--- MITgcm/doc/tag-index	2004/05/24 14:10:02	1.301
+++ MITgcm/doc/tag-index	2004/11/19 13:55:26	1.389
@@ -1,9 +1,324 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.301 2004/05/24 14:10:02 adcroft Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.389 2004/11/19 13:55:26 jmc Exp $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+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. 
+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)
+  output of: global_ocean.cs32x15, global_ocean_pressure & internal_wave
+o cnh's modifs to gad_advection.F for cube-sphere multi-dim advection
+o new parameter "nShapS": allow to treat differently S from T (nShapT)
+o separate Vert.Advec.Scheme from horizontal Advec.Scheme (T & S)
+o restore adjointability
+
+checkpoint53f_post
+o modifications that affect AIM experiment results (update output.txt):
+  - no advection of S at top interface Nr (pkg/generic_advdiff) 
+  - air surf. temp: use lower value between T0 & T1 (phy_suflux_prep.F)
+o AIM pkg:
+  - include stability function into surf.Flux derivative relative to Tsurf
+  - calculate clear-sky radiation & surface temp. change (for diagnostics)
+ 
+checkpoint53e_post
+o merged cylindrical coord configuration
+o added rotating_tank experiment
+checkpoint53e_pre
+
+checkpoint53d_post
+o faulks upgraded: re-generate output.txt that have changed:
+   global_ocean.cs32x15(.thsice), global_ocean_ebm, lab_sea, natl_box
+o Added Bryan and Lewis, 1979, vertical diffusivity profile
+o pkg/land: fix problem in land_impl_temp.F when Ts arround freezing. 
+o added Sadourny discretization of Coriolis
+  - moved some PARAMETERS from mom_*_coriolis.F to PARAMS.h
+  - re-enabled use of omega3 (useAbsVorticity)
+o added Leith (Phys. Fluids, 1968, 10, 1409-1416) variable viscosity for
+  vector-invariant equations
+  - note: does *NOT* yet use same variable visc. for no-slip BC's.
+o recoded the lateral boundary conditions for non-hydrostatic w, this time
+  hopefully without new bugs
+  - still to do: biharmonic friction for non-hydrostatic w
+o bug fix for mom_*_sidedrag: rA -> rAs,rAw
+o regenerated output for global_ocean_ebm (using -ieee)
 o fix mom_common/mom_*_sidedrag.F to recover numeric output prior to creation
   of mom_common/
   - simple re-arrangement of instructions within computing loop