoint iters.
+    If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
+    always goes to same record, meaning that the last forward field will be
+    the one used in the adjoint - an approximation.
+  - now produces non-zero LSR-related gradients, and acceptable gradients for
+    An's zonal (x-z) test case (to be checked in)
+  - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
+    (but these are screwed up by the thermodynamics in the first place);
+    reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
+    output_adm.txt also reflects changes to seaice_lsr
+  - global_ocean.cs32x15:
+    * the "default" input_ad.seaice has been re-defined to always exclude dynamics
+      (output_adm.seaice.txt was updated)
+    * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
+      (output_adm.seaice_dynmix.txt)
+o test-exp. exp4+stevens:
+  - switch off pTracers and nonHydrostatic (restart problems with NH); update output
+o pkg/seaice (lsr solver):
+  - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
+    update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
+  - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
+  - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
+    into initial guess for linearised solver; use weight ~ (1/err)^2,4.
+  - compute (with new S/R) and print initial (+ free-driff sol. if available)
+    and final residual of linearised system.
 o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
   (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
 o pkg/obcs: Stevens BCs (still only for east and west)
   - fix Stevens BCs by using intermediate velocities of previous
     time step as "baroclinic" contribution rather velocity of one grid cell
     inside the boundaries; more consistent but makes the entire treatment
-    more complicated, requires new pickup files and two new S/Rs: 
+    more complicated, requires new pickup files and two new S/Rs:
     obcs_copy_uv_n and obcs_save_uv_n
-    keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY 
+    keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
     (undefined by default)
-  - silently move computation of some grid factors into separate loops to 
+  - silently move computation of some grid factors into separate loops to
     save some recomputations
   - add a hack for non-linear free surface
   - add a verification experiment to exp4 that tests this code