--- MITgcm/doc/tag-index	2005/03/24 14:51:34	1.465
+++ MITgcm/doc/tag-index	2005/12/08 15:34:24	1.587
@@ -1,8 +1,344 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.465 2005/03/24 14:51:34 baylor Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.587 2005/12/08 15:34:24 heimbach Exp $
+$Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+checkpoint57y_pre
+
+o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
+o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
+o add new offset feature to offline pkg (plus minor cleanup)
+o cfc fixes for final year of integration
+o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
+  be in GCHEM_OPTIONS).
+
+checkpoint57x_post
+o fix testreport Pb in multiple test experiment.
+o cleanup our namelist syntax in verification:
+  - make it more F95 standards compliant (some work still needed)
+  - allows the vast majority of our tests to work with gfortran
+o Non-Hydrostatic:
+ - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
+ - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
+o Allow to apply AB on T,S rather than on AB(gT,gS):
+ - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
+ - use the same arrays (gtNm,gsNm) to hold tracer field at previous
+   time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
+ - need a "clever" read_pickup to restart from the other AB formulation
+o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h 
+o remove some unused variables (reduces number of compiler warnings)
+o adjoint
+  * Disable useVariableViscosity for adjoint for time being
+    (there are a number of extensive recomputations)
+  * Initialize certain variables needed for adjoint
+
+checkpoint57w_post
+o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
+             fix the singleCpuIO RS version of MDSWRITEFIELD
+   and add a WARNING if using globalFiles=T with multi-processors.
+o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
+  using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
+o tracer advection scheme:
+  add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get 
+   those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile, 
+   was not very convenient).
+  add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
+   (further tests needed for the implicit DST & Flux-Limiter schemes).
+o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
+  and sRef for convenience, handy, when you want to initialize
+  ptracers in a large domain with a constant non-zero value. Also,
+  untangle ptracers_init.F a little.
+
+checkpoint57v_post
+o change dome exp. to use variable viscosity in side-drag terms.
+o remove all the files from the cfc_offline test since they are now
+  incorporated into tutorial_cfc_offline which has been producing
+  identical results for a few days of testing
+o add new parameter: sideDragFactor to enable half-slip-side BC
+  and change side-drag S/R to use viscosity from mom_calc_visc
+  (can switch back by setting sideDragFactor=0.); affects results at 
+  truncation level; regenerate output for exp.: global_ocean.cs32x10(x3), 
+   global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
+o vorticity & strain are now computed without masking, to account for 
+  no-slip-side BC in variable viscosity calculation ; mask is applied
+  anyway later on, before computing advection/coriolis terms.
+o modify exp4 to test new obcs support for reading from external files
+  and for passive tracers
+o fix behavior of ptracers_monitor when monitor output is written to a 
+  netcdf-file; still not independent of monitor.F (writes in the same
+  file).
+o change default value of tRef (put a uniform, meaningful value for ocean 
+  & atmos) and initialize sRef (was missing, as Martin mentioned).
+o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity 
+  to be proportional to enstrophy dissipation length.  Thus,
+   viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
+  This is now consistent with Smagorinsky and with the manual.
+
+checkpoint57u_post
+o OBCS and PTRACERS: add open boundary support for passive tracers
+  - either use homogenous (pseudo) v.Neumann conditions or prescribe 
+    OB-values from file; this is not different from the way theta and salinity
+    are treated
+  - however, Orlanski-radiation conditions are not supported, and the model
+    will stop if you use pTracers and Orlanski at the same time. 
+  - beefed up the rountine obcs_external_fields_load: now only those open
+    boundary values are overwritten with values from files for which there 
+    are really files, otherwise the OB-fields remain untouched. This makes
+    it possible to use different OBs at different ends of the domain (as 
+    with EXF)
+o reduce number of exch calls in shap_filt (s2). 
+o CS-grid: fix divergence contribution to Leith viscosity. Affects (@ 
+  truncation level) 4/5 MLAdjust test results (11&12 digits match).
+
+checkpoint57t_post
+o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
+o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
+  same truncation, independent of the face number: affects affects several
+  test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
+o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
+  note that biharmonic viscosity + no-slip was not tested in any experiment.
+o fix bug in non-linear free-surf side-drag ; generate new output for
+  global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
+o make mnc honor the writeBinaryPrec flag for most kinds of output
+o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
+o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
+  error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
+o add brackets in multi-terms sum to get same truncation, independent of
+  the face number (manage to get exactly same value of gU,gV at the cs-edge)
+  affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
+o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
+  and viscA4Remax, which allow one to limit the minimum viscosity by specifying
+  a maximum grid-scale Reynolds number.  Also, changes all length calculations
+  in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
+  Suggested values of viscosity parameters found in mom_calc_visc. 
+  Many new viscosity diagnostics available.
+
+checkpoint57s_post
+o Add clearing-house for viscosity calculations, mom_calc_visc and 
+  correct numerous bugs in LeithD and Smagorinsky discretizations.  
+  mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be 
+  used simultaneously, and to be used in mom_vecinv and mom_fluxform. 
+  Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
+  and with Strain-Tension viscous term calculation (mom_hdissip.F).  
+  The Strain-Tension form is now called with useStrainTensonVisc=.true.
+  ViscAhStrain and viscAhTension are now retired.
+o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
+o In response to JMC's bug report, genmake2 now ignores any soft-links
+  that it finds in the *current* directory when searching for files.
+  Soft-links found in any other source directories will still work as
+  they did before.
+o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls 
+  a C routine to unlimit the stack size
+o mnc-ify pkg/aim snapshot vars
+o mnc-ify pkg/land as requested by Daniel
+o various changes to mnc including:
+  - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
+  - output can now be grouped so that all files within a group 
+      change the ITER portion of their names in lock-step together
+  - can now read ("global") PER-FACE (in addition to PER-TILE) files
+      and works with both EXCH1 and EXCH2 (but needs more testing)
+  - writing works for all verification test cases w/ g77 on Linux
+
+checkpoint57r_post
+o make MNC variable initialization happen earlier
+o add diagnostics for (almost) each term of the momentum Eq.
+o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
+o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
+o remove MINIMAL_TAVE_OUTPUT option ; 
+  add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
+o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
+  allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
+o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
+o add time-dependent SST, SSS control
+o cost terms in ecco/ modularized (new cost_generic.F)
+o cost_averages routines are modularized (new cost_averagesgeneric.F)
+o new infrastructure for seaice model vs. obs misfits in seaice/
+  * driver from the_main_loop.F is seaice_cost_driver.F
+  * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
+  * gradient check in Exp. 6a of natl_box_adjoint/
+o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
+  (see README file)
+
+checkpoint57q_post
+o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
+o fix annoying months-old bug in mnc/mdsio output for seaice pkg
+  - bug was reported by Jean-Michel and Ian Fenty
+o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
+  update exp. cpl_aim+ocn output. 
+o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
+  Needed for high-res. runs with large global files 
+  to be able to limit tapelev size
+o Changed some tests for adjoint:
+  * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
+  * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
+  * global_ocean.90x40x15/ back to default 3-level checkpointing
+o Modifications to enable scripted COMMON to MODULE conversion
+  * verification/OpenAD/code/ has necessary scripts and description;
+  * converts, compiles and runs successfully;
+
+checkpoint57p_post
+o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
+o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
+  (already the case for some pkgs, including recent MNC_init, e.g. thsice)
+o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
+o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
+  (was already the case for dissipation with mom_vecinv,
+   and also the case for grad.PhiHyd when staggered-timeStep)
+  This will allow to put dissipation out-off the AB time-stepping.
+ Unfortunately, affects truncation error. Update output of exp. that "fails"
+  (cg2d matching number) and leave the others for later: front_relax(10),
+  global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
+  matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
+
+checkpoint57o_post
+o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and 
+  (2) its ready to be documented during the 20050801 DocFest
+o MNC-ify the gmredi package -- tested and works w/ and w/o mnc 
+  for ideal_2D_oce and lab_sea on linux_ia32_g77
+o set to #undef CTRL_SET_OLD_MAXCVARS_30
+  in global1x1_tot/code_seaice_adj to access indices 32, 33
+  (worth another tag)
+
+checkpoint57n_post
+o adding precip control xx_precip 32
+o adding swflux control xx_swflux 33
+o Replacing 10 forcing penalty cost routines by 1 generic.
+o Implementing partitioning in time-mean and variable adjustment
+  for atmos. state.
+o Time-mean constant error is now read in data.ecco (instead of hard-coded)
+o in natl_box_adjoint:
+  * updated exp 1 to 10 
+    (but does not have time-mean vs. variable split results yet)
+o updated global1x1/*_seaice_adj/
+  to incorporate latest changes
+o enable useSingleCpuIO for mdsio vector routines
+  (applies in particular to tapelev I/O)
+o removed inefficient K-loop in all active_file*control*.F
+
+checkpoint57m_post
+o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
+  and advect_cs (use EXCH-2 and standard cs-32 grid files).
+o pkg/exch2: filling of face-corner halo regions is optional 
+  (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
+
+checkpoint57l_post
+ tag before updating tutorials (pre-release-2) 
+o add cos & sin of grid-direction orientation angle (curvilinear grid only,
+   for output and interpolation of input fields onto model grid)
+o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
+   Affects results of exp. rotating_tank ; update output.txt.
+o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
+      and taking the square quantity and/or using a fraction-weight field.
+o fix aim_diagnostics_init.F mate numbers.
+o add mnc output capability to diagnostics/diagstat and update
+  our cvsignore files for the ACSII output generated
+
+checkpoint57k_post
+o lab_sea now uses diagnostics package and provides a suite of
+  new EXF diagnostics output.
+
+checkpoint57j_post
+o exf
+  * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
+    Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
+    terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
+  * extended diagnostics output
+    - now includes all EXF variables
+    - hs, hl moved to common block
+    - separate S/R for diagnostics, called after ctrl vector is added
+    - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
+    - EXFqnet contains true Qnet (i.e. includes qsw)
+  * updated verif. lab_sea, global_with_exf
+  * Rearranging hflux (exf_mapfields -> exf_getforcing)
+    to ensure that diagnostics sees a true EXFqnet
+o add matlab scripts for CS-grid vectors (in utils/cs_grid)
+o diagnostics pkg: change pointers so that 1 diagnostic can be used
+  several times with different frequencies.
+o mnc-ify the thsice package as requested by Daniel Enderton
+  - the monitor--MNC output needs work
+  - many attributes need to be added (most are currently blank)
+o mnc-ify theaim_v23 package as requested by Daniel Enderton
+  - many attributes need to be added (most are currently blank)
+o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
+o add Sadourny like discretization to the 4th.O vorticity advection scheme
+o fix bug in rStar code (calc_r_star.F) when used with topo/bathy. 
+  update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
+     fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
+o fix few little things to avoid floating error with -ftrapuv (ifort v9)
+ (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
+
+checkpoint57i_post
+o Diagnostics package was changed: diagnostic allocation is now deactivated
+  by setting an empty file name in the namelist (used to be by setting 0 frequency)
+o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
+  add 1rst Order upwind vertical Shear.
+o add a quick fix for A/B checkpointing in OFFLINE mode
+o add IGNORE_TIME define and -ignore_time option to genmake2 as an
+  end-run around the C/Fortran linking horror in eesup/src/timers.F
+o added pkg/runclock: allows user to terminate run based on wall clock
+o added non-hydrostatic scaling parameter: nh_am2
+o pkg/my82: futile attempt to make results compiler-independent by adding
+  some "_d 0", etc. no effect.
+o for mnc output, fill the 'T' coordinate var with myTime and create a 
+  separate 'iter' variable for iteration count
+o pkg/diagnostics: 
+  add new capability: output of Global/Regional & per-level statistics ;
+  tested against monitor output (including land & thSIce) on various exp.
+o make seaice-pkg I/O type flags (MNC/MDS) more standard.
+
+checkpoint57h_done
+  tag after changing user customized files (DIAGNOSTICS_SIZE.h, 
+  data.diagnostics, data.gchem, data.ptracers) is done.
+
+o pkg/diagnostics: prepare for Global/Regional statistics. 
+  add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h 
+o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
+  and rename it: DIFFERENT_MULTIPLE
+
+checkpoint57h_post
+o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
+o pkg/diagnostics: change output frequency, now in seconds (instead
+  of Nb of iterations). This requires to change data.diagnostics.
+checkpoint57h_pre
+
+o in mnc, let the user create the output dir if both mnc_outdir_date
+  and mnc_outdir_num are false
+o add fflags() to pkg/diagnostics which allows one to specify, on a
+  per-file basis, the file precision [default behavior is unchanged]
+o added diagnostics to pkg/kpp, including computation of mixed layer
+  depth based on a temperature/density criterion
+o updated verification/natl_box to test the new pkg/kpp diagnostics
+o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
+o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
+o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
+  not mnc -- this mistake was found by JMC and is now corrected
+
+checkpoint57g_post
+o add Adams-Bashforth 3rd Order time stepping:
+  - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
+  - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
+checkpoint57g_pre
+
+o make lambda[Theta,Salt]ClimRelax spatially varying
+  (default remains spatially uniform constant based on tau)
+o added new control variables
+  * init. uVel, vVel, etanN
+  * lambda[Theta,Salt]ClimRelax
+o separate masks used for ctrl_pack/unpack 'from write_grid' output
+  (suggested by G. Forget)
+
+checkpoint57f_post
+o add parameter "baseTime" = model base time = time at iteration zero
+  new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to 
+  account for baseTime shift
+o move Coriolis arrays from PARAMS.h to GRID.h
+checkpoint57f_pre
+
+o mnc-ifying the seaice package
+o introduced an alternative length scale calculation for use in the limiting
+  maximum viscosity (off by default, see mom_vi_hdissip.F for details)
+o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
 o added modified Leith scheme with viscosity proportional to grad(Hdiv) 
   as well as grad(vort3).  Made it compatible with both approximate form
   for the cubed sphere and full form of these gradients.  Added flag
@@ -13,10 +349,14 @@
 o fix obscure MNC bug involving conversion between reals and integers
   - it caused no problems with certain (eg. gcc, ifc) compilers but the 
     new version is now more standards-compliant
+o adjoint-related modifications
+  * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
+  * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
+  * mom_vi_hdissip: to be able to use Leith scheme in adjoint
 
 checkpoint57e_post
 o Adding eddy stress controls a la Ferreira et al.
-checkpoint57e_pre
+checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
 
 o fizhi pkg: fix AtoC and CtoA when called with same input & output array
   update output.txt of exp. fizhi-gridalt-hs