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-revision 1.1228 by gforget,
Tue Feb 16 23:39:26 2010 UTC
+revision 1.1295 by jmc,
Sat Sep 11 21:39:13 2010 UTC
 Line 4 
 $Name$
      Notes on tags used in MITgcmUV
      ==============================
+ 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
+rst 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
+    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).
+ o pkg/offline:
+   fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
+   (bug was added in version 1.10 on 2007-08-23).
+ o pkg/offline:
+   - no need to specify periodicExternalForcing, etc ... to use offline pack
+   - offline input files no longer just single prec --> parameter offlineLoadPrec
+ o verification/lab_sea:
+   change AD test to multi-tile setup and update all 4 AD output.
+   NOTE: while cost function values remain very similar,
+   gradients are very different, although gradient checks are self-consistent
+   Should try to get to the bottom of this (cost function summation order?)
+ o pkg/dic:
+   in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
+   a weakness of TAF that drops part of double precision in log10 derivative.
+   <= changes removed since problem has been fixed in current TAF version 1.9.71
+   update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
+ o pkg/ecco:
+   add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
+   update all 4 lab_sea AD output.
+ checkpoint62d (2010/03/22)
+ o build_options:
+   remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
+ o remove unbalanced quote (single or double) in commented line of source code
+   (may cause some warning with some preprocessor/makedepend versions).
+ o pkg/seaice:
+   fix seaice_model.F for adjoint (gael) and update AD results of experiments
+    lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
+ o testreport:
+   add option '-runonly' (short: '-ro') to just do the run part (without make).
+ o eesupp: remove JAM communication code (obsolete).
+ o add option to genmake2 & testreport to switch "_RS" type to "real*4"
+   (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
+   to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
+   (update also the output).
+ checkpoint62c (2010/03/02)
+ o tools/build_options :
+    move (some) old optfiles from build_options/ to build_options/unsupported/
+ o model/src and pkg/exf
+    surface relaxation -- separating data and data.exf options
+    The point is to ensure that we specify the surface relaxation
+    either in data or in data.exf (but not half and half) and to
+    avoid an accidental relaxation to 0 (which happened if a time
+    scale was specified but the file name was left empty)
+ o model/src model/inc and pkg/mom_common
+    ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
+    => addition to the viscosity field as computed by others schemes
+ o tools/build_options:
+   - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
+     but keep the former optfile for few weeks for smooth transition
  o pkg/ecco
    - allow user defined cost function contributions
          CPP: ALLOW_USERCOST_CONTRIBUTION
-Line 12 
 o pkg/ecco
+Line 279 
 o pkg/ecco
        the two options are complementary.
  o pkg/smooth
    - migration from contrib to the main repository
  checkpoint62b (2010/01/26)
  o pkg/monitor:
    - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop

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