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revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.706 by jmc, Sun Jul 16 00:27:38 2006 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7  o adding precip control xx_precip  o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
8  o moved ptracer ctrl index 17 -> 32     keep global_ocean.90x40x15 (for AD testing) with former secondary test
9       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
10    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
11        add MITgcm_tutorials (= code + all the tutorials)
12    o ecco, option to compute cost for total ssh (mean+anom)
13    o consistent with addition of ptracer and ssh in pkg/profiles
14    o profiles: adding ptracer and ssh
15    o testreport: change multi-test output-file name
16      (from output.txt.{name} to output.{name}.txt)
17    o profiles: now ok for mutli-threaded case
18    o seaice: add 4 parameters for different advection schemes for area,
19      (effective) seaice thickness, enthalphy, and snow height. Their default
20      is the standard parameter SEAICEadvScheme
21    o calc_gw:
22     - add cosFacU in zonal viscous flux (harmonic.visc.).
23     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
24       of tutorial_plume_on_slope.
25    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
26    o calc_gw: true flux-form, account for horizontal grid spacing.
27      update rotating_tank results, but not plume_on_slope (affected at
28      truncation level, 11 digits).
29    
30    checkpoint58l_post
31    o calc_gw:
32     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
33     - remove side-drag for now (need to fix it); update plume_on_slope results.
34     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
35    o commit code to make SST/SSS weights spatially variable
36      (based on either variable in-situ or variable initial T/S weights)
37    o pkg/ecco:
38      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
39        now based on horizontally varying weights wthetaLev, wsaltLev
40      * cost_averagesflags now returns year indices in addition to day, month
41      * sflux balance is performed on annual basis
42        (sflxumm, sfluxmm2, bal_sfluxmm)
43      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
44        including separate counting and multipliers
45    o pkg/rbcs
46      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
47    
48    checkpoint58k_post
49    o testreport:
50     - always build in dir. "build" (if not there, mkdir build instead of building
51       & running in input)
52     - run in dir run (if it exists), in build otherwise.
53     - call prepare_run (if input/prepare_run exists)
54     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
55    o pkg/exf modifications to interpolation and rotation routines for more
56       reasonable treatment of North Pole singularity: for tracers North Pole
57       value is set to northernmost zonal-mean value, for zonal velocity it is
58       set to zero, and for meridional velocity it is set to northernmost value.
59    o pkg/exf/exf_check_range.F
60     - add tile index to diagnostics and move stop statement to the very
61       end of the routine.
62    o pkg/diagnostics: (diagnostics_main_init.F)
63      define title of isomorphic variables according to the current config.
64    o pkg/thsice with pkg/seaice dynamics:
65    - fix domain of computation (interior only, required for exf) and do exchanges
66    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
67    o towards a standard way of dealing with multi-threading in MONITOR
68      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
69    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
70       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
71    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
72    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
73    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
74       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
75    o tracer advection:
76     - clean-up and simplify calc_common_factors.F
77     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
78       advection subroutine (but still not used within DST advection S/R)
79    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
80    
81    checkpoint58j_post
82    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
83      from file (collects calls previously in FORWARD_STEP)
84    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
85    o adjoint store dir. adjusted accordingly
86    o genmake2
87      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
88    
89    checkpoint58i_post
90    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
91      on wind stress (SEAICEstressFactor defaults to 1.)
92    o Total number of Timers is finite (<=40): comment out 2 non-essential one
93      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
94    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
95      on CS-grid: no longer loosing mass.
96    o exf & curvilinear-grid: no longer modify longitude xC & xG.
97    o pkg/ggl90: fix sloppy output and fix a bug
98    o pkg/seaice: added SEAICEuseEVPpickup parameter
99      - Set to false in order to start EVP solver with
100        non-EVP pickup files when using SEAICEuseEVP
101      - fix sign error in diffusion in seaice_calc_rhs
102    
103    checkpoint58h_post
104    * Modifications for bottom topography control
105      o replace hFacC by _hFacC at various places
106      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
107      o add non-self-adjoint cg2d_nsa
108      o update autodiff support routines
109      o re-initialise hfac after ctrl_depth_ini
110      o works for 5x5 box, doesnt work for global_ocean.90x40x15
111    * Adding verification for 5x5 box (4-layer) bottom topography control
112    
113    checkpoint58g_post
114    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
115       used for mean seasonal cycle, mean diurnal cycle); add an example
116       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
117    o pkg/ggl90:
118      - add parameter (minimum surface kinetic energy)
119      - fix bug (avoiding division by zero)
120    o couple pkg/thsice to pkg/seaice:
121      - modify advection in seaice to accomodate new scalar fields to be advected
122      - only muliDimAdection scheme work with seaice/thsice
123      - mapping of thsice-variables to seaice-variables, back and forth
124      - does not break the verification experiments, but does not give the
125        desired results either
126    o pkg/seaice
127      - make (default) second order advection a bit less confusing?
128    
129    checkpoint58f_post
130    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
131      to pkg/seaice):
132      - new routines thsice_map_exf and thsice_get_exf provide the interface
133      - add an additional formal parameter to thsice_solve4temp
134    o pkg/exf:
135      - add new fields wspeed, snowprecip (to be able to couple to thsice)
136      - correct Stefan-Boltzmann constant
137      - new parameter for longwave surface emittance
138      - separate some stuff from exf_bulkformulae into new routines  
139        exf_radiation, exf_wind
140      - add new parameters and constants: longwave emissivity for ocean, ice
141        and snow, evaporation parameters over ice
142      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
143        either wind from stress or stress from wind
144    o pkg/thSIce:
145    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
146    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
147       and THSICE_CALC_THICKN
148    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
149    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
150      to make debugging easier.
151    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
152    o pkg/bulk_force:
153      - clean-up comments and parameters ;
154      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
155    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
156      generate new output for test-experiment: aim.5l_cs.thSI
157    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
158      testreport accordingly
159    
160    checkpoint58e_post
161    o SEAICE_CGRID adjoint done
162    o R_STAR adjoint implemented.
163      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
164      * need to sort out init. of h0facc, etc.
165    o Make pkg/profile fully independent of ecco,cost, etc. stuff
166      to be able to use it in pure forward.
167    
168    checkpoint58d_post
169    o upgrade simple test-experiment to tutorial example:
170     step.1: duplicate the experiment and (step.2) will remove the old copy.
171      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
172      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
173      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
174      tutorial_global_oce_biogeo    <- copy of dic_example
175      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
176      tutorial_plume_on_slope       <- copy of plume_on_slope
177      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
178      tutorial_global_oce_optim     <- empty for now (David ?)
179      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
180     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
181    o correct a sign problem in cost_scat.F
182    o obcs and ptracers: fix boundary conditions for advections schemes
183      with larger stencil
184    o thsice adjoint: start
185    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
186      completeness
187    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
188      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
189    o ptracers adjoint:
190      * avoid extensive recomputatations
191      * fix missing re-init. of gptr (missed by TAF)
192    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
193      me to turn off the excessive output to STDOUT that this package produces
194    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
195      and add those terms in Vector-Invariant formulation.
196    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
197      if the control period (xx_hfluxperiod etc) is 0
198    o in profiles pkg, clean routines and fix details
199    o in ecco pkg, reading ssh data:
200      fix problem in case the model does not start at iter0=0
201    o fix mnc-pickup/restart for ptracers
202    o new package prifiles:
203      code to compute profile-based cost by Gael Forget
204      (modifs in ecco, ctrl, autodiff)
205    o Benign bug fix in initialization (spotted by M. Mazloff) of
206      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
207    
208    checkpoint58c_post
209    o adjoint: finish NLFS adjoint and provide reference output in
210      verification/global_ocean.90x40x15/results_ad_nlfs
211    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
212      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
213      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
214      with SEAICE_CGRID defined.
215    o move calendarDumps from "data" to "data.cal" and clean-up the code
216      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
217    o add useEXF & useCAL flags (for now, set in hard-coded way)
218    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
219      (were missing in NH mode, and wrong in quasihydrostatic mode).
220      waiting for Chris updated version of calc_gw to add those CALLs.
221    o fix bug in quasihydrostatic S/R ;
222      add a test for this option: global_ocean.90x40x15.qshyd
223    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
224      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
225    o add on/off flag useOffLine for package OFFLINE
226    o seaice:
227      - modify advection so that it works also on the C-grid
228      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
229        problem in multi-tile runs with C-grid
230      - add flags for clipping ice velocities and/or masking solver forcing
231      - fix drag (ocean on ice) formulation and a bug that caused noise in the
232        C-grid solver
233      - added a few comments to seaice_diffusion.F
234      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
235        are now exclusive)
236      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
237        required re-ordering the code a little:
238       + make DAIRN global variable (defined in SEAICE)
239       + move computation of the viscosities eta and zeta into a new separate
240         routine (because I need to recompute them in seaice_ocean_stress.F)
241    
242    checkpoint58b_post
243    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
244      update output.txt of exp. aim.5l_cs.thSI
245    o various mnc cleanups and improvements:
246      + shrink lookup tables by factor of ~4
247      + better error reporting when running out of lookup space
248      + able to handle longer path/file names (up to 500 chars)
249    o adjoint:
250      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
251      - TBD: "hidden" mom_vecinv recomp. in dynamics
252    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
253     (allow to differentiate between forcing components using new integer flags:
254      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
255     and add new flag to put Dissipation tendency out of Adams-Bashforth.
256    o ecco
257      - enable trend removal from SSH anomaly obs.
258    o adjoint
259      - a fix for PmEpR when #undef EXACT_CONSERV
260      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
261      - try to fix "hidden" recomp. in forward_step for NLFS
262        (NLFS seems broken sometimes after I checked it in)
263    o seaice:
264     - add c-grid version of the dynamic solver:
265       + three new routines that are the c-grid substitute lsr, dynsolver
266         and ostres
267       + put a few fields that were local to dynsolver into global common
268         blocks, so that I can move the computation of stresses etc into
269         seaice_lsr (saves coding but may break the adjoint).
270     - replace more hardwired parameters by runtime parameters
271     - add ice masks that mask the rhs of the implicit solvers where there
272       is no ice (commented out in seaice_dynsolver, because i am not sure
273       if this works properly), eventually this should replace the clipping
274       of ice velocities in seaice_dynsolver to +/-40cm/s.
275    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
276      include it only where its needed
277    o move balancing of fluxes before the call of external_forcing_surf
278    o seaice:
279      - correct units of turning angles (now they are really in degrees)
280      - move computation of GWATX/Y out of main routine into dynsolver
281      - initialize GWATX/Y in seaice_init
282    o Apply mask on Fresh-Water flux (needed for SSH forcing).
283      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
284    o seaice: add runtime flags for turning angles (default to zero)
285    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
286      and trend from exf forcing and ctrl control adjustments
287    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
288      (since checkpoint57x_post)
289    o change the default rotation period to 86164.s = the Earth rotation
290    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
291      and based on a reference stratification. Tested within hs94.cs-32x32x5.
292    o seaice advection: add code for choosing between the default (2nd order
293      central differences) and multiDim advection schemes provided by
294      pkg/generic_advdiff
295    o seaice:
296      - removed all references to SEAICE_GRID.h fields from
297        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
298        (cubed-sphere configuration will change a little)
299      - grid computations in seaice_init are obsolete now.
300      - cleaned up code a little so that is easier to read (hopefully).
301      - added new (better?) discretizations of default advection and diffusion
302        (turn on with SEAICEuseFluxForm)
303      - replace 1 in 3d global fields by kSurface in growth.F
304      
305    checkpoint58a_post
306    o seaice:
307      - bug fix in advect.F
308    o shelfice:
309      - separate shelfice load anomaly from pload (breaks with time
310        dependent forcing), => introduce constant field shelficeLoadAnomaly.
311        Its default is 0., but it may be computed more cleverly from (unknown)
312        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
313        done offline. A good approximation of the pressure load anomaly is
314        necessary to avoid large initial adjustment processes underneath
315        deep-reaching shelfice.
316      - small fix in ISOMIP shelfice_thermodynamics
317      - add more sophisticated thermodynamics of Hellmer (1989), this is
318        now the default
319      - give a few constants more intuitive names
320    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
321      if bulk formulae are used in long integration (especially EmPmR). Turn
322      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
323      if balancePrintMean, the imbalance that is substracted is printed to
324      STDOUT.
325    o fix bug (typo) in obcs_apply_eta.F
326    o add a new package shelfice which enables us to model the circulation
327      underneath shelf-ice with draughts of hundreds of meters.
328     - works
329     - to do: + include improved thermodynamics
330              + check whether kSurfC (from model/inc/SURFACE.h) can be used
331                instead of new field kTopC
332              + can we use topoFile, Ro_surf and existing code in ini_depth.F
333                instead of new field R_shelfIce and new code in ini_depth.F
334                and ini_mask_etc.F?
335              + adjust vertical mixing schemes?
336    o seaice pkg:
337     - add a cpp-flag to include a simple formula for a salinity dependent
338       freezing point of sea water at the surface
339     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
340       meridional stresses are now different (and hopefully correct)
341    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
342       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
343       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
344    o pkg/diagnostics: add options and parameters for regional-statistics
345       diagnostics ; define regions by reading a region-mask from a file
346       (might add other options later)
347    o pkg/bulk_force:
348     - add option and parameters to use AIM surface-flux formulae.
349     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
350       others forcing fields (defined in PARM05, parameter file "data") are loaded
351       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
352     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
353     - use the right EXCH call for uwind,vwind (to work on CS-grid).
354     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
355       and parameters (note: calcWindStress replaces .NOT.readwindstress).
356     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
357    
358    checkpoint58
359    o add "--embed-source" option to genmake2 which, when the supporting
360      tools can be compiled (as determined by genmake2) will turn on the
361      embed_files package which then embeds the entire MITgcm source code
362      (*.[fFhc] + Makefile) used for the build within the executable
363      - requested by CNH but off by default
364      - adds a paltry <9MB to the mitgcmuv executable in most cases
365      - only writes the output when useEMBEDSRC in eedata is true
366    o clean up 3-dim. relaxation codes:
367      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
368      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
369      * Thanks to Tom Haine for testing!
370    
371    checkpoint57z_post
372    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
373      affects output (@ truncation level) of exp. plume_on_slope ; updated.
374    o fix the pickup behavior for obcs in combination with ptracers
375    o fix a bug in ptracers_external_fields_load
376    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
377      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
378    o transfered surface NH pressure to eta field (if exactConserv).
379    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
380         and update lab_sea output.txt file.
381    o completing 3-dim. relaxation code: additional term
382         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
383      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
384      * At compile time, in "EXF_OPTIONS.h" set
385          #define  ALLOW_CLIMTEMP_RELAXATION
386          #define  ALLOW_CLIMSALT_RELAXATION
387      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
388          tauThetaClimRelax3Dim = 15552000.0,
389          tauSaltClimRelax3Dim  = 15552000.0,
390      * 3 cases:
391          1) Use a constant-in-time 3-dim. field
392          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
393          3) Real-time relax. to time-evolving prescribed field
394    o Adding Laplacian-type smoothness constraint on
395      initial and boundary (forcing) controls (ic, bc)
396      * enable at compile-time via
397        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
398      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
399      * Absolute scale somewhat unclear so far
400      * no area weighting was included since no other cost term does so far
401    
402    checkpoint57y_post
403    First step for a NLFS adjoint
404    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
405    o new init. routines for calc_r_star, calc_surf_dr
406    o still need to deal with ini_masks_etc
407    o testreport seemed happy
408    checkpoint57y_pre
409    
410    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
411    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
412    o add new offset feature to offline pkg (plus minor cleanup)
413    o cfc fixes for final year of integration
414    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
415      be in GCHEM_OPTIONS).
416    
417    checkpoint57x_post
418    o fix testreport Pb in multiple test experiment.
419    o cleanup our namelist syntax in verification:
420      - make it more F95 standards compliant (some work still needed)
421      - allows the vast majority of our tests to work with gfortran
422    o Non-Hydrostatic:
423     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
424     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
425    o Allow to apply AB on T,S rather than on AB(gT,gS):
426     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
427     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
428       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
429     - need a "clever" read_pickup to restart from the other AB formulation
430    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
431    o remove some unused variables (reduces number of compiler warnings)
432    o adjoint
433      * Disable useVariableViscosity for adjoint for time being
434        (there are a number of extensive recomputations)
435      * Initialize certain variables needed for adjoint
436    
437    checkpoint57w_post
438    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
439                 fix the singleCpuIO RS version of MDSWRITEFIELD
440       and add a WARNING if using globalFiles=T with multi-processors.
441    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
442      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
443    o tracer advection scheme:
444      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
445       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
446       was not very convenient).
447      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
448       (further tests needed for the implicit DST & Flux-Limiter schemes).
449    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
450      and sRef for convenience, handy, when you want to initialize
451      ptracers in a large domain with a constant non-zero value. Also,
452      untangle ptracers_init.F a little.
453    
454    checkpoint57v_post
455    o change dome exp. to use variable viscosity in side-drag terms.
456    o remove all the files from the cfc_offline test since they are now
457      incorporated into tutorial_cfc_offline which has been producing
458      identical results for a few days of testing
459    o add new parameter: sideDragFactor to enable half-slip-side BC
460      and change side-drag S/R to use viscosity from mom_calc_visc
461      (can switch back by setting sideDragFactor=0.); affects results at
462      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
463       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
464    o vorticity & strain are now computed without masking, to account for
465      no-slip-side BC in variable viscosity calculation ; mask is applied
466      anyway later on, before computing advection/coriolis terms.
467    o modify exp4 to test new obcs support for reading from external files
468      and for passive tracers
469    o fix behavior of ptracers_monitor when monitor output is written to a
470      netcdf-file; still not independent of monitor.F (writes in the same
471      file).
472    o change default value of tRef (put a uniform, meaningful value for ocean
473      & atmos) and initialize sRef (was missing, as Martin mentioned).
474    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
475      to be proportional to enstrophy dissipation length.  Thus,
476       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
477      This is now consistent with Smagorinsky and with the manual.
478    
479    checkpoint57u_post
480    o OBCS and PTRACERS: add open boundary support for passive tracers
481      - either use homogenous (pseudo) v.Neumann conditions or prescribe
482        OB-values from file; this is not different from the way theta and salinity
483        are treated
484      - however, Orlanski-radiation conditions are not supported, and the model
485        will stop if you use pTracers and Orlanski at the same time.
486      - beefed up the rountine obcs_external_fields_load: now only those open
487        boundary values are overwritten with values from files for which there
488        are really files, otherwise the OB-fields remain untouched. This makes
489        it possible to use different OBs at different ends of the domain (as
490        with EXF)
491    o reduce number of exch calls in shap_filt (s2).
492    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
493      truncation level) 4/5 MLAdjust test results (11&12 digits match).
494    
495    checkpoint57t_post
496    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
497    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
498      same truncation, independent of the face number: affects affects several
499      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
500    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
501      note that biharmonic viscosity + no-slip was not tested in any experiment.
502    o fix bug in non-linear free-surf side-drag ; generate new output for
503      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
504    o make mnc honor the writeBinaryPrec flag for most kinds of output
505    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
506    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
507      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
508    o add brackets in multi-terms sum to get same truncation, independent of
509      the face number (manage to get exactly same value of gU,gV at the cs-edge)
510      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
511    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
512      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
513      a maximum grid-scale Reynolds number.  Also, changes all length calculations
514      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
515      Suggested values of viscosity parameters found in mom_calc_visc.
516      Many new viscosity diagnostics available.
517    
518    checkpoint57s_post
519    o Add clearing-house for viscosity calculations, mom_calc_visc and
520      correct numerous bugs in LeithD and Smagorinsky discretizations.  
521      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
522      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
523      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
524      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
525      The Strain-Tension form is now called with useStrainTensonVisc=.true.
526      ViscAhStrain and viscAhTension are now retired.
527    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
528    o In response to JMC's bug report, genmake2 now ignores any soft-links
529      that it finds in the *current* directory when searching for files.
530      Soft-links found in any other source directories will still work as
531      they did before.
532    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
533      a C routine to unlimit the stack size
534    o mnc-ify pkg/aim snapshot vars
535    o mnc-ify pkg/land as requested by Daniel
536    o various changes to mnc including:
537      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
538      - output can now be grouped so that all files within a group
539          change the ITER portion of their names in lock-step together
540      - can now read ("global") PER-FACE (in addition to PER-TILE) files
541          and works with both EXCH1 and EXCH2 (but needs more testing)
542      - writing works for all verification test cases w/ g77 on Linux
543    
544    checkpoint57r_post
545    o make MNC variable initialization happen earlier
546    o add diagnostics for (almost) each term of the momentum Eq.
547    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
548    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
549    o remove MINIMAL_TAVE_OUTPUT option ;
550      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
551    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
552      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
553    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
554    o add time-dependent SST, SSS control
555    o cost terms in ecco/ modularized (new cost_generic.F)
556    o cost_averages routines are modularized (new cost_averagesgeneric.F)
557    o new infrastructure for seaice model vs. obs misfits in seaice/
558      * driver from the_main_loop.F is seaice_cost_driver.F
559      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
560      * gradient check in Exp. 6a of natl_box_adjoint/
561    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
562      (see README file)
563    
564    checkpoint57q_post
565    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
566    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
567      - bug was reported by Jean-Michel and Ian Fenty
568    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
569      update exp. cpl_aim+ocn output.
570    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
571      Needed for high-res. runs with large global files
572      to be able to limit tapelev size
573    o Changed some tests for adjoint:
574      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
575      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
576      * global_ocean.90x40x15/ back to default 3-level checkpointing
577    o Modifications to enable scripted COMMON to MODULE conversion
578      * verification/OpenAD/code/ has necessary scripts and description;
579      * converts, compiles and runs successfully;
580    
581    checkpoint57p_post
582    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
583    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
584      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
585    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
586    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
587      (was already the case for dissipation with mom_vecinv,
588       and also the case for grad.PhiHyd when staggered-timeStep)
589      This will allow to put dissipation out-off the AB time-stepping.
590     Unfortunately, affects truncation error. Update output of exp. that "fails"
591      (cg2d matching number) and leave the others for later: front_relax(10),
592      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
593      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
594    
595    checkpoint57o_post
596    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
597      (2) its ready to be documented during the 20050801 DocFest
598    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
599      for ideal_2D_oce and lab_sea on linux_ia32_g77
600    o set to #undef CTRL_SET_OLD_MAXCVARS_30
601      in global1x1_tot/code_seaice_adj to access indices 32, 33
602      (worth another tag)
603    
604    checkpoint57n_post
605    o adding precip control xx_precip 32
606    o adding swflux control xx_swflux 33
607    o Replacing 10 forcing penalty cost routines by 1 generic.
608    o Implementing partitioning in time-mean and variable adjustment
609      for atmos. state.
610    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
611  o in natl_box_adjoint:  o in natl_box_adjoint:
612    * updated: results_bulk/    * updated exp 1 to 10
613    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
614    o updated global1x1/*_seaice_adj/
615      to incorporate latest changes
616    o enable useSingleCpuIO for mdsio vector routines
617      (applies in particular to tapelev I/O)
618    o removed inefficient K-loop in all active_file*control*.F
619    
620  checkpoint57m_post  checkpoint57m_post
621  o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)  o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
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