--- MITgcm/doc/tag-index	2012/09/18 21:26:19	1.1739
+++ MITgcm/doc/tag-index	2013/02/05 15:02:34	1.1818
@@ -1,9 +1,395 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1739 2012/09/18 21:26:19 jmc Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1818 2013/02/05 15:02:34 gforget Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o pkg/ecco : 
+  - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
+o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk : 
+  - modifications for ALLOW_GENTIM2D_CONTROL
+  -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
+  -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
+  -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
+  -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
+o model/src:
+  - account for moist thermodynamics in (dry) potential temperature equation;
+    update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
+    and cpl_aim+ocn.
+  - also switch to standard compiler (gfortran, was using ifort previously)
+    for fizhi-cs experiments reference output.
+o pkg/ctrl:
+  - 1st step toward generic time-varying control variable (2D) via CPP option
+    ALLOW_GENTIM2D_CONTROL
+  - note new namelist ctrl_nml_genarr in data.ctrl
+o verification/global_ocean.cs32x15:
+  - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
+    thsice calling sequence and update "output.icedyn.txt" output file.
+o pkg/ptracers:
+  - from Ryan A.: code to allow to restart a tracer at regular time interval
+    specifying a reset frequency and a reset-phase (for each tracers).
+o pkg/thsice:
+  - implement new sequence of calls for thsice+seaice:
+      previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
+      new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
+  - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
+    in CPP_OPTIONS.h) to recover old sequence;
+  - update diagnostics for Intermediate State thsice diagnostics: now filled
+    just before advection (instead of just after advection in old sequence);
+  - update output of experiment offline_exf_seaice (standard test);
+  - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
+    by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
+o pkg/aim_v23:
+  - use tiled array for aim_CO2 and surface wind speed for export to coupler;
+  - use standard pkg/mdsio routines to read & write CO2 pickup file;
+  - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
+  - Implement new sequence of calls for seaice advection (with thsice and
+    seaice diffusion): do ice advection after ice-Thermodynamic (previously
+    was done before); change aim_do_physics.F (split the bi,bj loops block);
+  - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
+o pkg/thsice:
+  - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
+    where just seaice diffusion is used without seaice-dynamics.
+
+checkpoint64c (2013/01/18)
+o pkg/seaice:
+  - add a parameter JFNKres_tFac that can replace JFNKres_t
+    (= JFNKres_tFac*JFNKresidual before JFNK solver)
+  - add a line search option to the JFNK solver
+  - move update of u/vIce and computation of initial residual into a separate
+    routine (same file); makes the code a little easier to read (?)
+  - the line search requires computation of the residual and for some reason
+    I cannot do the update of u/vIce at the beginning of the Newton loop
+    without changing the results, so we move computation of the new residual
+    also to the end of the Newton loop, even without the line search
+o pkg/mdsio:
+  - write missing value (corresponding to undefined array value) to meta files;
+    skip this if missing value is one (UNSET_RL would be a better value for the
+    case of undefined missing value but it's current the default missing-value);
+    Also update mdsio_read_meta.F (reading timeInterval & missing-value).
+o pkg/exf & thsice:
+  - for diagnostics purpose, fill-up and update Qsw array (+ fill the
+    diagnostics) even when SHORTWAVE_HEATING is #undef;
+o verification/cfc_example:
+  - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
+    illustrate how to use it).
+o verification/offline_exf_seaice:
+  in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
+    files to only one time-record.
+  in input.thermo: narrow the 2 bands of low initial ice-concentration near
+    N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
+    snapshot output; same mcPheePiston value as in thsice with
+    surf-current=0.2m/s.
+  in input.thsice: similar set-up as in input.thermo (channel with same seaice
+    initial conditions).
+o verification/cfc_example:
+  - update file "data" with more standard choice (default rotationPeriod,
+    exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
+    set deltaTFreeSurf to deltaTtracer) and update the output.
+o pkg/layers:
+  - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
+  - ensure that "layers_bolus" is switched to False when useGMRedi=False.
+o verification/offline_exf_seaice:
+  - set all {field}period to zero for constant-in-time forcing (not tested
+    anywhere else).
+o verification/offline_exf_seaice:
+  - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
+  - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
+o model/src:
+  - implement Finite-Volume method for (hydrostatic) presure gradient
+    from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
+o pkg/seaice: implement EVP* by Lemieux et al. (2012).
+  - In order to be compatible with the default EVP code, this requires changing
+    the EVP code around a little; and because any small change immediately
+    breaks the lab_sea.hb87 verification experiment, the reference output is
+    updated two times (each time the remaining aggrement was only 2 digits):
+    - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
+    - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
+    The adjoint test lab_sea.evp also needed to be updated.
+  - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
+    SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
+    a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
+    explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
+    INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
+    kept obscure, because I need to test it a little more.
+o pkg/cheapaml:
+  - fix few incorrect type (_RL/_RS) in subroutine calls.
+o pkg/seaice:
+  - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
+    to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
+o model/src:
+  - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
+    change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
+    experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
+o pkg/cheapaml:
+  - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
+    update output of experiment cheapAML_box.
+  - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
+    and set them only in one place (cheapaml_readparms.F).
+  - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
+  - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
+    and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
+o model/src/the_main_loop.F:
+  - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
+o pkg/seaice:
+  - remove legacy branch code.
+  - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
+o verification/*/code*/SEAICE_OPTIONS.h:
+  - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
+    SEAICE_CAP_HEFF).
+o pkg/cheapaml:
+  - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
+    to load new forcing fields.
+  - add missing "_d 0" where it's needed; + some editing (improve indentation).
+  - remove switch to "-r8" compiler option (no longer needed) in verification
+    cheapAML_box, keep same output (small trucation error differences).
+o verification/offline_exf_seaice:
+  - add thermodynamics only test.
+o verification/cheapAML_box:
+  - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
+    keep same output (same 14 digits for cg2d).
+  - switch on "-r8" compiler option (some numerical values are missing
+    the "_d 0") and update output (only 6 digits for cg2d were preserved).
+
+checkpoint64b (2012/12/24)
+o pkg/cheapaml:
+  - remove un-used variables (Qnet,EmPmR) from pickup files.
+  - store tendency of advected variables into cheapaml pickup file
+    and fix the AB-2 restart.
+o verification/offline_exf_seaice and lab_sea adjoint:
+  - switch to new code (#undef SEAICE_GROWTH_LEGACY).
+  - switch to 4 time steps in offline, consistent with lab_sea.
+  - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
+  - update results after change of experiment seaice.
+o pkg/seaice:
+  - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
+    parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
+    still defined since SEAICE_multDim needs to be set to MULTDIM value (from
+    SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
+o model/src:
+  - add run-time parameter to select CG2D solver minimum-residual solution
+    (in case of a poor convergence).
+o pkg/seaice/seaice_lsr.F
+  - move calculation of matrix coefficients into new
+    S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
+    file; the main purpose of this change is to be able to reuse the code
+    in S/R SEAICE_PRECONDITIONER
+  - modify the computation of the residual so that the mass of sea-ice
+    is not used twice; this simplifies the calculations, but since
+    the residual is never used except when LSR_mixIniGuess.ge.4---and this is
+    not tested in testreport---this does not affect the testreport results.
+o verification/seaice_obcs:
+  - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
+    verification/lab_sea/input.salt_plume; changes results/output.txt*
+o model/src:
+  - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
+o pkg/seaice:
+  - improve description of parameters in seaice_fgmres.F and start
+    cleaning up the code
+  - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
+    second argument
+  - add a metric based on grid cell area to SEAICE_SCALPROD; update
+    results of offline_exf_seaice.dyn_jfnk
+  - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
+o pkg/aim_v23:
+  - fix an other bug in dissipation heating (grid-cell area was missing).
+o model/src + pkg/seaice:
+  - add global (multi-tile) linear solver for pair of tri-diagonal system
+    along X and Y lines, respectively for U and V component.
+    Note: 1) MPI and cube-exchange not yet coded.
+        2) probably not accurate for poorly conditioned / large size problem.
+  - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
+    default: not compiled and not used.
+o pkg/seaice:
+  - first attempt at a multi-threaded fgmres solver for the JFNK solver:
+    introduce bi/bj loops and use global_sum_tile_rl instead of
+    mpi_allreduce in seaice_fgmres.F
+  - improve diagnostics output for fgmres solver (seaice_fgmres.F)
+  - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
+  - add a verification experiment for JFNK in offline_exf_seaice
+o verification:
+  - change (for now, only fwd test) offline_exf_seaice experiment:
+    use a re-entrant channel with idealized coastline (trapezoidal shape)
+    at southern boundary to explore seaice dynamics and thermodynamics
+    with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
+    secondary test (input.thsice) use thermodynamics only with SST relaxation.
+  - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
+o pkg/exf:
+  - disable "sstExtrapol" when Nr=1
+o verification:
+  - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
+    to test pkg/cheapaml.
+o pkg/aim_v23 & pkg/shap_filt:
+  - fix dissipation heating (erroneous gravity multiplication factor).
+o pkg/seaice:
+  - remove unused field pressPre from jfnk solver
+  - rename two subroutines in seaice_preconditioner.F
+o eesupp/src:
+   - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
+o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
+   - remove wrong parts of the rhs and the lhs (were in there
+     because I did not understand the concept of this preconditioner)
+   - add an exchange between u- and v-sweep. This increases communication
+     by a factor of two but improves the convergence of jfnk. Ideally,
+     one would like the u- and v-sweep to be independent. So far within
+     undocumented ifdefs
+   - reorganize the extra computations for printing the residuals
+o tools/genmake2:
+  - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
+    since it's not necessary (and was preventing to use MNC in some cases).
+
+checkpoint64a (2012/11/16)
+o pkg/autodiff:
+  - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
+    autodiff_readparms.F no longer depends on calling order (within
+    packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
+    rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
+    and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
+o pkg/obcs:
+  - adding tidal velocity forcing capability to obcs
+    for usage example, see verification/seaice_obcs/input.tides
+o pkg/seaice:
+  - turn the LSR-relaxation parameters WFAU/V into runtime parameters
+    SEAICE_LSRrelaxU/V
+  - introduce runtime parameter SEAICEetaZmethod (=0 by default)
+o pkg/aim_v23:
+  - implement heating from friction (bottom friction and stratospheric drag).
+o pkg/shap_filt:
+  - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
+    dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
+o model/src:
+  - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
+    time-constant addMass field from file (addMassFile);
+  - support for heating due to friction (and Kinetic Energy dissipation):
+    add option, run-time switch and 3-D field array + support code ; each pkg
+    or S/R can add heating contribution (if there is a sink of KE); the sum is
+    accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
+o pkg/seaice:
+  - complete merge of ITD code into seaice_growth.F
+    from MITgcm_contrib/torge/itd/code/
+    no verification so far, but Torge Martin tested
+    "1-D test case and Beaufort set up;
+    deliver okay results after 1 model year."
+  - complete merge of SEAICE_SIZE.h into all relevant routines
+  - move computation of eta at Z-points into calc_viscosities
+    + introduce global field etaZ
+    + add different methods for computing etaZ, for now the old
+      method (simple averages of eta to Z-points) is hardwired
+    + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
+      seaice_preconditioner
+  - simplify computations for SEAICE_ZETA_SMOOTHREG
+  - seaice_preconditioner:
+    + replace one remaining press by pressLoc (mistake)
+    + adjust printing of residuals
+  - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
+    + add (SEAICE.h) and rename some counters (initiliased in
+      seaice_init_fixed.F)
+    + add _BEGIN/END_MASTER (myThid)  around print statements
+    + print total number of iterations and failures over SEAICE_monFreq
+      interval to STDOUT
+  - move control over output-messages by fgmres to seaice_jfnk to save
+    some operations
+  - move resetting initial guess for fgmres outside of seaice_fgmres_driver
+    in order to make restarts with sol .ne. zero (fgmres with restarts)
+    (seaice_jfnk.F, seaice_fgmres.F)
+  - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
+    a serious convergence problem when open boundaries are involved
+o pkg/ggl90: fix computation of control volumes for the case of
+  ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
+  up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
+o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
+o pkg/autodiff
+  - Add inAdMode switch for SEAICEuseDYNAMICS:
+    SEAICEuseDYNAMICSinAdMode
+    (extend logic in ADAUTODIFF_INADMODE_SET)
+o pkg/seaice
+  - Step 1 of merging ice-thickness distribution (ITD) code from
+    MITgcm_contrib/torge/itd/ (author: Torge Martin)
+    The code implements concept laid out in Thorndike et al. (1975);
+    code is enabled via CPP flag SEAICE_ITD
+    nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
+    code is not complete yet!!
+  - SEAICE_SIZE.h now included in almost all seaice routines
+o verification (using seaice):
+  - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
+    global_ocean.cs32x15.seaice ; update results.
+  - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
+  - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
+    offline_exf_seaice (previously compiling B-grid).
+o pkg/exf:
+  - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
+    to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
+    forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
+o pkg/layers (adjust changes from Sept 19):
+  - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
+    this allows to remove "layers_maxNum" dimension from all layers arrays.
+o pkg/layers (adjust changes from Sept 19):
+  - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
+  - snap-shot extended to all type of layers (not just the 1rst type);
+  - remove layers variables when corresponding CPP option is undef.
+o pkg/layers:
+  - rename pkg/layers variable and add new output (layer exist & un-weighted
+    velocity in layer)
+o pkg/seaice:
+  - simplify (?) ocean-drag coefficent computations by using
+    the same routine in all three solvers (saves some code lines)
+  - remove global fields DRAGA and DRAGS from C-grid code and
+    declare them locally in lsr.F (the only place where they are
+    still used)
+  - update AD output of lab_sea.evp (very sensitive anyway).
+o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
+  (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
+  and SEAICEuseJFNK=.true. A few things to note:
+  - involves a FGMRES, that is parallel but very inefficient,
+    because of many scalar products (global sums) in the Gram-Schmidt
+    orthogonalization method. Needs to be replaced. Original code
+    from J.-F. Lemieux
+  - preconditioner for FGMRES is a stripped down version of LSOR
+  - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
+    preconditioner. For the preconditioner, the default is set to 10.
+  - Jacobian times vector is computed with finite differences
+  - marginally related to JFNK-solver: add a smooth regularization for
+    zeta with tanh that will improve convergence (Lemieux and Tremblay,
+    2009) for any implicit solver (not implemented for EVP because EVP
+    does not need this regularization in the first place). Define
+    SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
+o eesupp/src:
+  - check in genmake2 that intrinsic S/R flush is available.
+  - add S/R to flush IO unit (if intrinsic S/R flush is available)
+  - flush standard & error msg unit before MPI termination
+  - if debugMode, flush IO unit after printing msg
+o pkg/ctrl:
+  - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
+    to ctrl_set_unpack_xyz.
+
+checkpoint64 (2012/10/09)
+o pkg/shelfice
+  - in mom_fluxform.F, mom_vecinv.F:
+    CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
+    Bug fix KappaRU -> KappaRV
+    does not change verification/isomip but may change other setups
+    (presumably constant KappaRU=KappaRV)
+  - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
+o pkg/obcs:
+  - fixed some indexing bugs in obcs_seaice_sponge.F
+  - added obcs relaxation subroutines for HSALT and HSNOW
+  - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
+o pkg/seaice:
+  - add "multicategory" parameterization for snow in analogy to ice,
+    default is off for now.
+o pkg/obcs:
+  - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
+    see verification/seaice_obcs/input.seaiceSponge for example application.
+  - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
+    index setting by master-thread. This fix multi-threads Pb in previous modifs.
+o pkg/layers :
+  - add diagnostics to pkg/layers
+  - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
+    (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
+o pkg/generic_advdiff/gad_implicit_r.F :
+  - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
+o pkg/seaice/seaice_growth.F:
+  - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
 o pkg/obcs:
   - change default setting of OBCS_UVICE_OLD from defined to undef;
   - use new parameter OB_indexNone for null index value (instead of hard-coded 0)