--- MITgcm/doc/tag-index	2010/04/04 14:28:20	1.1246
+++ MITgcm/doc/tag-index	2010/09/26 13:48:19	1.1305
@@ -1,13 +1,270 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1246 2010/04/04 14:28:20 jmc Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1305 2010/09/26 13:48:19 jmc Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o pkg/seaice:
+  -fix the USE_ORIGINAL_SBI version (for variable freezing point);
+  -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
+   version (with USE_ORIGINAL_SBI undef);
+o add hooks for new packages OASIS, the package will follow
+  (hooks exclude the seaice pkg for now)
+o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
+  Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
+  rather than mdsio_readvector.F/mdsio_writevector.F, within
+  adread_adwrite.F to read/write adjoint-related tapes to disk.
+o eesupp and pkg/mdsio: ALLOW_WHIO
+  Option to write/read 2D fields to files including tiles halos.
+  The main purpose is for adjoint related "tape I/O".
+  The secondary purpose is for debugging phases.
+  A word on those rather specifically intended purposes.
+  The code was meant to be stripped down to the bare minimum.
+  Typically, there is a unique and basic mapping to the global
+  buffer (tile by tile, then proc by proc, then level by level), and
+  byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
+  meant to generate user friendly outputs of various shapes and forms.
+  Rather it is intended, for the knowledgeabale developers,
+  to be largely independent of the many mdsio options, to allow
+  outputs of tiles+halos in debugging phases and in adjoint runs,
+  and to allow some flexibility in tuning (adoint) I/O depending on each
+  file system behavior. With regard to tuning, most of the potential knobs
+  (to leave files open, to allocate the I/O indep. of usesinglecpuio,
+  to specify directories, to specify the typical size of I/O calls, etc.)
+  are not yet included, and will be added if they prove useful.
+o pkg/seaice:
+   fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
+o pkg/seaice:
+   new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
+   code (seaice_budget_ice_if.F) which enable to recover old standard
+   code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
+   temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
+o model/src (rStar):
+   use simple average (not area weighted) of rStarFac at U,V point when using
+   vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
+   update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
+
+checkpoint62k (2010/09/17)
+o adjoint
+   * changed verification/global_ocean.cs32x15 ; adjoint now tests
+     Adams-Bashforth 3 + NLFS + RSTAR
+   * some more modifs required for ECCO-GODAE v4
+o pkg/seaice
+   add SEAICE_AGE_VOL option to use volume instead of area for
+   integrating SEAICE_AGE
+o model/src:
+   first check-in of sigma & hybrid-sigma coordinate code ; also includes
+   non-linear free-surface parts ; but pressure-gradient not yet coded.
+o pkg/ptracers:
+   option for ptracer to convert Salt Relax into additional EmP.
+    tested in exp. global_ocean.90x40x15.dwnslp (update output)
+
+checkpoint62j (2010/08/25)
+o pkg/ggl90:
+   other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
+o pkg/dic: car_flux.F, phos_flux.F
+  - reduce number of exp-calls in order to improve performance
+  - clean up a little (replace fields by their macros, etc., fix
+    typo in CPP-flag)
+o pkg/ggl90: minor changes
+  - GGL90diffKrS was removed --> always use GGL90diffKr
+  - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
+  - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
+    (commented out for now)
+  - change in max/min operations to ensure that smoothing is ok
+  - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
+  - always use diffKrNrT as background profile (i.e. never use diffKr field)
+o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
+o pkg/dic:
+  - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
+    vectorization
+  - small bug fix in insol for the unlikely case of a cartesian grid
+  - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
+    + now vectorize, which also removes adjoint recomputations;
+    + replace integer maksp1 by _RL maskp1
+    + replace a**x by exp(x*log(a)) in phos_flux.F for speed
+
+checkpoint62i (2010/07/21)
+o pkg/flt:
+  - with OBCS: stop floats which enter the OB region
+o model/src:
+  - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
+    for implicit vertical advection.
+o pkg/seaice:
+ - account for melting in seaice age evolution.
+ - remove double counting of seaice ridging effect on seaice age.
+
+checkpoint62h (2010/06/18)
+o pkg/exch2:
+ - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
+o tools/genmake2
+  - remove "-pdefault" option: redundant with the use of "packages.conf";
+  - remove file pkg/pkg_default : set the default as a pkg group
+    ("default_pkg_list") defined in pkg/pkg_groups;
+  - fix for case pkg/pkg_depend is missing (was hanging before);
+  - add option "-pgroups" to specify a different pkg_groups than the default.
+o verification/adjustment.cs-32x32x1:
+   add a "minimal" set-up test (code_min & input_min) which only compiles
+   eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
+o tools/genmake2
+  - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
+  - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
+o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
+  files are nearly the same anyway.
+  Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
+   - redefinition of tau(i,i) (by a factor of ustar)
+   - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
+   - replace rhonil by rhoConstFresh in computation of evap (bug fix)
+   - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
+   - replace
+     rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
+     shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
+     by
+     shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
+     (changes results)
+   -> exf_bulkformulae v1.22,
+      update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
+      (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
+                output.txt 1.63
+       offline_exf_seaice: output.seaicetd.txt 1.7
+       seaice_obcs: output.txt 1.10)
+  Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
+   -> exf_bulkformulae v1.23,
+      unfortunately requires updating lab_sea.salt_plume (6 matching digits),
+      and global_ocean.cs32x15.icedyn (only 11 matching digits)
+  Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
+o adjoint of exch-1:
+ - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
+   (note: was already like this when using EXCH-2) and remove flow dir
+   and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
+ - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
+ - update pkg/exch2 diff list.
+
+checkpoint62g (2010/05/19)
+o eesupp/src (exch-1):
+ - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
+   and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
+   (renamed to exch1_*rx_cube.F).
+ - change accordingly exch_*_rx.template and AD version in pkg/autodiff
+   to call new exch1 S/R ; update Makefile and .cvsignore.
+ - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
+   exch2_xy_rx later)
+  Note: after updating your code, need to run "make clean" in eesupp/src
+o test experiment bottom_ctrl_5x5:
+   new output_adm.txt with fewer grdchk & less monitor output.
+o model/src:
+  remove the call to ini_cori in initialise_varia.F (just keep the usual one
+   in initialise_fixed.F). More consistent with coriolis & horizontal grid
+   beeing treated in the same way (ini_grid is not called a 2nd time).
+o pkg/exf:
+  - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
+  global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
+  - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
+  - cosmetic changes to exf_bulkformulae.F to make it look more like 
+    exf_bulk_largeyeager04.F 
+o eesupp/src (exch-1):
+  - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
+  - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
+    array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
+    (even without using MPI).
+  - Message mode: move RecvAck setting (indicator of buffer being ready)
+    from send_put to recv_get S/R (was useless before, but not sure if
+    it's much more useful now);
+  - Switch the order of sync: MPI-proc 1rst and then threads;
+  - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
+  - fix AD code for communication mode ='get' (but not used).
+o model/src:
+  initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
+  not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
+o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
+o pkg/ctrl: require a specific set of control variables and exf-flags for
+  adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
+o model/src:
+ a) 1rst version of a new driver S/R to turn-off output freq and flags after the
+   1rst forward sweep, to avoid over-writing output files during recomputations
+   recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
+ b) 2nd version:
+  - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
+  - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
+     writePickupAtEnd) + seaice & ptracers output;
+  - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
+o model/src:
+  - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
+o pkg/exch2:
+  - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
+  - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
+o pkg/autodiff & exch2:
+  process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
+  (for now, only if ALLOW_EXCH2 is defined).
+o pkg/autodiff:
+  - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
+    (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
+   + clean-up comments (_RS is not always real*4)
+  - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
+  - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
+    was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
+o testreport (AD-tests):
+  no longer link files from dir "../input" (1rst link files from
+  "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
+
+checkpoint62f (2010/04/29)
+o model/src/the_main_loop.F:
+  adjust store directives for seaice evp and multicategory according to
+  pkg/ecco/the_main_loop.F
+o adjoint:
+  global_sum_ad was incomplete (noted many times by many people ;)
+  nice description by Jean U. as follows:
+  * allreduce(var) in global_sum.F can be interpreted as
+    reduce(sum) followed by broadcast of sum.
+  * The adjoint of that is
+    sum(adjoint) followed by broadcast(summed adjoint value)
+    or in other words, allreduce(sum, adjoint vars)
+  We were missing the sum(adjoint)!
+  Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
+  (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
+  The fix should produce 16-digit accuracy between
+  single-CPU multi-tile (e.g. nSx=2, nPx=1) and
+  multi-CPU single-tile (e.g. nSx=1, nPx-2)
+  We'll probably change this yet again shortly
+o eesupp/src:
+  - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
+o pkg/icefront
+  - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
+    specification of addmass array based on a 2D field, which is added
+    at bottommost wet level at each horizontal location.
+o model/src:
+ horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
+ layout; (not always compatible with delX,delY setting; commented out for now).
+o pkg/exch2:
+ change tile to processor setting (case nSy*nPy > 1): allows default model mapping
+ (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
+
+checkpoint62e (2010/04/15)
+o pkg/obcs:
+  - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
+o pkg/dic:
+  -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
+    (note: not presently tested in any forward verification exp.)
+   update tutorial_global_oce_biogeo AD output file.
+o pkg/exf:
+  - account for the variation of albedo as a function of zenith angle
+    by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
+o build_options:
+ - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
+o pkg/dic:
+  change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
+  - use binary pickup file for restart;
+  - initialise atmos-CO2 box from dic_pCO2 parameter;
+  - fix multi-threaded.
+o pkg/rbcs:
+ - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
+   change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
+ - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
+   and update output.txt
 o pkg/kpp:
  - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
  - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
-   (= ratio of KPP non-local (salt) flux relative to surface-flux) when 
+   (= ratio of KPP non-local (salt) flux relative to surface-flux) when
    using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
  - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
    KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).