--- MITgcm/doc/tag-index	2004/07/02 16:00:06	1.318
+++ MITgcm/doc/tag-index	2004/12/17 19:17:56	1.418
@@ -1,8 +1,414 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.318 2004/07/02 16:00:06 heimbach Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.418 2004/12/17 19:17:56 dimitri Exp $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
+o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
+o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
+  this is based directly on what the model compute, so that the content of
+  each diagnostics might be affected by switching options (e.g., implicitDiffusion)
+o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
+o clean up build options files for SunOS, in particular 
+  - remove -traditional from xmakedepend
+  - change -xarch=v9 to -xarch=native for f77
+  - restore use of make (not gmake)
+  - add CC=gcc if using g77
+o changes per discussion of AM, JMC, & EH3 today:
+  - move redundant "grid" variables out of "state" -- in preparation of 
+    creating proper CF-style coordinate variables and in recognition 
+    that any/all grid variables can be easily copied (eg. w/NCO) from 
+    the grid files into any of the other NetCDF files
+  - *always* output grid variables with MDSIO (this will eventually be 
+    changed)
+  - output MNC grid file if useMNC is true
+o every instance of _END_MASTER() has been found and replaced with 
+  _END_MASTER( myThid ) in order to satisfy certain picky Sun 
+  preprocessors
+o re-arrange diagnostics pkg initialisation:
+ - allow each package to extend the available diagnostics list
+ - add some checking and fix small problems (multi-threaded, ...)
+ - new S/R diagnostics_fill (replace fill_diagnostics):
+   look through the short list of active diag. (instead of the long list)
+   create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
+
+checkpoint57a_post
+o this set of changes restores TAMC compatibility
+  tested for global_ocean.90x40x15 adjoint on trough
+  (what a pain)
+
+checkpoint57a_pre
+o some modifs in tools/build_options for sunos
+o call ctrl_pack for ctrl at end for optimcycle=0
+
+checkpoint57
+o add horizontal bi-harmonic viscosity for vertical velocity
+  - new parameter viscA4W (defaults to viscA4)
+  - affects only non-hydrostatic code
+  - to be done: no-slip lateral boundary conditions
+o switch back to "sflux = sflux - runoff" in exf_getforcing.F
+o implement Implicit Vertical advection for pTracers
+o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
+  (implemented also for implicit vertical diffusion & advection)
+o OBCS: extend application of tracer open boundary conditions
+  to a strip beyond the boundary of width Olx/Oly
+o add call monitor to TAF set of required calls (flow directives)
+  and include in natl_box_adjoint
+o untangle a few ifdefs related to cost, ctrl, autodiff
+  untangel a few ALLOW_ECCO_OPTIMIZATION
+o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
+  (theta2, salt2 in ecco_cost_weights)
+
+checkpoint56c_post
+o OBCS as control variables
+  - update ctrl_ad_diff.list, obcs_ad_diff.list
+  - remove balance of obcs controls from default
+  - fix index bug nobcs in ctrl_init
+  - fix dummy fields filen in ctrl_pack
+  - add dummy weights for obcs
+o lsopt: comment out fort.94 output
+o optim: 
+  - remove unnecessary header files
+  - adjusted namelists
+  - add xerbla.F to Makefile
+o exf: 
+  - multiple modifications of exf_check_range
+  - unit change in exf_init_runoff from [m/year] to [m/s]
+o mdsio:
+  - i/o-vector change debugLevel from debLevA to debLevB
+
+checkpoint56b_post
+o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
+  is called from DO_THE_MODEL_IO
+  - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
+  - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
+  - clean up PTRACERS_WRITE_TIMEAVE a little
+o add another verification experiment that tests both the cfc-pkg and
+  the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with 
+  reactive tendencies treated inline with regular timestepping
+o testreport previously did a lousy job of comparing small numbers, so
+  we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
+  implemented in the little c-progam tmp_cmpnum.c which is embedded in
+  testreport. 
+o ptracers_monitor: bug fix for MPI
+
+checkpoint56a_post
+o GCHEM: finish reorganizating the package
+  - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency 
+    (introduces another 3D-array for each passive tracer, but only if
+    GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
+    gchemTendency is not needed because the timestep is done separately)
+  - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
+  - GCHEM is now---more or less cleanly---separate from PTRACERS
+  - to bo done: handling of surfaceForcingPtr that is needed for KPP not
+    so clear to me how that should be done in a general way.
+o CFC: improve formatting of output in CFC_ATMOS
+o PTRACERS:
+  - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
+    that ALL experiments with ptracers enable can be checked. This makes
+    GCHEM_MONITOR obsolete.
+  - include a runtime parameter PTRACERS_monitorFreq that defaults to
+    monitorFreq
+  - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true 
+o add PTRACERS (PTR0[1-5]) to testreport output
+o exf_check_range:
+  * default changed to .TRUE.
+  * will check values for niter0 if debLevA, every timestep if debLevB
+  * STOP in exf_check_range if 'out of range'
+  * range chosen generous to allow for potential extema
+  TBD: a version with stricter range
+       permitted range would be runtime parameters
+o GMredi:
+  - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
+  - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
+  - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
+o GCHEM: 
+  - move call to GCHEM_FORCING_SEP, so that it is now called before
+    the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
+  - introduced a useGCHEM runtime flag and applied it everywhere. 
+  - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
+    this flag is now only visible within GCHEM-pkg routines.
+  - moved gchem_forcing_int temporarily into ptracers_forcing, this will
+    be replaced by a 3D array that is computed before thermodynamics; for 
+    this, the tracer ID iTracer had to be included into the parameter list
+    of ptracers_forcing
+  - set up forward_step to call gchem_forcing, that will replace 
+    gchem_forcing_int in ptracers_forcing
+  - cleaning up
+o small cleaning of exch2: remove files that are also in eesupp/src
+
+checkpoint56
+o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
+o mnc: cleanup "full" files--fixes out-of-memory problem
+o ECCO-GODAE
+  * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
+  * fully merged and updated from SIO code
+    windstress sign change affects
+    - exf_inscal_[u/v]stress
+    - sign of xx_tau[u/v] adjustments
+    - signs in cost_scat
+  * ctrl_get_gen: avoid update of tau[u/v] for first few days
+  * natl_box_adjoint updated and compressed
+  * 2-level checkpoint switch added
+    (tested in EXP. 1 of natl_box_adjoint)
+  * new switch doInitXX to avoid init. of xx_... in optimcycle=0
+o SVD
+  * first complete, non-hacked version for SVD calculations
+  * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
+    performed via direct access files admtlm_vector.it????
+    (via ctrl_[un]pack)
+  * optimcycle is used for ARPACK iteration counter
+    (note: adxx_... is iterated, rather than xx_...; latter is constant!)
+  * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
+    and add linear transforms where necessary 
+  * controls are initial/final SST, SSS (can be extended; need to check
+    ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
+o mdsio: filename info to both stderr, stdout
+o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
+  from sign change 
+
+checkpoint55j_post
+o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
+  affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
+o add consistent build directories and .cvsignore files to verification
+o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
+o make all subroutines 30 or less characters in length for certain older 
+  compilers to work (a thorough search only turns up two routines in 
+  pkg/ptracers)
+o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity; 
+  affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
+
+checkpoint55i_post
+o change arrays for total vertical diffusivity (2.D if explicit,
+  3.D if implicit) ; each ptracer uses its own background value.
+o added mnc/NetCDF output capability to ocn_compon_interf
+  - added bits to verification/cpl_aim+ocn so that it can run on 
+    ITRDA and other clusters without the mpirun "-wd" option
+o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
+  configuration 
+o give MNC the ability to create additional files rather than 
+  exceeding a specified file size limit "MNC_MAX_FILESIZE" 
+  - the default is just less than 2GB which is a practical limit 
+    on many systems
+o Compute the non-local term using either KPP vertical diffusivity (=default) 
+   or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
+
+checkpoint55h_post
+o add verification test "vermix"
+o remove all the *_ioinc flags and replace with the single global
+  outputTypesInclusive flag
+o allow to set a vertical profile of vertical diffusivity for T & S
+o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
+o useMNC moved from data.mnc to data.pkg
+
+checkpoint55g_post
+o Renaming carbon AD experiments to comply with testreport conventions
+o Updating adjoint of Held-Suarez hs94.1x64x5
+o Fixing directives for non-ECCO forward_step, after ECCO directives
+  have been fixed to avoid recomp. of do_oceanic_phys
+  Works well for global_ocean.90x40x15,
+  but recomp. issue remains for carbon
+o Updating adjoint output for natl_box_adjoint after 
+  pkg/ecco has been modified (see taga c55d_post)
+
+checkpoint55f_post
+o rename to timeave_init_fixed
+
+checkpoint55e_post
+o some delicate re-shuffle of store directives to avoid one
+  extra call of do_oceanic_physics
+  affects ecco_the_main_loop.F, do_oceanic_physics.F
+  checkpoint_lev1_directives.h
+o NB: this may break global_ocean adjoint temporarily,
+  but it is clear how to fix it. Will do later, need this now.
+
+checkpoint55d_post
+o ECCO specific cost function terms (up-to-date with 1x1 runs)
+o ecco_cost_weights is modified to 1x1 runs
+o modifs to allow observations to be read in as
+  single file or yearly files
+o enable to read exf forcing fields as either
+  single file or yearly files (flag useExfYearlyFields)
+checkpoint55d_pre
+
+o switch between 2-level and 3-level checkpointing
+o add ability of MNC to write local and "partial" (eg. 2D slices where 
+  the full 3D field is never actually stored) arrays to NetCDF files
+  with the correct (that is, the complete multi-dimensional) set of 
+  array indicies
+  - used in mom_vecinv() to write the diagFreq output
+  - tested (demonstrated) in verification/aim.5l_cs
+o further mnc-ification
+  - add verification/lab_sea to the list with mnc setups
+  - fix undefined mnc v-names in cd_code
+  - add kpp to mnc output (both snapshot and timeave)
+o non-hydrostatic code
+  - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
+    in calc_gw.F
+  - defaults to viscAh
+  - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
+    friction or Leith) in non-hydrostatic mode, as long as there is 
+    no biharmonic friction and/or Leigth or equivalent for vertical velocity.
+o pkg/cost
+  extend simple cost functions to treat time mean quantities
+  (T,U,V) via cost_accumulate_state from cost_tile
+o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
+    be 2 times larger than the minimum size the advection scheme requires.
+    now get a perfect conservation of salt in advect_cs test-exp (updated)
+o GGL90 (Gaspar's TKE mixed layer)
+  - add horizontal diffusion of TKE, requires exchanges in 
+    do_fields_blocking_exchanges, horizontal diffusivity is zero by 
+    default. In OPA there is no horizontal diffusion of TKE but the 
+    mixing coefficients are computed from a horizontal average of TKE of
+    6 points or so. I think that diffusion has a little more physical
+    justification.
+  - clean up ggl90_calc in the hope of reducing memory usage (this hope 
+    was in vain)
+  - mask tke-variable in ggl90_init
+o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
+o fix biharmonic diffusion on CS-grid.
+o more obcs stuff
+  - added obcs_external_fields_load as an alternative to the EXF-pkg option
+    for reading boundary values. This routine is called from 
+    obcs_prescribe_read
+  - updated obcs_check
+  - changed sponge layer relaxation parameter units for days to seconds
+  - turned off sponge layer by default
+  - changed argument list of OBCS_CALC to myTime+deltaTclock
+  - fixed about 35 bugs in obcs_external_fields_load
+
+checkpoint55c_post
+o obcs stuff
+  - new runtime flags useOBCSprescribe, useOBCSbalance
+  - re-arranged obcs_calc
+  - moved exf_getobcs to obcs_prescibe_read
+    obcs_prescibe_read is called after ORLANSKI stuff
+    and independent of it (executable can contain all).
+  - updated obcs_check
+  - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
+    These may be necessary only if tangential velocities are
+    prescribed at OB, not sure, needs testing.
+o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
+  which simplifies the calls and passes the ifc check-bounds test
+
+checkpoint55b_post
+o add a 2D scalar, Z location, exchange_2 routine.
+o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
+  to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
+  affects advect_cs results (for the wrong reason): update output.txt
+o use a more standard discretization for biharmonic viscosity ; 
+ (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
+  affects results of dome set-up: update output.txt 
+o fix gad_advection.F (CubedSphere part), back to version 1.23
+o fix bug in mom_vi_del2uv.F (CubedSphere part).
+
+checkpoint55a_post
+o merged code to 
+  * prescribe/read time-dependent open boundaries
+    (works in conjunction with exf, cal)
+  * sponge layer code for open boundaries
+  * each boundary N/S/E/W now has its own CPP option
+    (healthy for the adjoint)
+
+checkpoint55
+o up-to-date adjoint of previous breaks
+  - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
+  - global_ocean_ebm: adjoint still needs fix (TLM ok)
+  - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
+  - carbon: * remove tr1-related adjoint verification
+            * add ptracer as control variable
+o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
+  (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
+
+checkpoint54f_post
+o in verification/carbin/ remove experiment related to
+  ALLOW_PASSIVE_TRACER (array tr1 etc)
+  code_ad/ input_ad/ results_ad
+
+o add two new packages
+  - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
+    + subject to optimization (memory)
+  - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
+    + subject to reordering (many GOTOs in the original code)
+    + so far opps is called for every (i,j) point, and then operates in
+      the vertical; one may want to reorder the scheme in order operate in
+      horizontal slabs at the cost of (a lot of) memory, at least ten new 3D 
+      fields)
+o overhaul of IO so that we now have flags for MDSIO and/or MNC
+  - all verification tests compile and run with linux_ia32_g77
+  - defaults are compatible with current input files--nothing 
+    should change if you were not previously using MNC
+  - MNC output has been added in numerous places (eg. timeave)
+    but there are still a few writes not yet do-able with MNC
+    (this is in progress)
+  - flags now allow for either/or/both use of MDSIO and MNC and 
+    documentation will soon follow
+  - numerous small formatting cleanups for ProTeX
+o add version info (via BUILD_INFO.h) to MNC and stdout
+
+checkpoint54e_post
+o add two new packages
+  - pp81 (Packanowski and Philander, 1981), Richardson number and 
+    stratification dependent mixing
+  - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
+  - these scheme operate in a similar manner as KPP (without ghat, of 
+    course), however there is only one diffusivity that is used for both
+    temperature and salinity (and passive tracers)ç
+o add offline package
+o add "verification/dic_example" which contains a dic-gchem-ptracer setup
+  provided by Stephanie Dutkiewicz
+o genmake2: add ability to search for C compilers and cleanup test output
+  - fixes recent SX-6 problems and should help with others (eg. HP-UX)
+
+checkpoint54d_post
+o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
+o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong, 
+  leading to additional shift by 5 days each year of integration
+   (i.e. leading to considerable offset over the years)
+o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
+o start with no AB and no initial filtering (staggerTimeStep):
+  change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
+o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
+  (external loading & cpl import/export stay in forward_step.F)
+o update coupling interface to work with new staggerTimeStep
+o change MDSIO ptracers_pickup.
+o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
+o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
+o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
+
+checkpoint54c_post
+o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
+  this affects (truncation error) output.txt of test-exp:
+   global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
+o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
+o change Qnet to always be the net heat flux, (+upward).
+  affects (truncation error) output of natl_box exp.: updated
+o define the max number of passive tracers in PTRACERS_SIZE.h
+o start to test mnc routinely in exp0
+o add sea-ice loading (sIceLoad) as a new forcing field.
+
+checkpoint54b_post
+o add testreport "-j JOBS" option for parallel builds (tested and pretty 
+   impressive on Altix and Opteron systems)
+o diagnostics can now write NetCDF files through the mnc package
+o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
+o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added 
+o staggerTimeStep & NLFS: rescale T & S surface tendencies.
+  affects (truncation error) output of lab_sea & natl_box exp.: updated
+o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
+
+checkpoint54a_post
+o re-write staggerTimeStep: step fwd U,V and then T,S (reverse the order).
+o change pickup file (to restart from old pickup, set usePickupBeforeC54=.T.)
+o get a perfect restart when using RealFreshWaterFlux + NLFS (not finished)
+o update output of all exp. that use staggerTimeStep (except hs94.cs & 2D)
+  + internal_wave (shift in writing cg2d_ini_res)
+checkpoint54a_pre
+
+o require forcing_In_AB=.FALSE. and remove surfaceTendencyTice from pkg/seaice
+  - modified verification/lab_sea and natl_box_adjoint accordingly
+
+checkpoint54
 checkpoint53g_post
 o prepare splitting of thermodynamics: store convect.counter in common block
 o store d.etaH/dt (instead of Div.hV) in common ; affects (truncation error)