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revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.692 by jmc, Thu Jul 6 00:29:49 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 testreport:
8  o moved ptracer ctrl index 17 -> 32   - always build in dir. "build" (if not there, mkdir build instead of building
9       & running in input)
10     - run in dir run (if it exists), in build otherwise.
11     - call prepare_run (if input/prepare_run exists)
12     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
13    o pkg/exf modifications to interpolation and rotation routines for more
14       reasonable treatment of North Pole singularity: for tracers North Pole
15       value is set to northernmost zonal-mean value, for zonal velocity it is
16       set to zero, and for meridional velocity it is set to northernmost value.
17    o pkg/exf/exf_check_range.F
18     - add tile index to diagnostics and move stop statement to the very
19       end of the routine.
20    o pkg/diagnostics: (diagnostics_main_init.F)
21      define title of isomorphic variables according to the current config.
22    o pkg/thsice with pkg/seaice dynamics:
23    - fix domain of computation (interior only, required for exf) and do exchanges
24    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
25    o towards a standard way of dealing with multi-threading in MONITOR
26      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
27    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
28       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
29    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
30    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
31    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
32       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
33    o tracer advection:
34     - clean-up and simplify calc_common_factors.F
35     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
36       advection subroutine (but still not used within DST advection S/R)
37    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
38    
39    checkpoint58j_post
40    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
41      from file (collects calls previously in FORWARD_STEP)
42    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
43    o adjoint store dir. adjusted accordingly
44    o genmake2
45      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
46    
47    checkpoint58i_post
48    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
49      on wind stress (SEAICEstressFactor defaults to 1.)
50    o Total number of Timers is finite (<=40): comment out 2 non-essential one
51      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
52    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
53      on CS-grid: no longer loosing mass.
54    o exf & curvilinear-grid: no longer modify longitude xC & xG.
55    o pkg/ggl90: fix sloppy output and fix a bug
56    o pkg/seaice: added SEAICEuseEVPpickup parameter
57      - Set to false in order to start EVP solver with
58        non-EVP pickup files when using SEAICEuseEVP
59      - fix sign error in diffusion in seaice_calc_rhs
60    
61    checkpoint58h_post
62    * Modifications for bottom topography control
63      o replace hFacC by _hFacC at various places
64      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
65      o add non-self-adjoint cg2d_nsa
66      o update autodiff support routines
67      o re-initialise hfac after ctrl_depth_ini
68      o works for 5x5 box, doesnt work for global_ocean.90x40x15
69    * Adding verification for 5x5 box (4-layer) bottom topography control
70    
71    checkpoint58g_post
72    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
73       used for mean seasonal cycle, mean diurnal cycle); add an example
74       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
75    o pkg/ggl90:
76      - add parameter (minimum surface kinetic energy)
77      - fix bug (avoiding division by zero)
78    o couple pkg/thsice to pkg/seaice:
79      - modify advection in seaice to accomodate new scalar fields to be advected
80      - only muliDimAdection scheme work with seaice/thsice
81      - mapping of thsice-variables to seaice-variables, back and forth
82      - does not break the verification experiments, but does not give the
83        desired results either
84    o pkg/seaice
85      - make (default) second order advection a bit less confusing?
86    
87    checkpoint58f_post
88    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
89      to pkg/seaice):
90      - new routines thsice_map_exf and thsice_get_exf provide the interface
91      - add an additional formal parameter to thsice_solve4temp
92    o pkg/exf:
93      - add new fields wspeed, snowprecip (to be able to couple to thsice)
94      - correct Stefan-Boltzmann constant
95      - new parameter for longwave surface emittance
96      - separate some stuff from exf_bulkformulae into new routines  
97        exf_radiation, exf_wind
98      - add new parameters and constants: longwave emissivity for ocean, ice
99        and snow, evaporation parameters over ice
100      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
101        either wind from stress or stress from wind
102    o pkg/thSIce:
103    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
104    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
105       and THSICE_CALC_THICKN
106    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
107    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
108      to make debugging easier.
109    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
110    o pkg/bulk_force:
111      - clean-up comments and parameters ;
112      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
113    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
114      generate new output for test-experiment: aim.5l_cs.thSI
115    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
116      testreport accordingly
117    
118    checkpoint58e_post
119    o SEAICE_CGRID adjoint done
120    o R_STAR adjoint implemented.
121      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
122      * need to sort out init. of h0facc, etc.
123    o Make pkg/profile fully independent of ecco,cost, etc. stuff
124      to be able to use it in pure forward.
125    
126    checkpoint58d_post
127    o upgrade simple test-experiment to tutorial example:
128     step.1: duplicate the experiment and (step.2) will remove the old copy.
129      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
130      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
131      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
132      tutorial_global_oce_biogeo    <- copy of dic_example
133      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
134      tutorial_plume_on_slope       <- copy of plume_on_slope
135      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
136      tutorial_global_oce_optim     <- empty for now (David ?)
137      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
138     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
139    o correct a sign problem in cost_scat.F
140    o obcs and ptracers: fix boundary conditions for advections schemes
141      with larger stencil
142    o thsice adjoint: start
143    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
144      completeness
145    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
146      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
147    o ptracers adjoint:
148      * avoid extensive recomputatations
149      * fix missing re-init. of gptr (missed by TAF)
150    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
151      me to turn off the excessive output to STDOUT that this package produces
152    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
153      and add those terms in Vector-Invariant formulation.
154    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
155      if the control period (xx_hfluxperiod etc) is 0
156    o in profiles pkg, clean routines and fix details
157    o in ecco pkg, reading ssh data:
158      fix problem in case the model does not start at iter0=0
159    o fix mnc-pickup/restart for ptracers
160    o new package prifiles:
161      code to compute profile-based cost by Gael Forget
162      (modifs in ecco, ctrl, autodiff)
163    o Benign bug fix in initialization (spotted by M. Mazloff) of
164      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
165    
166    checkpoint58c_post
167    o adjoint: finish NLFS adjoint and provide reference output in
168      verification/global_ocean.90x40x15/results_ad_nlfs
169    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
170      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
171      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
172      with SEAICE_CGRID defined.
173    o move calendarDumps from "data" to "data.cal" and clean-up the code
174      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
175    o add useEXF & useCAL flags (for now, set in hard-coded way)
176    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
177      (were missing in NH mode, and wrong in quasihydrostatic mode).
178      waiting for Chris updated version of calc_gw to add those CALLs.
179    o fix bug in quasihydrostatic S/R ;
180      add a test for this option: global_ocean.90x40x15.qshyd
181    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
182      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
183    o add on/off flag useOffLine for package OFFLINE
184    o seaice:
185      - modify advection so that it works also on the C-grid
186      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
187        problem in multi-tile runs with C-grid
188      - add flags for clipping ice velocities and/or masking solver forcing
189      - fix drag (ocean on ice) formulation and a bug that caused noise in the
190        C-grid solver
191      - added a few comments to seaice_diffusion.F
192      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
193        are now exclusive)
194      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
195        required re-ordering the code a little:
196       + make DAIRN global variable (defined in SEAICE)
197       + move computation of the viscosities eta and zeta into a new separate
198         routine (because I need to recompute them in seaice_ocean_stress.F)
199    
200    checkpoint58b_post
201    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
202      update output.txt of exp. aim.5l_cs.thSI
203    o various mnc cleanups and improvements:
204      + shrink lookup tables by factor of ~4
205      + better error reporting when running out of lookup space
206      + able to handle longer path/file names (up to 500 chars)
207    o adjoint:
208      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
209      - TBD: "hidden" mom_vecinv recomp. in dynamics
210    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
211     (allow to differentiate between forcing components using new integer flags:
212      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
213     and add new flag to put Dissipation tendency out of Adams-Bashforth.
214    o ecco
215      - enable trend removal from SSH anomaly obs.
216    o adjoint
217      - a fix for PmEpR when #undef EXACT_CONSERV
218      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
219      - try to fix "hidden" recomp. in forward_step for NLFS
220        (NLFS seems broken sometimes after I checked it in)
221    o seaice:
222     - add c-grid version of the dynamic solver:
223       + three new routines that are the c-grid substitute lsr, dynsolver
224         and ostres
225       + put a few fields that were local to dynsolver into global common
226         blocks, so that I can move the computation of stresses etc into
227         seaice_lsr (saves coding but may break the adjoint).
228     - replace more hardwired parameters by runtime parameters
229     - add ice masks that mask the rhs of the implicit solvers where there
230       is no ice (commented out in seaice_dynsolver, because i am not sure
231       if this works properly), eventually this should replace the clipping
232       of ice velocities in seaice_dynsolver to +/-40cm/s.
233    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
234      include it only where its needed
235    o move balancing of fluxes before the call of external_forcing_surf
236    o seaice:
237      - correct units of turning angles (now they are really in degrees)
238      - move computation of GWATX/Y out of main routine into dynsolver
239      - initialize GWATX/Y in seaice_init
240    o Apply mask on Fresh-Water flux (needed for SSH forcing).
241      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
242    o seaice: add runtime flags for turning angles (default to zero)
243    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
244      and trend from exf forcing and ctrl control adjustments
245    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
246      (since checkpoint57x_post)
247    o change the default rotation period to 86164.s = the Earth rotation
248    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
249      and based on a reference stratification. Tested within hs94.cs-32x32x5.
250    o seaice advection: add code for choosing between the default (2nd order
251      central differences) and multiDim advection schemes provided by
252      pkg/generic_advdiff
253    o seaice:
254      - removed all references to SEAICE_GRID.h fields from
255        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
256        (cubed-sphere configuration will change a little)
257      - grid computations in seaice_init are obsolete now.
258      - cleaned up code a little so that is easier to read (hopefully).
259      - added new (better?) discretizations of default advection and diffusion
260        (turn on with SEAICEuseFluxForm)
261      - replace 1 in 3d global fields by kSurface in growth.F
262      
263    checkpoint58a_post
264    o seaice:
265      - bug fix in advect.F
266    o shelfice:
267      - separate shelfice load anomaly from pload (breaks with time
268        dependent forcing), => introduce constant field shelficeLoadAnomaly.
269        Its default is 0., but it may be computed more cleverly from (unknown)
270        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
271        done offline. A good approximation of the pressure load anomaly is
272        necessary to avoid large initial adjustment processes underneath
273        deep-reaching shelfice.
274      - small fix in ISOMIP shelfice_thermodynamics
275      - add more sophisticated thermodynamics of Hellmer (1989), this is
276        now the default
277      - give a few constants more intuitive names
278    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
279      if bulk formulae are used in long integration (especially EmPmR). Turn
280      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
281      if balancePrintMean, the imbalance that is substracted is printed to
282      STDOUT.
283    o fix bug (typo) in obcs_apply_eta.F
284    o add a new package shelfice which enables us to model the circulation
285      underneath shelf-ice with draughts of hundreds of meters.
286     - works
287     - to do: + include improved thermodynamics
288              + check whether kSurfC (from model/inc/SURFACE.h) can be used
289                instead of new field kTopC
290              + can we use topoFile, Ro_surf and existing code in ini_depth.F
291                instead of new field R_shelfIce and new code in ini_depth.F
292                and ini_mask_etc.F?
293              + adjust vertical mixing schemes?
294    o seaice pkg:
295     - add a cpp-flag to include a simple formula for a salinity dependent
296       freezing point of sea water at the surface
297     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
298       meridional stresses are now different (and hopefully correct)
299    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
300       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
301       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
302    o pkg/diagnostics: add options and parameters for regional-statistics
303       diagnostics ; define regions by reading a region-mask from a file
304       (might add other options later)
305    o pkg/bulk_force:
306     - add option and parameters to use AIM surface-flux formulae.
307     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
308       others forcing fields (defined in PARM05, parameter file "data") are loaded
309       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
310     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
311     - use the right EXCH call for uwind,vwind (to work on CS-grid).
312     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
313       and parameters (note: calcWindStress replaces .NOT.readwindstress).
314     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
315    
316    checkpoint58
317    o add "--embed-source" option to genmake2 which, when the supporting
318      tools can be compiled (as determined by genmake2) will turn on the
319      embed_files package which then embeds the entire MITgcm source code
320      (*.[fFhc] + Makefile) used for the build within the executable
321      - requested by CNH but off by default
322      - adds a paltry <9MB to the mitgcmuv executable in most cases
323      - only writes the output when useEMBEDSRC in eedata is true
324    o clean up 3-dim. relaxation codes:
325      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
326      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
327      * Thanks to Tom Haine for testing!
328    
329    checkpoint57z_post
330    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
331      affects output (@ truncation level) of exp. plume_on_slope ; updated.
332    o fix the pickup behavior for obcs in combination with ptracers
333    o fix a bug in ptracers_external_fields_load
334    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
335      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
336    o transfered surface NH pressure to eta field (if exactConserv).
337    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
338         and update lab_sea output.txt file.
339    o completing 3-dim. relaxation code: additional term
340         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
341      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
342      * At compile time, in "EXF_OPTIONS.h" set
343          #define  ALLOW_CLIMTEMP_RELAXATION
344          #define  ALLOW_CLIMSALT_RELAXATION
345      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
346          tauThetaClimRelax3Dim = 15552000.0,
347          tauSaltClimRelax3Dim  = 15552000.0,
348      * 3 cases:
349          1) Use a constant-in-time 3-dim. field
350          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
351          3) Real-time relax. to time-evolving prescribed field
352    o Adding Laplacian-type smoothness constraint on
353      initial and boundary (forcing) controls (ic, bc)
354      * enable at compile-time via
355        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
356      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
357      * Absolute scale somewhat unclear so far
358      * no area weighting was included since no other cost term does so far
359    
360    checkpoint57y_post
361    First step for a NLFS adjoint
362    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
363    o new init. routines for calc_r_star, calc_surf_dr
364    o still need to deal with ini_masks_etc
365    o testreport seemed happy
366    checkpoint57y_pre
367    
368    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
369    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
370    o add new offset feature to offline pkg (plus minor cleanup)
371    o cfc fixes for final year of integration
372    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
373      be in GCHEM_OPTIONS).
374    
375    checkpoint57x_post
376    o fix testreport Pb in multiple test experiment.
377    o cleanup our namelist syntax in verification:
378      - make it more F95 standards compliant (some work still needed)
379      - allows the vast majority of our tests to work with gfortran
380    o Non-Hydrostatic:
381     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
382     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
383    o Allow to apply AB on T,S rather than on AB(gT,gS):
384     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
385     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
386       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
387     - need a "clever" read_pickup to restart from the other AB formulation
388    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
389    o remove some unused variables (reduces number of compiler warnings)
390    o adjoint
391      * Disable useVariableViscosity for adjoint for time being
392        (there are a number of extensive recomputations)
393      * Initialize certain variables needed for adjoint
394    
395    checkpoint57w_post
396    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
397                 fix the singleCpuIO RS version of MDSWRITEFIELD
398       and add a WARNING if using globalFiles=T with multi-processors.
399    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
400      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
401    o tracer advection scheme:
402      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
403       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
404       was not very convenient).
405      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
406       (further tests needed for the implicit DST & Flux-Limiter schemes).
407    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
408      and sRef for convenience, handy, when you want to initialize
409      ptracers in a large domain with a constant non-zero value. Also,
410      untangle ptracers_init.F a little.
411    
412    checkpoint57v_post
413    o change dome exp. to use variable viscosity in side-drag terms.
414    o remove all the files from the cfc_offline test since they are now
415      incorporated into tutorial_cfc_offline which has been producing
416      identical results for a few days of testing
417    o add new parameter: sideDragFactor to enable half-slip-side BC
418      and change side-drag S/R to use viscosity from mom_calc_visc
419      (can switch back by setting sideDragFactor=0.); affects results at
420      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
421       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
422    o vorticity & strain are now computed without masking, to account for
423      no-slip-side BC in variable viscosity calculation ; mask is applied
424      anyway later on, before computing advection/coriolis terms.
425    o modify exp4 to test new obcs support for reading from external files
426      and for passive tracers
427    o fix behavior of ptracers_monitor when monitor output is written to a
428      netcdf-file; still not independent of monitor.F (writes in the same
429      file).
430    o change default value of tRef (put a uniform, meaningful value for ocean
431      & atmos) and initialize sRef (was missing, as Martin mentioned).
432    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
433      to be proportional to enstrophy dissipation length.  Thus,
434       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
435      This is now consistent with Smagorinsky and with the manual.
436    
437    checkpoint57u_post
438    o OBCS and PTRACERS: add open boundary support for passive tracers
439      - either use homogenous (pseudo) v.Neumann conditions or prescribe
440        OB-values from file; this is not different from the way theta and salinity
441        are treated
442      - however, Orlanski-radiation conditions are not supported, and the model
443        will stop if you use pTracers and Orlanski at the same time.
444      - beefed up the rountine obcs_external_fields_load: now only those open
445        boundary values are overwritten with values from files for which there
446        are really files, otherwise the OB-fields remain untouched. This makes
447        it possible to use different OBs at different ends of the domain (as
448        with EXF)
449    o reduce number of exch calls in shap_filt (s2).
450    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
451      truncation level) 4/5 MLAdjust test results (11&12 digits match).
452    
453    checkpoint57t_post
454    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
455    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
456      same truncation, independent of the face number: affects affects several
457      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
458    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
459      note that biharmonic viscosity + no-slip was not tested in any experiment.
460    o fix bug in non-linear free-surf side-drag ; generate new output for
461      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
462    o make mnc honor the writeBinaryPrec flag for most kinds of output
463    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
464    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
465      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
466    o add brackets in multi-terms sum to get same truncation, independent of
467      the face number (manage to get exactly same value of gU,gV at the cs-edge)
468      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
469    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
470      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
471      a maximum grid-scale Reynolds number.  Also, changes all length calculations
472      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
473      Suggested values of viscosity parameters found in mom_calc_visc.
474      Many new viscosity diagnostics available.
475    
476    checkpoint57s_post
477    o Add clearing-house for viscosity calculations, mom_calc_visc and
478      correct numerous bugs in LeithD and Smagorinsky discretizations.  
479      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
480      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
481      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
482      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
483      The Strain-Tension form is now called with useStrainTensonVisc=.true.
484      ViscAhStrain and viscAhTension are now retired.
485    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
486    o In response to JMC's bug report, genmake2 now ignores any soft-links
487      that it finds in the *current* directory when searching for files.
488      Soft-links found in any other source directories will still work as
489      they did before.
490    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
491      a C routine to unlimit the stack size
492    o mnc-ify pkg/aim snapshot vars
493    o mnc-ify pkg/land as requested by Daniel
494    o various changes to mnc including:
495      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
496      - output can now be grouped so that all files within a group
497          change the ITER portion of their names in lock-step together
498      - can now read ("global") PER-FACE (in addition to PER-TILE) files
499          and works with both EXCH1 and EXCH2 (but needs more testing)
500      - writing works for all verification test cases w/ g77 on Linux
501    
502    checkpoint57r_post
503    o make MNC variable initialization happen earlier
504    o add diagnostics for (almost) each term of the momentum Eq.
505    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
506    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
507    o remove MINIMAL_TAVE_OUTPUT option ;
508      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
509    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
510      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
511    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
512    o add time-dependent SST, SSS control
513    o cost terms in ecco/ modularized (new cost_generic.F)
514    o cost_averages routines are modularized (new cost_averagesgeneric.F)
515    o new infrastructure for seaice model vs. obs misfits in seaice/
516      * driver from the_main_loop.F is seaice_cost_driver.F
517      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
518      * gradient check in Exp. 6a of natl_box_adjoint/
519    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
520      (see README file)
521    
522    checkpoint57q_post
523    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
524    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
525      - bug was reported by Jean-Michel and Ian Fenty
526    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
527      update exp. cpl_aim+ocn output.
528    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
529      Needed for high-res. runs with large global files
530      to be able to limit tapelev size
531    o Changed some tests for adjoint:
532      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
533      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
534      * global_ocean.90x40x15/ back to default 3-level checkpointing
535    o Modifications to enable scripted COMMON to MODULE conversion
536      * verification/OpenAD/code/ has necessary scripts and description;
537      * converts, compiles and runs successfully;
538    
539    checkpoint57p_post
540    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
541    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
542      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
543    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
544    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
545      (was already the case for dissipation with mom_vecinv,
546       and also the case for grad.PhiHyd when staggered-timeStep)
547      This will allow to put dissipation out-off the AB time-stepping.
548     Unfortunately, affects truncation error. Update output of exp. that "fails"
549      (cg2d matching number) and leave the others for later: front_relax(10),
550      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
551      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
552    
553    checkpoint57o_post
554    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
555      (2) its ready to be documented during the 20050801 DocFest
556    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
557      for ideal_2D_oce and lab_sea on linux_ia32_g77
558    o set to #undef CTRL_SET_OLD_MAXCVARS_30
559      in global1x1_tot/code_seaice_adj to access indices 32, 33
560      (worth another tag)
561    
562    checkpoint57n_post
563    o adding precip control xx_precip 32
564    o adding swflux control xx_swflux 33
565    o Replacing 10 forcing penalty cost routines by 1 generic.
566    o Implementing partitioning in time-mean and variable adjustment
567      for atmos. state.
568    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
569  o in natl_box_adjoint:  o in natl_box_adjoint:
570    * updated: results_bulk/    * updated exp 1 to 10
571    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
572    o updated global1x1/*_seaice_adj/
573      to incorporate latest changes
574    o enable useSingleCpuIO for mdsio vector routines
575      (applies in particular to tapelev I/O)
576    o removed inefficient K-loop in all active_file*control*.F
577    
578  checkpoint57m_post  checkpoint57m_post
579  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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