--- MITgcm/doc/tag-index	2007/10/28 21:39:40	1.900
+++ MITgcm/doc/tag-index	2008/05/22 12:22:13	1.994
@@ -1,9 +1,271 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.900 2007/10/28 21:39:40 jmc Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.994 2008/05/22 12:22:13 mlosch Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o pkg/diagnostics: enforce missing_value attribute for scalar variables at
+  mass points, when using mnc for output
+  - add runtime parameter (missing_value, missing_value_int) to override 
+    default (which is the value of getcon('UNDEF'))
+o pkg/mnc: prepare mnc for the actual use of missing values with the
+  diagnostics package: small fix in mnc_cw_readwrite.template and more
+  initialisation of never used fields
+  - replace mnc_common.h and mnc_id_header.h with corresponding upper case
+  versions
+o pkg/thsice/thsice_ini_vars.F added default initial values so that 
+  thermodynamics sea ice solver does not blow up when some initial fields 
+  are missing.
+o move from external_forcing_surf.F to ini_forcing.F
+  the p-coord. hack consisting in using pLoad to set phi0surf ;
+  update output of tutorial_global_oce_in_p (affected @ truncation level).
+o Freshen up a bit hs94.1x64x5, notably: 
+  remove rotationPeriod and tRef=5*0. (adjoint only), and add 
+  exactConserv=.TRUE.
+o pkg/generic_advdiff:
+  change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
+  applies to files where Temperature & Salinity 2nd Order moments are used.
+o pkg/ptracers: add second-order moment advection schemes (80 and 81);
+  this uses a dynamically allocated internal state data structure
+  (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h) 
+  and requires a fortran 90 compiler
+
+checkpoint59q
+o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
+   (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
+o Refresh tutorial_global_oce_biogeo, notably:
+  - change bathymetry (put back seamounts in ACC, use hFacs)
+  - change EOS (POLY3 --> JMD95Z)
+  - use Bryan-Lewis vertical diffusivity
+  - use multidimensional advection
+  - remove old virtual virtual in dic pkg, now done through ptracer pkg
+  - change a couple of parameters in dic pkg
+o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
+o pkg/obcs: change default to OBCSfixTopo = .true., 
+  - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
+  - replace "debugMode" with "debugLevel .GE. debLevB"
+o implementation of TAF directives for gchem,cfc,dic 
+o remove "exp5" (replaced by tutorial_deep_convection).
+o pkg/obcs: add code to fix topography gradients normal to open boundaries;
+  this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
+  the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
+  --> changes results in exp4, seaice_obcs
+o tutorial_deep_convection :
+  update the set-up and increase resolution and domain size ; start
+  from pseudo initial conditions = output at t=120mn in order to see
+  something happening when running testreport.
+o pkg/seaice: add os7mp as an advection scheme
+              add check for advection schemes
+              add a flag for restoring T and S underneath sea ice
+o pkg/my82: add netcdf-support and diagnostics 
+o thsice pkg:
+  - Now hsMax limits snow height by turning it into ice following
+    flooding scheme (and now conserving energy)
+  - Slight rewriting of the formula in thsice_calc_thick.F
+  - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
+  --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice 
+
+checkpoint59p
+o gchem / dic / cfc :
+  - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
+  - add new parameter files: "data.dic" & "data.cfc" ;
+  - various re-arrangement in initialisation & header file ;
+  - fix tutorial_global_oce_biogeo for multi-threaded test.
+o pkg/dic: test for "pickup_dic" file when restarting ;
+  if no pickup-file, can restart with a re-initialised pH (same as it did
+  before) providing pickupStrictlyMatch is set to False.
+o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
+  + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
+o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
+  and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
+o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
+ & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
+   (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
+o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
+   scheme to use for vorticty-term ;
+ - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F 
+   (with default selectVortScheme, return to original discretisation)
+ - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
+o pkg/seaice: add a line to the summary to indicate grid type (B/C)
+o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
+  bottom ; only used with variable horizontal viscosity and non-hydrostatic.
+  also fix diagnostics VISCAHW & VISCA4W.
+
+checkpoint59o
+o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
+o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
+  move a few statemens out the main loop into separate loops
+o pkg/shelfice: 
+  - sort out freshwater flux; convert freshwater fluxes to mass fluxes 
+    (kg/m^2/s), does not break tests, because in verification/isomip,
+    rhoConstFresh=rhoConst (by accident)
+  - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
+  - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
+    new file model/src/seawater.F, so that they are available for all pkgs.
+  - convert potential temperature into in-situ temperature. This changes the
+    isomip tests => update tests
+o add a flag writePickupAtEnd (default=true) to be able to suppress 
+  writing a pickup at the last timestep
+o tools/mpack-1.6 : 
+  - disable automake (not working) and autoconf (not needed).
+  - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
+    also cleaner with much less compilation warnings.
+o pkg/profiles: 
+  rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
+  (for "less than 32 characters name" compiler requirement)
+o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
+  conditions that have a different sampling frequency than S/T/U/V obcs
+o pkg/diagnostics (stats-diags): 
+  - fix global Min/Max in case 1 processor get only empty tiles
+o genmake2: replace (4 times)
+     make genmake_tc_1.o >> genmake_warnings 2>&1
+  with
+     COMM="$CC $CFLAGS -c genmake_tc_1.c"
+     echo $COMM >> genmake_warnings
+     $COMM >> genmake_warnings 2>&1
+  to make genmake2 always see the value of CC as specified in the optfile.
+o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
+  - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
+  - modify verification advect_cs test to test SOM-advection on CS-grid.
+o pkg/ctrl:
+  - Rewrite of ctrl_map_ini_ecco.F, 
+    introducing a generic routine (ctrl_map_ini_gen.F).
+  - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
+
+checkpoint59n
+o pkg/diagnostics: for large number of diagnostics, store diagnostic mate 
+  number in dedicate array "hdiag":
+  - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
+    with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
+  - many small changes (integer format) for large number of diagnostics
+  - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
+    a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
+o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
+  usingSphericalGrid, this allows to define the rotated grid coordinates
+  via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
+  geographical coordinates according to the inverse of the rotation defined
+  by the Euler angles, so that Coriolis parameter and online-interpolation by 
+  exf works with the geographical coordinates on XC/YC/XG/YG.
+  Naturally, this feature does not work with all packages, so some 
+  combinations are prohibited in config_summary (flt, flt_zonal, ecco, 
+  profiles), because there the coordinates are assumed to be regular 
+  spherical grid coordinates. 
+o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
+  - introduce isopycnal diffusion coefficient control.
+o tools/adjoint_options: 
+  - additional control vector components.
+o pkg/mnc: have mnc create marginally meaning full coordinate variables
+  (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2 
+o pkg/mypackage: 
+  - add example of read/write pickup for state-var ; 
+  - add entry points to the main code for state-vars diags & write-pickup.
+o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
+  transitions for useExfYearlyFields
+  - add new subroutine that determines the file to read from for 
+    use*YearlyFields = .TRUE. and .FALSE.
+  - add a verification experiment to global_with_exf that tests 
+    useExfYearlyFields with USE_EXF_INTERPOLATION defined
+o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in 
+  analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new 
+  subroutines (which could be generated from a template, because they are 
+  almost identical), for now they are included in obcs_prescribe_read.F for
+  simplicity
+o pkg/exf:
+  - add a little more diagnostic to exf_interp_read (in analogy to 
+    mds_read_field, can be turned off with debugLevel < debugLevA=1)
+  - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
+    ugly but fast by unrolling short inner loops, inserting a unroll=8 
+    directive in routine lagran, and splitting a loop and making do while the
+    outermost loop (the latter requires the intoduction of index arrays)
+o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
+o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
+  http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
+o verification/seaice_obcs: updated for restart test and latest options
+o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
+  ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
+  for now this is only available for the C-grid code and also within
+  #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
+
+checkpoint59m
+o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
+  and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
+o gad_som : fix flux output (& diagnostics) to have same units as other   
+  advection scheme fluxes (was previously multiplied by deltaT).   
+o added verification/seaice_obcs both to test seaice open boundaries
+  and to provide an example matlab scrpt for generating them
+o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
+o pkg/salt_plume: clean up salt_plume_frac.F to
+  remove redundancy in PlumeMethod 1 and 4
+o pkg/kpp: added saltplume diagnostics
+o pkg/obcs and pkg/seaice:
+  - do not set uice and vice to zero when OB*icefile are unspecified
+  - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
+  - moved seaice tracer obcs after call to seaice_growth
+o pkg/salt_plume: added various options for salt plume depth
+  criterion and for vertical distribution of the salt
+
+checkpoint59l
+o pkg/ptracers: new version of ptracers pickup:
+  read meta file and write only fields which are needed to restart.
+  ( same logic as main pickup file ; also using pickupStrictlyMatch )
+o pkg/seaice:
+  - add timescale for melting due to warm mixed layer as a means of
+    setting SEAICE_availHeatFrac more conveniently
+  - add a CPP-flag/runtime parameter check for flooding algorithm
+  - reformulated availHeat in seaice_growth.F to be independent of AREA
+o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
+  unit changes
+o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
+o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
+  SX vector computer.
+o pkg/seaice:
+  - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
+    seaice forcing fields can now be read only through pkg/exf
+  - removed some unused halos
+o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
+o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
+  or U/VICE from U/VWIND before computing U/VSTRESS
+
+checkpoint59k
+o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
+  dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
+o fix un-initialised variable problem (in mom_vecinv & shap_filt):
+  all experiments pass when compile with un-initialised var. checking option.
+o added pkg/salt_plume
+o script to test restart (for now, in MITgcm_contrib/jmc_script)
+o pkg/seaice: new read/write pickup version. 
+  read meta file and write only fields which are needed to restart.
+  ( same logic as main pickup file ; also using pickupStrictlyMatch )
+o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
+o lab_sea.hb87: modify the domain & update output.hb87.txt :
+  lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
+  at j=1 & j=Ny+1 : this case is not treated correctly in the restart
+  process. Fixed here by closing the domain at the Northern boundary.
+o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
+o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
+  a set of consecutive levels in/from a 3-D array.
+o pkg/ptracers: 
+  use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
+  to-do: fix pkg/diagnostics when large number of diagnostics are defined.
+
+checkpoint59j
+o in pkgs: dic, obcs, offline, rbcs:
+  standard way to compute coeff. for time interpolation between 2 time reccords
+  which retains full precision (& make results less dependent on compiler).
+  update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
+o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
+  packages instead of reading ice cover and wind speed separately
+o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
+ (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
+  to allow to compile customized code before the update)
+o cleaning-up: 
+  - fix CPP instruction syntax in pkg/obcs
+  - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
+    add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
+  - fix some threads issue in IO parts.
+o pkg/dic:
+  - add tons of "_d 0" (--> much better testreports !)
+   and then update outputs of tutorial_global_oce_biogeo
 o pkg/mom_fluxform:
   add a special version of momentum advection intended to conserve momentum
   next to a bathymetry step or a coastline edge. (default = off = #undef)
@@ -61,11 +323,13 @@
 o add new diagnostics to seaice: advective, diffusive fluxes (only for
   multidim-advection, for scheme 2 they are not filled) and transports, 
   thermodynamic growth rates
-o change units of EmPmR (inside the code) from m/s to kg/m2/s (mass flux) but
-  leave input file unchanged. Affects results @ truncation level (cg2d match)
-  and update output of experiments: lab_sea(6), global_ocean.90x40x15(10),
+o change units of EmPmR (inside the code, + within coupling interface)
+  from m/s to kg/m2/s (mass flux) but leave input file unchanged.
+  Affects results @ truncation level (cg2d match) and update output of 
+   experiments: lab_sea(6), global_ocean.90x40x15(10),
   global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
   + adjoint results: global_ocean_ebm(11) and lab_sea (12).
+  Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
   Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
 
 checkpoint59h