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revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.672 by dimitri, Thu Jun 8 23:09:55 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 pkg/ggl90: fix sloppy output and fix a bug
8  o moved ptracer ctrl index 17 -> 32  o pkg/seaice: added SEAICEuseEVPpickup parameter
9      - Set to false in order to start EVP solver with
10        non-EVP pickup files when using SEAICEuseEVP
11    
12    checkpoint58h_post
13    * Modifications for bottom topography control
14      o replace hFacC by _hFacC at various places
15      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
16      o add non-self-adjoint cg2d_nsa
17      o update autodiff support routines
18      o re-initialise hfac after ctrl_depth_ini
19      o works for 5x5 box, doesnt work for global_ocean.90x40x15
20    * Adding verification for 5x5 box (4-layer) bottom topography control
21    
22    checkpoint58g_post
23    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
24       used for mean seasonal cycle, mean diurnal cycle); add an example
25       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
26    o pkg/ggl90:
27      - add parameter (minimum surface kinetic energy)
28      - fix bug (avoiding division by zero)
29    o couple pkg/thsice to pkg/seaice:
30      - modify advection in seaice to accomodate new scalar fields to be advected
31      - only muliDimAdection scheme work with seaice/thsice
32      - mapping of thsice-variables to seaice-variables, back and forth
33      - does not break the verification experiments, but does not give the
34        desired results either
35    o pkg/seaice
36      - make (default) second order advection a bit less confusing?
37    
38    checkpoint58f_post
39    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
40      to pkg/seaice):
41      - new routines thsice_map_exf and thsice_get_exf provide the interface
42      - add an additional formal parameter to thsice_solve4temp
43    o pkg/exf:
44      - add new fields wspeed, snowprecip (to be able to couple to thsice)
45      - correct Stefan-Boltzmann constant
46      - new parameter for longwave surface emittance
47      - separate some stuff from exf_bulkformulae into new routines  
48        exf_radiation, exf_wind
49      - add new parameters and constants: longwave emissivity for ocean, ice
50        and snow, evaporation parameters over ice
51      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
52        either wind from stress or stress from wind
53    o pkg/thSIce:
54    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
55    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
56       and THSICE_CALC_THICKN
57    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
58    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
59      to make debugging easier.
60    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
61    o pkg/bulk_force:
62      - clean-up comments and parameters ;
63      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
64    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
65      generate new output for test-experiment: aim.5l_cs.thSI
66    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
67      testreport accordingly
68    
69    checkpoint58e_post
70    o SEAICE_CGRID adjoint done
71    o R_STAR adjoint implemented.
72      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
73      * need to sort out init. of h0facc, etc.
74    o Make pkg/profile fully independent of ecco,cost, etc. stuff
75      to be able to use it in pure forward.
76    
77    checkpoint58d_post
78    o upgrade simple test-experiment to tutorial example:
79     step.1: duplicate the experiment and (step.2) will remove the old copy.
80      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
81      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
82      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
83      tutorial_global_oce_biogeo    <- copy of dic_example
84      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
85      tutorial_plume_on_slope       <- copy of plume_on_slope
86      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
87      tutorial_global_oce_optim     <- empty for now (David ?)
88      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
89     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
90    o correct a sign problem in cost_scat.F
91    o obcs and ptracers: fix boundary conditions for advections schemes
92      with larger stencil
93    o thsice adjoint: start
94    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
95      completeness
96    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
97      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
98    o ptracers adjoint:
99      * avoid extensive recomputatations
100      * fix missing re-init. of gptr (missed by TAF)
101    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
102      me to turn off the excessive output to STDOUT that this package produces
103    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
104      and add those terms in Vector-Invariant formulation.
105    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
106      if the control period (xx_hfluxperiod etc) is 0
107    o in profiles pkg, clean routines and fix details
108    o in ecco pkg, reading ssh data:
109      fix problem in case the model does not start at iter0=0
110    o fix mnc-pickup/restart for ptracers
111    o new package prifiles:
112      code to compute profile-based cost by Gael Forget
113      (modifs in ecco, ctrl, autodiff)
114    o Benign bug fix in initialization (spotted by M. Mazloff) of
115      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
116    
117    checkpoint58c_post
118    o adjoint: finish NLFS adjoint and provide reference output in
119      verification/global_ocean.90x40x15/results_ad_nlfs
120    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
121      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
122      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
123      with SEAICE_CGRID defined.
124    o move calendarDumps from "data" to "data.cal" and clean-up the code
125      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
126    o add useEXF & useCAL flags (for now, set in hard-coded way)
127    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
128      (were missing in NH mode, and wrong in quasihydrostatic mode).
129      waiting for Chris updated version of calc_gw to add those CALLs.
130    o fix bug in quasihydrostatic S/R ;
131      add a test for this option: global_ocean.90x40x15.qshyd
132    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
133      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
134    o add on/off flag useOffLine for package OFFLINE
135    o seaice:
136      - modify advection so that it works also on the C-grid
137      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
138        problem in multi-tile runs with C-grid
139      - add flags for clipping ice velocities and/or masking solver forcing
140      - fix drag (ocean on ice) formulation and a bug that caused noise in the
141        C-grid solver
142      - added a few comments to seaice_diffusion.F
143      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
144        are now exclusive)
145      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
146        required re-ordering the code a little:
147       + make DAIRN global variable (defined in SEAICE)
148       + move computation of the viscosities eta and zeta into a new separate
149         routine (because I need to recompute them in seaice_ocean_stress.F)
150    
151    checkpoint58b_post
152    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
153      update output.txt of exp. aim.5l_cs.thSI
154    o various mnc cleanups and improvements:
155      + shrink lookup tables by factor of ~4
156      + better error reporting when running out of lookup space
157      + able to handle longer path/file names (up to 500 chars)
158    o adjoint:
159      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
160      - TBD: "hidden" mom_vecinv recomp. in dynamics
161    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
162     (allow to differentiate between forcing components using new integer flags:
163      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
164     and add new flag to put Dissipation tendency out of Adams-Bashforth.
165    o ecco
166      - enable trend removal from SSH anomaly obs.
167    o adjoint
168      - a fix for PmEpR when #undef EXACT_CONSERV
169      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
170      - try to fix "hidden" recomp. in forward_step for NLFS
171        (NLFS seems broken sometimes after I checked it in)
172    o seaice:
173     - add c-grid version of the dynamic solver:
174       + three new routines that are the c-grid substitute lsr, dynsolver
175         and ostres
176       + put a few fields that were local to dynsolver into global common
177         blocks, so that I can move the computation of stresses etc into
178         seaice_lsr (saves coding but may break the adjoint).
179     - replace more hardwired parameters by runtime parameters
180     - add ice masks that mask the rhs of the implicit solvers where there
181       is no ice (commented out in seaice_dynsolver, because i am not sure
182       if this works properly), eventually this should replace the clipping
183       of ice velocities in seaice_dynsolver to +/-40cm/s.
184    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
185      include it only where its needed
186    o move balancing of fluxes before the call of external_forcing_surf
187    o seaice:
188      - correct units of turning angles (now they are really in degrees)
189      - move computation of GWATX/Y out of main routine into dynsolver
190      - initialize GWATX/Y in seaice_init
191    o Apply mask on Fresh-Water flux (needed for SSH forcing).
192      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
193    o seaice: add runtime flags for turning angles (default to zero)
194    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
195      and trend from exf forcing and ctrl control adjustments
196    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
197      (since checkpoint57x_post)
198    o change the default rotation period to 86164.s = the Earth rotation
199    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
200      and based on a reference stratification. Tested within hs94.cs-32x32x5.
201    o seaice advection: add code for choosing between the default (2nd order
202      central differences) and multiDim advection schemes provided by
203      pkg/generic_advdiff
204    o seaice:
205      - removed all references to SEAICE_GRID.h fields from
206        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
207        (cubed-sphere configuration will change a little)
208      - grid computations in seaice_init are obsolete now.
209      - cleaned up code a little so that is easier to read (hopefully).
210      - added new (better?) discretizations of default advection and diffusion
211        (turn on with SEAICEuseFluxForm)
212      - replace 1 in 3d global fields by kSurface in growth.F
213      
214    checkpoint58a_post
215    o seaice:
216      - bug fix in advect.F
217    o shelfice:
218      - separate shelfice load anomaly from pload (breaks with time
219        dependent forcing), => introduce constant field shelficeLoadAnomaly.
220        Its default is 0., but it may be computed more cleverly from (unknown)
221        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
222        done offline. A good approximation of the pressure load anomaly is
223        necessary to avoid large initial adjustment processes underneath
224        deep-reaching shelfice.
225      - small fix in ISOMIP shelfice_thermodynamics
226      - add more sophisticated thermodynamics of Hellmer (1989), this is
227        now the default
228      - give a few constants more intuitive names
229    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
230      if bulk formulae are used in long integration (especially EmPmR). Turn
231      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
232      if balancePrintMean, the imbalance that is substracted is printed to
233      STDOUT.
234    o fix bug (typo) in obcs_apply_eta.F
235    o add a new package shelfice which enables us to model the circulation
236      underneath shelf-ice with draughts of hundreds of meters.
237     - works
238     - to do: + include improved thermodynamics
239              + check whether kSurfC (from model/inc/SURFACE.h) can be used
240                instead of new field kTopC
241              + can we use topoFile, Ro_surf and existing code in ini_depth.F
242                instead of new field R_shelfIce and new code in ini_depth.F
243                and ini_mask_etc.F?
244              + adjust vertical mixing schemes?
245    o seaice pkg:
246     - add a cpp-flag to include a simple formula for a salinity dependent
247       freezing point of sea water at the surface
248     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
249       meridional stresses are now different (and hopefully correct)
250    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
251       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
252       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
253    o pkg/diagnostics: add options and parameters for regional-statistics
254       diagnostics ; define regions by reading a region-mask from a file
255       (might add other options later)
256    o pkg/bulk_force:
257     - add option and parameters to use AIM surface-flux formulae.
258     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
259       others forcing fields (defined in PARM05, parameter file "data") are loaded
260       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
261     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
262     - use the right EXCH call for uwind,vwind (to work on CS-grid).
263     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
264       and parameters (note: calcWindStress replaces .NOT.readwindstress).
265     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
266    
267    checkpoint58
268    o add "--embed-source" option to genmake2 which, when the supporting
269      tools can be compiled (as determined by genmake2) will turn on the
270      embed_files package which then embeds the entire MITgcm source code
271      (*.[fFhc] + Makefile) used for the build within the executable
272      - requested by CNH but off by default
273      - adds a paltry <9MB to the mitgcmuv executable in most cases
274      - only writes the output when useEMBEDSRC in eedata is true
275    o clean up 3-dim. relaxation codes:
276      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
277      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
278      * Thanks to Tom Haine for testing!
279    
280    checkpoint57z_post
281    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
282      affects output (@ truncation level) of exp. plume_on_slope ; updated.
283    o fix the pickup behavior for obcs in combination with ptracers
284    o fix a bug in ptracers_external_fields_load
285    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
286      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
287    o transfered surface NH pressure to eta field (if exactConserv).
288    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
289         and update lab_sea output.txt file.
290    o completing 3-dim. relaxation code: additional term
291         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
292      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
293      * At compile time, in "EXF_OPTIONS.h" set
294          #define  ALLOW_CLIMTEMP_RELAXATION
295          #define  ALLOW_CLIMSALT_RELAXATION
296      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
297          tauThetaClimRelax3Dim = 15552000.0,
298          tauSaltClimRelax3Dim  = 15552000.0,
299      * 3 cases:
300          1) Use a constant-in-time 3-dim. field
301          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
302          3) Real-time relax. to time-evolving prescribed field
303    o Adding Laplacian-type smoothness constraint on
304      initial and boundary (forcing) controls (ic, bc)
305      * enable at compile-time via
306        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
307      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
308      * Absolute scale somewhat unclear so far
309      * no area weighting was included since no other cost term does so far
310    
311    checkpoint57y_post
312    First step for a NLFS adjoint
313    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
314    o new init. routines for calc_r_star, calc_surf_dr
315    o still need to deal with ini_masks_etc
316    o testreport seemed happy
317    checkpoint57y_pre
318    
319    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
320    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
321    o add new offset feature to offline pkg (plus minor cleanup)
322    o cfc fixes for final year of integration
323    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
324      be in GCHEM_OPTIONS).
325    
326    checkpoint57x_post
327    o fix testreport Pb in multiple test experiment.
328    o cleanup our namelist syntax in verification:
329      - make it more F95 standards compliant (some work still needed)
330      - allows the vast majority of our tests to work with gfortran
331    o Non-Hydrostatic:
332     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
333     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
334    o Allow to apply AB on T,S rather than on AB(gT,gS):
335     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
336     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
337       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
338     - need a "clever" read_pickup to restart from the other AB formulation
339    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
340    o remove some unused variables (reduces number of compiler warnings)
341    o adjoint
342      * Disable useVariableViscosity for adjoint for time being
343        (there are a number of extensive recomputations)
344      * Initialize certain variables needed for adjoint
345    
346    checkpoint57w_post
347    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
348                 fix the singleCpuIO RS version of MDSWRITEFIELD
349       and add a WARNING if using globalFiles=T with multi-processors.
350    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
351      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
352    o tracer advection scheme:
353      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
354       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
355       was not very convenient).
356      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
357       (further tests needed for the implicit DST & Flux-Limiter schemes).
358    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
359      and sRef for convenience, handy, when you want to initialize
360      ptracers in a large domain with a constant non-zero value. Also,
361      untangle ptracers_init.F a little.
362    
363    checkpoint57v_post
364    o change dome exp. to use variable viscosity in side-drag terms.
365    o remove all the files from the cfc_offline test since they are now
366      incorporated into tutorial_cfc_offline which has been producing
367      identical results for a few days of testing
368    o add new parameter: sideDragFactor to enable half-slip-side BC
369      and change side-drag S/R to use viscosity from mom_calc_visc
370      (can switch back by setting sideDragFactor=0.); affects results at
371      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
372       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
373    o vorticity & strain are now computed without masking, to account for
374      no-slip-side BC in variable viscosity calculation ; mask is applied
375      anyway later on, before computing advection/coriolis terms.
376    o modify exp4 to test new obcs support for reading from external files
377      and for passive tracers
378    o fix behavior of ptracers_monitor when monitor output is written to a
379      netcdf-file; still not independent of monitor.F (writes in the same
380      file).
381    o change default value of tRef (put a uniform, meaningful value for ocean
382      & atmos) and initialize sRef (was missing, as Martin mentioned).
383    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
384      to be proportional to enstrophy dissipation length.  Thus,
385       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
386      This is now consistent with Smagorinsky and with the manual.
387    
388    checkpoint57u_post
389    o OBCS and PTRACERS: add open boundary support for passive tracers
390      - either use homogenous (pseudo) v.Neumann conditions or prescribe
391        OB-values from file; this is not different from the way theta and salinity
392        are treated
393      - however, Orlanski-radiation conditions are not supported, and the model
394        will stop if you use pTracers and Orlanski at the same time.
395      - beefed up the rountine obcs_external_fields_load: now only those open
396        boundary values are overwritten with values from files for which there
397        are really files, otherwise the OB-fields remain untouched. This makes
398        it possible to use different OBs at different ends of the domain (as
399        with EXF)
400    o reduce number of exch calls in shap_filt (s2).
401    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
402      truncation level) 4/5 MLAdjust test results (11&12 digits match).
403    
404    checkpoint57t_post
405    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
406    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
407      same truncation, independent of the face number: affects affects several
408      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
409    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
410      note that biharmonic viscosity + no-slip was not tested in any experiment.
411    o fix bug in non-linear free-surf side-drag ; generate new output for
412      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
413    o make mnc honor the writeBinaryPrec flag for most kinds of output
414    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
415    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
416      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
417    o add brackets in multi-terms sum to get same truncation, independent of
418      the face number (manage to get exactly same value of gU,gV at the cs-edge)
419      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
420    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
421      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
422      a maximum grid-scale Reynolds number.  Also, changes all length calculations
423      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
424      Suggested values of viscosity parameters found in mom_calc_visc.
425      Many new viscosity diagnostics available.
426    
427    checkpoint57s_post
428    o Add clearing-house for viscosity calculations, mom_calc_visc and
429      correct numerous bugs in LeithD and Smagorinsky discretizations.  
430      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
431      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
432      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
433      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
434      The Strain-Tension form is now called with useStrainTensonVisc=.true.
435      ViscAhStrain and viscAhTension are now retired.
436    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
437    o In response to JMC's bug report, genmake2 now ignores any soft-links
438      that it finds in the *current* directory when searching for files.
439      Soft-links found in any other source directories will still work as
440      they did before.
441    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
442      a C routine to unlimit the stack size
443    o mnc-ify pkg/aim snapshot vars
444    o mnc-ify pkg/land as requested by Daniel
445    o various changes to mnc including:
446      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
447      - output can now be grouped so that all files within a group
448          change the ITER portion of their names in lock-step together
449      - can now read ("global") PER-FACE (in addition to PER-TILE) files
450          and works with both EXCH1 and EXCH2 (but needs more testing)
451      - writing works for all verification test cases w/ g77 on Linux
452    
453    checkpoint57r_post
454    o make MNC variable initialization happen earlier
455    o add diagnostics for (almost) each term of the momentum Eq.
456    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
457    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
458    o remove MINIMAL_TAVE_OUTPUT option ;
459      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
460    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
461      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
462    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
463    o add time-dependent SST, SSS control
464    o cost terms in ecco/ modularized (new cost_generic.F)
465    o cost_averages routines are modularized (new cost_averagesgeneric.F)
466    o new infrastructure for seaice model vs. obs misfits in seaice/
467      * driver from the_main_loop.F is seaice_cost_driver.F
468      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
469      * gradient check in Exp. 6a of natl_box_adjoint/
470    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
471      (see README file)
472    
473    checkpoint57q_post
474    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
475    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
476      - bug was reported by Jean-Michel and Ian Fenty
477    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
478      update exp. cpl_aim+ocn output.
479    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
480      Needed for high-res. runs with large global files
481      to be able to limit tapelev size
482    o Changed some tests for adjoint:
483      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
484      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
485      * global_ocean.90x40x15/ back to default 3-level checkpointing
486    o Modifications to enable scripted COMMON to MODULE conversion
487      * verification/OpenAD/code/ has necessary scripts and description;
488      * converts, compiles and runs successfully;
489    
490    checkpoint57p_post
491    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
492    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
493      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
494    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
495    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
496      (was already the case for dissipation with mom_vecinv,
497       and also the case for grad.PhiHyd when staggered-timeStep)
498      This will allow to put dissipation out-off the AB time-stepping.
499     Unfortunately, affects truncation error. Update output of exp. that "fails"
500      (cg2d matching number) and leave the others for later: front_relax(10),
501      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
502      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
503    
504    checkpoint57o_post
505    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
506      (2) its ready to be documented during the 20050801 DocFest
507    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
508      for ideal_2D_oce and lab_sea on linux_ia32_g77
509    o set to #undef CTRL_SET_OLD_MAXCVARS_30
510      in global1x1_tot/code_seaice_adj to access indices 32, 33
511      (worth another tag)
512    
513    checkpoint57n_post
514    o adding precip control xx_precip 32
515    o adding swflux control xx_swflux 33
516    o Replacing 10 forcing penalty cost routines by 1 generic.
517    o Implementing partitioning in time-mean and variable adjustment
518      for atmos. state.
519    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
520  o in natl_box_adjoint:  o in natl_box_adjoint:
521    * updated: results_bulk/    * updated exp 1 to 10
522    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
523    o updated global1x1/*_seaice_adj/
524      to incorporate latest changes
525    o enable useSingleCpuIO for mdsio vector routines
526      (applies in particular to tapelev I/O)
527    o removed inefficient K-loop in all active_file*control*.F
528    
529  checkpoint57m_post  checkpoint57m_post
530  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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