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revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.700 by mlosch, Fri Jul 14 13:01:31 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 seaice: add 4 parameters for different advection schemes for area,
8  o moved ptracer ctrl index 17 -> 32    (effective) seaice thickness, enthalphy, and snow height. Their default
9      is the standard parameter SEAICEadvScheme
10    o calc_gw:
11     - add cosFacU in zonal viscous flux (harmonic.visc.).
12     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
13       of tutorial_plume_on_slope.
14    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
15    o calc_gw: true flux-form, account for horizontal grid spacing.
16      update rotating_tank results, but not plume_on_slope (affected at
17      truncation level, 11 digits).
18    
19    checkpoint58l_post
20    o calc_gw:
21     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
22     - remove side-drag for now (need to fix it); update plume_on_slope results.
23     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
24    o commit code to make SST/SSS weights spatially variable
25      (based on either variable in-situ or variable initial T/S weights)
26    o pkg/ecco:
27      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
28        now based on horizontally varying weights wthetaLev, wsaltLev
29      * cost_averagesflags now returns year indices in addition to day, month
30      * sflux balance is performed on annual basis
31        (sflxumm, sfluxmm2, bal_sfluxmm)
32      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
33        including separate counting and multipliers
34    o pkg/rbcs
35      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
36    
37    checkpoint58k_post
38    o testreport:
39     - always build in dir. "build" (if not there, mkdir build instead of building
40       & running in input)
41     - run in dir run (if it exists), in build otherwise.
42     - call prepare_run (if input/prepare_run exists)
43     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
44    o pkg/exf modifications to interpolation and rotation routines for more
45       reasonable treatment of North Pole singularity: for tracers North Pole
46       value is set to northernmost zonal-mean value, for zonal velocity it is
47       set to zero, and for meridional velocity it is set to northernmost value.
48    o pkg/exf/exf_check_range.F
49     - add tile index to diagnostics and move stop statement to the very
50       end of the routine.
51    o pkg/diagnostics: (diagnostics_main_init.F)
52      define title of isomorphic variables according to the current config.
53    o pkg/thsice with pkg/seaice dynamics:
54    - fix domain of computation (interior only, required for exf) and do exchanges
55    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
56    o towards a standard way of dealing with multi-threading in MONITOR
57      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
58    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
59       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
60    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
61    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
62    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
63       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
64    o tracer advection:
65     - clean-up and simplify calc_common_factors.F
66     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
67       advection subroutine (but still not used within DST advection S/R)
68    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
69    
70    checkpoint58j_post
71    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
72      from file (collects calls previously in FORWARD_STEP)
73    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
74    o adjoint store dir. adjusted accordingly
75    o genmake2
76      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
77    
78    checkpoint58i_post
79    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
80      on wind stress (SEAICEstressFactor defaults to 1.)
81    o Total number of Timers is finite (<=40): comment out 2 non-essential one
82      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
83    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
84      on CS-grid: no longer loosing mass.
85    o exf & curvilinear-grid: no longer modify longitude xC & xG.
86    o pkg/ggl90: fix sloppy output and fix a bug
87    o pkg/seaice: added SEAICEuseEVPpickup parameter
88      - Set to false in order to start EVP solver with
89        non-EVP pickup files when using SEAICEuseEVP
90      - fix sign error in diffusion in seaice_calc_rhs
91    
92    checkpoint58h_post
93    * Modifications for bottom topography control
94      o replace hFacC by _hFacC at various places
95      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
96      o add non-self-adjoint cg2d_nsa
97      o update autodiff support routines
98      o re-initialise hfac after ctrl_depth_ini
99      o works for 5x5 box, doesnt work for global_ocean.90x40x15
100    * Adding verification for 5x5 box (4-layer) bottom topography control
101    
102    checkpoint58g_post
103    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
104       used for mean seasonal cycle, mean diurnal cycle); add an example
105       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
106    o pkg/ggl90:
107      - add parameter (minimum surface kinetic energy)
108      - fix bug (avoiding division by zero)
109    o couple pkg/thsice to pkg/seaice:
110      - modify advection in seaice to accomodate new scalar fields to be advected
111      - only muliDimAdection scheme work with seaice/thsice
112      - mapping of thsice-variables to seaice-variables, back and forth
113      - does not break the verification experiments, but does not give the
114        desired results either
115    o pkg/seaice
116      - make (default) second order advection a bit less confusing?
117    
118    checkpoint58f_post
119    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
120      to pkg/seaice):
121      - new routines thsice_map_exf and thsice_get_exf provide the interface
122      - add an additional formal parameter to thsice_solve4temp
123    o pkg/exf:
124      - add new fields wspeed, snowprecip (to be able to couple to thsice)
125      - correct Stefan-Boltzmann constant
126      - new parameter for longwave surface emittance
127      - separate some stuff from exf_bulkformulae into new routines  
128        exf_radiation, exf_wind
129      - add new parameters and constants: longwave emissivity for ocean, ice
130        and snow, evaporation parameters over ice
131      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
132        either wind from stress or stress from wind
133    o pkg/thSIce:
134    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
135    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
136       and THSICE_CALC_THICKN
137    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
138    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
139      to make debugging easier.
140    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
141    o pkg/bulk_force:
142      - clean-up comments and parameters ;
143      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
144    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
145      generate new output for test-experiment: aim.5l_cs.thSI
146    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
147      testreport accordingly
148    
149    checkpoint58e_post
150    o SEAICE_CGRID adjoint done
151    o R_STAR adjoint implemented.
152      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
153      * need to sort out init. of h0facc, etc.
154    o Make pkg/profile fully independent of ecco,cost, etc. stuff
155      to be able to use it in pure forward.
156    
157    checkpoint58d_post
158    o upgrade simple test-experiment to tutorial example:
159     step.1: duplicate the experiment and (step.2) will remove the old copy.
160      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
161      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
162      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
163      tutorial_global_oce_biogeo    <- copy of dic_example
164      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
165      tutorial_plume_on_slope       <- copy of plume_on_slope
166      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
167      tutorial_global_oce_optim     <- empty for now (David ?)
168      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
169     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
170    o correct a sign problem in cost_scat.F
171    o obcs and ptracers: fix boundary conditions for advections schemes
172      with larger stencil
173    o thsice adjoint: start
174    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
175      completeness
176    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
177      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
178    o ptracers adjoint:
179      * avoid extensive recomputatations
180      * fix missing re-init. of gptr (missed by TAF)
181    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
182      me to turn off the excessive output to STDOUT that this package produces
183    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
184      and add those terms in Vector-Invariant formulation.
185    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
186      if the control period (xx_hfluxperiod etc) is 0
187    o in profiles pkg, clean routines and fix details
188    o in ecco pkg, reading ssh data:
189      fix problem in case the model does not start at iter0=0
190    o fix mnc-pickup/restart for ptracers
191    o new package prifiles:
192      code to compute profile-based cost by Gael Forget
193      (modifs in ecco, ctrl, autodiff)
194    o Benign bug fix in initialization (spotted by M. Mazloff) of
195      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
196    
197    checkpoint58c_post
198    o adjoint: finish NLFS adjoint and provide reference output in
199      verification/global_ocean.90x40x15/results_ad_nlfs
200    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
201      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
202      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
203      with SEAICE_CGRID defined.
204    o move calendarDumps from "data" to "data.cal" and clean-up the code
205      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
206    o add useEXF & useCAL flags (for now, set in hard-coded way)
207    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
208      (were missing in NH mode, and wrong in quasihydrostatic mode).
209      waiting for Chris updated version of calc_gw to add those CALLs.
210    o fix bug in quasihydrostatic S/R ;
211      add a test for this option: global_ocean.90x40x15.qshyd
212    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
213      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
214    o add on/off flag useOffLine for package OFFLINE
215    o seaice:
216      - modify advection so that it works also on the C-grid
217      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
218        problem in multi-tile runs with C-grid
219      - add flags for clipping ice velocities and/or masking solver forcing
220      - fix drag (ocean on ice) formulation and a bug that caused noise in the
221        C-grid solver
222      - added a few comments to seaice_diffusion.F
223      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
224        are now exclusive)
225      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
226        required re-ordering the code a little:
227       + make DAIRN global variable (defined in SEAICE)
228       + move computation of the viscosities eta and zeta into a new separate
229         routine (because I need to recompute them in seaice_ocean_stress.F)
230    
231    checkpoint58b_post
232    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
233      update output.txt of exp. aim.5l_cs.thSI
234    o various mnc cleanups and improvements:
235      + shrink lookup tables by factor of ~4
236      + better error reporting when running out of lookup space
237      + able to handle longer path/file names (up to 500 chars)
238    o adjoint:
239      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
240      - TBD: "hidden" mom_vecinv recomp. in dynamics
241    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
242     (allow to differentiate between forcing components using new integer flags:
243      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
244     and add new flag to put Dissipation tendency out of Adams-Bashforth.
245    o ecco
246      - enable trend removal from SSH anomaly obs.
247    o adjoint
248      - a fix for PmEpR when #undef EXACT_CONSERV
249      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
250      - try to fix "hidden" recomp. in forward_step for NLFS
251        (NLFS seems broken sometimes after I checked it in)
252    o seaice:
253     - add c-grid version of the dynamic solver:
254       + three new routines that are the c-grid substitute lsr, dynsolver
255         and ostres
256       + put a few fields that were local to dynsolver into global common
257         blocks, so that I can move the computation of stresses etc into
258         seaice_lsr (saves coding but may break the adjoint).
259     - replace more hardwired parameters by runtime parameters
260     - add ice masks that mask the rhs of the implicit solvers where there
261       is no ice (commented out in seaice_dynsolver, because i am not sure
262       if this works properly), eventually this should replace the clipping
263       of ice velocities in seaice_dynsolver to +/-40cm/s.
264    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
265      include it only where its needed
266    o move balancing of fluxes before the call of external_forcing_surf
267    o seaice:
268      - correct units of turning angles (now they are really in degrees)
269      - move computation of GWATX/Y out of main routine into dynsolver
270      - initialize GWATX/Y in seaice_init
271    o Apply mask on Fresh-Water flux (needed for SSH forcing).
272      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
273    o seaice: add runtime flags for turning angles (default to zero)
274    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
275      and trend from exf forcing and ctrl control adjustments
276    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
277      (since checkpoint57x_post)
278    o change the default rotation period to 86164.s = the Earth rotation
279    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
280      and based on a reference stratification. Tested within hs94.cs-32x32x5.
281    o seaice advection: add code for choosing between the default (2nd order
282      central differences) and multiDim advection schemes provided by
283      pkg/generic_advdiff
284    o seaice:
285      - removed all references to SEAICE_GRID.h fields from
286        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
287        (cubed-sphere configuration will change a little)
288      - grid computations in seaice_init are obsolete now.
289      - cleaned up code a little so that is easier to read (hopefully).
290      - added new (better?) discretizations of default advection and diffusion
291        (turn on with SEAICEuseFluxForm)
292      - replace 1 in 3d global fields by kSurface in growth.F
293      
294    checkpoint58a_post
295    o seaice:
296      - bug fix in advect.F
297    o shelfice:
298      - separate shelfice load anomaly from pload (breaks with time
299        dependent forcing), => introduce constant field shelficeLoadAnomaly.
300        Its default is 0., but it may be computed more cleverly from (unknown)
301        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
302        done offline. A good approximation of the pressure load anomaly is
303        necessary to avoid large initial adjustment processes underneath
304        deep-reaching shelfice.
305      - small fix in ISOMIP shelfice_thermodynamics
306      - add more sophisticated thermodynamics of Hellmer (1989), this is
307        now the default
308      - give a few constants more intuitive names
309    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
310      if bulk formulae are used in long integration (especially EmPmR). Turn
311      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
312      if balancePrintMean, the imbalance that is substracted is printed to
313      STDOUT.
314    o fix bug (typo) in obcs_apply_eta.F
315    o add a new package shelfice which enables us to model the circulation
316      underneath shelf-ice with draughts of hundreds of meters.
317     - works
318     - to do: + include improved thermodynamics
319              + check whether kSurfC (from model/inc/SURFACE.h) can be used
320                instead of new field kTopC
321              + can we use topoFile, Ro_surf and existing code in ini_depth.F
322                instead of new field R_shelfIce and new code in ini_depth.F
323                and ini_mask_etc.F?
324              + adjust vertical mixing schemes?
325    o seaice pkg:
326     - add a cpp-flag to include a simple formula for a salinity dependent
327       freezing point of sea water at the surface
328     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
329       meridional stresses are now different (and hopefully correct)
330    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
331       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
332       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
333    o pkg/diagnostics: add options and parameters for regional-statistics
334       diagnostics ; define regions by reading a region-mask from a file
335       (might add other options later)
336    o pkg/bulk_force:
337     - add option and parameters to use AIM surface-flux formulae.
338     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
339       others forcing fields (defined in PARM05, parameter file "data") are loaded
340       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
341     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
342     - use the right EXCH call for uwind,vwind (to work on CS-grid).
343     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
344       and parameters (note: calcWindStress replaces .NOT.readwindstress).
345     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
346    
347    checkpoint58
348    o add "--embed-source" option to genmake2 which, when the supporting
349      tools can be compiled (as determined by genmake2) will turn on the
350      embed_files package which then embeds the entire MITgcm source code
351      (*.[fFhc] + Makefile) used for the build within the executable
352      - requested by CNH but off by default
353      - adds a paltry <9MB to the mitgcmuv executable in most cases
354      - only writes the output when useEMBEDSRC in eedata is true
355    o clean up 3-dim. relaxation codes:
356      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
357      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
358      * Thanks to Tom Haine for testing!
359    
360    checkpoint57z_post
361    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
362      affects output (@ truncation level) of exp. plume_on_slope ; updated.
363    o fix the pickup behavior for obcs in combination with ptracers
364    o fix a bug in ptracers_external_fields_load
365    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
366      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
367    o transfered surface NH pressure to eta field (if exactConserv).
368    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
369         and update lab_sea output.txt file.
370    o completing 3-dim. relaxation code: additional term
371         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
372      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
373      * At compile time, in "EXF_OPTIONS.h" set
374          #define  ALLOW_CLIMTEMP_RELAXATION
375          #define  ALLOW_CLIMSALT_RELAXATION
376      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
377          tauThetaClimRelax3Dim = 15552000.0,
378          tauSaltClimRelax3Dim  = 15552000.0,
379      * 3 cases:
380          1) Use a constant-in-time 3-dim. field
381          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
382          3) Real-time relax. to time-evolving prescribed field
383    o Adding Laplacian-type smoothness constraint on
384      initial and boundary (forcing) controls (ic, bc)
385      * enable at compile-time via
386        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
387      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
388      * Absolute scale somewhat unclear so far
389      * no area weighting was included since no other cost term does so far
390    
391    checkpoint57y_post
392    First step for a NLFS adjoint
393    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
394    o new init. routines for calc_r_star, calc_surf_dr
395    o still need to deal with ini_masks_etc
396    o testreport seemed happy
397    checkpoint57y_pre
398    
399    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
400    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
401    o add new offset feature to offline pkg (plus minor cleanup)
402    o cfc fixes for final year of integration
403    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
404      be in GCHEM_OPTIONS).
405    
406    checkpoint57x_post
407    o fix testreport Pb in multiple test experiment.
408    o cleanup our namelist syntax in verification:
409      - make it more F95 standards compliant (some work still needed)
410      - allows the vast majority of our tests to work with gfortran
411    o Non-Hydrostatic:
412     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
413     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
414    o Allow to apply AB on T,S rather than on AB(gT,gS):
415     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
416     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
417       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
418     - need a "clever" read_pickup to restart from the other AB formulation
419    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
420    o remove some unused variables (reduces number of compiler warnings)
421    o adjoint
422      * Disable useVariableViscosity for adjoint for time being
423        (there are a number of extensive recomputations)
424      * Initialize certain variables needed for adjoint
425    
426    checkpoint57w_post
427    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
428                 fix the singleCpuIO RS version of MDSWRITEFIELD
429       and add a WARNING if using globalFiles=T with multi-processors.
430    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
431      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
432    o tracer advection scheme:
433      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
434       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
435       was not very convenient).
436      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
437       (further tests needed for the implicit DST & Flux-Limiter schemes).
438    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
439      and sRef for convenience, handy, when you want to initialize
440      ptracers in a large domain with a constant non-zero value. Also,
441      untangle ptracers_init.F a little.
442    
443    checkpoint57v_post
444    o change dome exp. to use variable viscosity in side-drag terms.
445    o remove all the files from the cfc_offline test since they are now
446      incorporated into tutorial_cfc_offline which has been producing
447      identical results for a few days of testing
448    o add new parameter: sideDragFactor to enable half-slip-side BC
449      and change side-drag S/R to use viscosity from mom_calc_visc
450      (can switch back by setting sideDragFactor=0.); affects results at
451      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
452       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
453    o vorticity & strain are now computed without masking, to account for
454      no-slip-side BC in variable viscosity calculation ; mask is applied
455      anyway later on, before computing advection/coriolis terms.
456    o modify exp4 to test new obcs support for reading from external files
457      and for passive tracers
458    o fix behavior of ptracers_monitor when monitor output is written to a
459      netcdf-file; still not independent of monitor.F (writes in the same
460      file).
461    o change default value of tRef (put a uniform, meaningful value for ocean
462      & atmos) and initialize sRef (was missing, as Martin mentioned).
463    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
464      to be proportional to enstrophy dissipation length.  Thus,
465       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
466      This is now consistent with Smagorinsky and with the manual.
467    
468    checkpoint57u_post
469    o OBCS and PTRACERS: add open boundary support for passive tracers
470      - either use homogenous (pseudo) v.Neumann conditions or prescribe
471        OB-values from file; this is not different from the way theta and salinity
472        are treated
473      - however, Orlanski-radiation conditions are not supported, and the model
474        will stop if you use pTracers and Orlanski at the same time.
475      - beefed up the rountine obcs_external_fields_load: now only those open
476        boundary values are overwritten with values from files for which there
477        are really files, otherwise the OB-fields remain untouched. This makes
478        it possible to use different OBs at different ends of the domain (as
479        with EXF)
480    o reduce number of exch calls in shap_filt (s2).
481    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
482      truncation level) 4/5 MLAdjust test results (11&12 digits match).
483    
484    checkpoint57t_post
485    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
486    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
487      same truncation, independent of the face number: affects affects several
488      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
489    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
490      note that biharmonic viscosity + no-slip was not tested in any experiment.
491    o fix bug in non-linear free-surf side-drag ; generate new output for
492      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
493    o make mnc honor the writeBinaryPrec flag for most kinds of output
494    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
495    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
496      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
497    o add brackets in multi-terms sum to get same truncation, independent of
498      the face number (manage to get exactly same value of gU,gV at the cs-edge)
499      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
500    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
501      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
502      a maximum grid-scale Reynolds number.  Also, changes all length calculations
503      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
504      Suggested values of viscosity parameters found in mom_calc_visc.
505      Many new viscosity diagnostics available.
506    
507    checkpoint57s_post
508    o Add clearing-house for viscosity calculations, mom_calc_visc and
509      correct numerous bugs in LeithD and Smagorinsky discretizations.  
510      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
511      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
512      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
513      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
514      The Strain-Tension form is now called with useStrainTensonVisc=.true.
515      ViscAhStrain and viscAhTension are now retired.
516    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
517    o In response to JMC's bug report, genmake2 now ignores any soft-links
518      that it finds in the *current* directory when searching for files.
519      Soft-links found in any other source directories will still work as
520      they did before.
521    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
522      a C routine to unlimit the stack size
523    o mnc-ify pkg/aim snapshot vars
524    o mnc-ify pkg/land as requested by Daniel
525    o various changes to mnc including:
526      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
527      - output can now be grouped so that all files within a group
528          change the ITER portion of their names in lock-step together
529      - can now read ("global") PER-FACE (in addition to PER-TILE) files
530          and works with both EXCH1 and EXCH2 (but needs more testing)
531      - writing works for all verification test cases w/ g77 on Linux
532    
533    checkpoint57r_post
534    o make MNC variable initialization happen earlier
535    o add diagnostics for (almost) each term of the momentum Eq.
536    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
537    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
538    o remove MINIMAL_TAVE_OUTPUT option ;
539      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
540    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
541      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
542    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
543    o add time-dependent SST, SSS control
544    o cost terms in ecco/ modularized (new cost_generic.F)
545    o cost_averages routines are modularized (new cost_averagesgeneric.F)
546    o new infrastructure for seaice model vs. obs misfits in seaice/
547      * driver from the_main_loop.F is seaice_cost_driver.F
548      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
549      * gradient check in Exp. 6a of natl_box_adjoint/
550    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
551      (see README file)
552    
553    checkpoint57q_post
554    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
555    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
556      - bug was reported by Jean-Michel and Ian Fenty
557    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
558      update exp. cpl_aim+ocn output.
559    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
560      Needed for high-res. runs with large global files
561      to be able to limit tapelev size
562    o Changed some tests for adjoint:
563      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
564      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
565      * global_ocean.90x40x15/ back to default 3-level checkpointing
566    o Modifications to enable scripted COMMON to MODULE conversion
567      * verification/OpenAD/code/ has necessary scripts and description;
568      * converts, compiles and runs successfully;
569    
570    checkpoint57p_post
571    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
572    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
573      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
574    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
575    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
576      (was already the case for dissipation with mom_vecinv,
577       and also the case for grad.PhiHyd when staggered-timeStep)
578      This will allow to put dissipation out-off the AB time-stepping.
579     Unfortunately, affects truncation error. Update output of exp. that "fails"
580      (cg2d matching number) and leave the others for later: front_relax(10),
581      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
582      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
583    
584    checkpoint57o_post
585    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
586      (2) its ready to be documented during the 20050801 DocFest
587    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
588      for ideal_2D_oce and lab_sea on linux_ia32_g77
589    o set to #undef CTRL_SET_OLD_MAXCVARS_30
590      in global1x1_tot/code_seaice_adj to access indices 32, 33
591      (worth another tag)
592    
593    checkpoint57n_post
594    o adding precip control xx_precip 32
595    o adding swflux control xx_swflux 33
596    o Replacing 10 forcing penalty cost routines by 1 generic.
597    o Implementing partitioning in time-mean and variable adjustment
598      for atmos. state.
599    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
600  o in natl_box_adjoint:  o in natl_box_adjoint:
601    * updated: results_bulk/    * updated exp 1 to 10
602    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
603    o updated global1x1/*_seaice_adj/
604      to incorporate latest changes
605    o enable useSingleCpuIO for mdsio vector routines
606      (applies in particular to tapelev I/O)
607    o removed inefficient K-loop in all active_file*control*.F
608    
609  checkpoint57m_post  checkpoint57m_post
610  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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