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revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.683 by jmc, Mon Jun 19 15:56:42 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/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
8  o moved ptracer ctrl index 17 -> 32  o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
9       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
10    o tracer advection:
11     - clean-up and simplify calc_common_factors.F
12     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
13       advection subroutine (but still not used within DST advection S/R)
14    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
15    
16    checkpoint58j_post
17    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
18      from file (collects calls previously in FORWARD_STEP)
19    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
20    o adjoint store dir. adjusted accordingly
21    o genmake2
22      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
23    
24    checkpoint58i_post
25    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
26      on wind stress (SEAICEstressFactor defaults to 1.)
27    o Total number of Timers is finite (<=40): comment out 2 non-essential one
28      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
29    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
30      on CS-grid: no longer loosing mass.
31    o exf & curvilinear-grid: no longer modify longitude xC & xG.
32    o pkg/ggl90: fix sloppy output and fix a bug
33    o pkg/seaice: added SEAICEuseEVPpickup parameter
34      - Set to false in order to start EVP solver with
35        non-EVP pickup files when using SEAICEuseEVP
36      - fix sign error in diffusion in seaice_calc_rhs
37    
38    checkpoint58h_post
39    * Modifications for bottom topography control
40      o replace hFacC by _hFacC at various places
41      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
42      o add non-self-adjoint cg2d_nsa
43      o update autodiff support routines
44      o re-initialise hfac after ctrl_depth_ini
45      o works for 5x5 box, doesnt work for global_ocean.90x40x15
46    * Adding verification for 5x5 box (4-layer) bottom topography control
47    
48    checkpoint58g_post
49    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
50       used for mean seasonal cycle, mean diurnal cycle); add an example
51       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
52    o pkg/ggl90:
53      - add parameter (minimum surface kinetic energy)
54      - fix bug (avoiding division by zero)
55    o couple pkg/thsice to pkg/seaice:
56      - modify advection in seaice to accomodate new scalar fields to be advected
57      - only muliDimAdection scheme work with seaice/thsice
58      - mapping of thsice-variables to seaice-variables, back and forth
59      - does not break the verification experiments, but does not give the
60        desired results either
61    o pkg/seaice
62      - make (default) second order advection a bit less confusing?
63    
64    checkpoint58f_post
65    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
66      to pkg/seaice):
67      - new routines thsice_map_exf and thsice_get_exf provide the interface
68      - add an additional formal parameter to thsice_solve4temp
69    o pkg/exf:
70      - add new fields wspeed, snowprecip (to be able to couple to thsice)
71      - correct Stefan-Boltzmann constant
72      - new parameter for longwave surface emittance
73      - separate some stuff from exf_bulkformulae into new routines  
74        exf_radiation, exf_wind
75      - add new parameters and constants: longwave emissivity for ocean, ice
76        and snow, evaporation parameters over ice
77      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
78        either wind from stress or stress from wind
79    o pkg/thSIce:
80    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
81    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
82       and THSICE_CALC_THICKN
83    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
84    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
85      to make debugging easier.
86    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
87    o pkg/bulk_force:
88      - clean-up comments and parameters ;
89      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
90    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
91      generate new output for test-experiment: aim.5l_cs.thSI
92    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
93      testreport accordingly
94    
95    checkpoint58e_post
96    o SEAICE_CGRID adjoint done
97    o R_STAR adjoint implemented.
98      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
99      * need to sort out init. of h0facc, etc.
100    o Make pkg/profile fully independent of ecco,cost, etc. stuff
101      to be able to use it in pure forward.
102    
103    checkpoint58d_post
104    o upgrade simple test-experiment to tutorial example:
105     step.1: duplicate the experiment and (step.2) will remove the old copy.
106      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
107      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
108      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
109      tutorial_global_oce_biogeo    <- copy of dic_example
110      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
111      tutorial_plume_on_slope       <- copy of plume_on_slope
112      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
113      tutorial_global_oce_optim     <- empty for now (David ?)
114      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
115     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
116    o correct a sign problem in cost_scat.F
117    o obcs and ptracers: fix boundary conditions for advections schemes
118      with larger stencil
119    o thsice adjoint: start
120    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
121      completeness
122    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
123      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
124    o ptracers adjoint:
125      * avoid extensive recomputatations
126      * fix missing re-init. of gptr (missed by TAF)
127    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
128      me to turn off the excessive output to STDOUT that this package produces
129    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
130      and add those terms in Vector-Invariant formulation.
131    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
132      if the control period (xx_hfluxperiod etc) is 0
133    o in profiles pkg, clean routines and fix details
134    o in ecco pkg, reading ssh data:
135      fix problem in case the model does not start at iter0=0
136    o fix mnc-pickup/restart for ptracers
137    o new package prifiles:
138      code to compute profile-based cost by Gael Forget
139      (modifs in ecco, ctrl, autodiff)
140    o Benign bug fix in initialization (spotted by M. Mazloff) of
141      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
142    
143    checkpoint58c_post
144    o adjoint: finish NLFS adjoint and provide reference output in
145      verification/global_ocean.90x40x15/results_ad_nlfs
146    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
147      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
148      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
149      with SEAICE_CGRID defined.
150    o move calendarDumps from "data" to "data.cal" and clean-up the code
151      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
152    o add useEXF & useCAL flags (for now, set in hard-coded way)
153    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
154      (were missing in NH mode, and wrong in quasihydrostatic mode).
155      waiting for Chris updated version of calc_gw to add those CALLs.
156    o fix bug in quasihydrostatic S/R ;
157      add a test for this option: global_ocean.90x40x15.qshyd
158    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
159      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
160    o add on/off flag useOffLine for package OFFLINE
161    o seaice:
162      - modify advection so that it works also on the C-grid
163      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
164        problem in multi-tile runs with C-grid
165      - add flags for clipping ice velocities and/or masking solver forcing
166      - fix drag (ocean on ice) formulation and a bug that caused noise in the
167        C-grid solver
168      - added a few comments to seaice_diffusion.F
169      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
170        are now exclusive)
171      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
172        required re-ordering the code a little:
173       + make DAIRN global variable (defined in SEAICE)
174       + move computation of the viscosities eta and zeta into a new separate
175         routine (because I need to recompute them in seaice_ocean_stress.F)
176    
177    checkpoint58b_post
178    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
179      update output.txt of exp. aim.5l_cs.thSI
180    o various mnc cleanups and improvements:
181      + shrink lookup tables by factor of ~4
182      + better error reporting when running out of lookup space
183      + able to handle longer path/file names (up to 500 chars)
184    o adjoint:
185      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
186      - TBD: "hidden" mom_vecinv recomp. in dynamics
187    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
188     (allow to differentiate between forcing components using new integer flags:
189      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
190     and add new flag to put Dissipation tendency out of Adams-Bashforth.
191    o ecco
192      - enable trend removal from SSH anomaly obs.
193    o adjoint
194      - a fix for PmEpR when #undef EXACT_CONSERV
195      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
196      - try to fix "hidden" recomp. in forward_step for NLFS
197        (NLFS seems broken sometimes after I checked it in)
198    o seaice:
199     - add c-grid version of the dynamic solver:
200       + three new routines that are the c-grid substitute lsr, dynsolver
201         and ostres
202       + put a few fields that were local to dynsolver into global common
203         blocks, so that I can move the computation of stresses etc into
204         seaice_lsr (saves coding but may break the adjoint).
205     - replace more hardwired parameters by runtime parameters
206     - add ice masks that mask the rhs of the implicit solvers where there
207       is no ice (commented out in seaice_dynsolver, because i am not sure
208       if this works properly), eventually this should replace the clipping
209       of ice velocities in seaice_dynsolver to +/-40cm/s.
210    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
211      include it only where its needed
212    o move balancing of fluxes before the call of external_forcing_surf
213    o seaice:
214      - correct units of turning angles (now they are really in degrees)
215      - move computation of GWATX/Y out of main routine into dynsolver
216      - initialize GWATX/Y in seaice_init
217    o Apply mask on Fresh-Water flux (needed for SSH forcing).
218      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
219    o seaice: add runtime flags for turning angles (default to zero)
220    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
221      and trend from exf forcing and ctrl control adjustments
222    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
223      (since checkpoint57x_post)
224    o change the default rotation period to 86164.s = the Earth rotation
225    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
226      and based on a reference stratification. Tested within hs94.cs-32x32x5.
227    o seaice advection: add code for choosing between the default (2nd order
228      central differences) and multiDim advection schemes provided by
229      pkg/generic_advdiff
230    o seaice:
231      - removed all references to SEAICE_GRID.h fields from
232        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
233        (cubed-sphere configuration will change a little)
234      - grid computations in seaice_init are obsolete now.
235      - cleaned up code a little so that is easier to read (hopefully).
236      - added new (better?) discretizations of default advection and diffusion
237        (turn on with SEAICEuseFluxForm)
238      - replace 1 in 3d global fields by kSurface in growth.F
239      
240    checkpoint58a_post
241    o seaice:
242      - bug fix in advect.F
243    o shelfice:
244      - separate shelfice load anomaly from pload (breaks with time
245        dependent forcing), => introduce constant field shelficeLoadAnomaly.
246        Its default is 0., but it may be computed more cleverly from (unknown)
247        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
248        done offline. A good approximation of the pressure load anomaly is
249        necessary to avoid large initial adjustment processes underneath
250        deep-reaching shelfice.
251      - small fix in ISOMIP shelfice_thermodynamics
252      - add more sophisticated thermodynamics of Hellmer (1989), this is
253        now the default
254      - give a few constants more intuitive names
255    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
256      if bulk formulae are used in long integration (especially EmPmR). Turn
257      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
258      if balancePrintMean, the imbalance that is substracted is printed to
259      STDOUT.
260    o fix bug (typo) in obcs_apply_eta.F
261    o add a new package shelfice which enables us to model the circulation
262      underneath shelf-ice with draughts of hundreds of meters.
263     - works
264     - to do: + include improved thermodynamics
265              + check whether kSurfC (from model/inc/SURFACE.h) can be used
266                instead of new field kTopC
267              + can we use topoFile, Ro_surf and existing code in ini_depth.F
268                instead of new field R_shelfIce and new code in ini_depth.F
269                and ini_mask_etc.F?
270              + adjust vertical mixing schemes?
271    o seaice pkg:
272     - add a cpp-flag to include a simple formula for a salinity dependent
273       freezing point of sea water at the surface
274     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
275       meridional stresses are now different (and hopefully correct)
276    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
277       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
278       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
279    o pkg/diagnostics: add options and parameters for regional-statistics
280       diagnostics ; define regions by reading a region-mask from a file
281       (might add other options later)
282    o pkg/bulk_force:
283     - add option and parameters to use AIM surface-flux formulae.
284     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
285       others forcing fields (defined in PARM05, parameter file "data") are loaded
286       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
287     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
288     - use the right EXCH call for uwind,vwind (to work on CS-grid).
289     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
290       and parameters (note: calcWindStress replaces .NOT.readwindstress).
291     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
292    
293    checkpoint58
294    o add "--embed-source" option to genmake2 which, when the supporting
295      tools can be compiled (as determined by genmake2) will turn on the
296      embed_files package which then embeds the entire MITgcm source code
297      (*.[fFhc] + Makefile) used for the build within the executable
298      - requested by CNH but off by default
299      - adds a paltry <9MB to the mitgcmuv executable in most cases
300      - only writes the output when useEMBEDSRC in eedata is true
301    o clean up 3-dim. relaxation codes:
302      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
303      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
304      * Thanks to Tom Haine for testing!
305    
306    checkpoint57z_post
307    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
308      affects output (@ truncation level) of exp. plume_on_slope ; updated.
309    o fix the pickup behavior for obcs in combination with ptracers
310    o fix a bug in ptracers_external_fields_load
311    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
312      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
313    o transfered surface NH pressure to eta field (if exactConserv).
314    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
315         and update lab_sea output.txt file.
316    o completing 3-dim. relaxation code: additional term
317         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
318      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
319      * At compile time, in "EXF_OPTIONS.h" set
320          #define  ALLOW_CLIMTEMP_RELAXATION
321          #define  ALLOW_CLIMSALT_RELAXATION
322      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
323          tauThetaClimRelax3Dim = 15552000.0,
324          tauSaltClimRelax3Dim  = 15552000.0,
325      * 3 cases:
326          1) Use a constant-in-time 3-dim. field
327          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
328          3) Real-time relax. to time-evolving prescribed field
329    o Adding Laplacian-type smoothness constraint on
330      initial and boundary (forcing) controls (ic, bc)
331      * enable at compile-time via
332        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
333      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
334      * Absolute scale somewhat unclear so far
335      * no area weighting was included since no other cost term does so far
336    
337    checkpoint57y_post
338    First step for a NLFS adjoint
339    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
340    o new init. routines for calc_r_star, calc_surf_dr
341    o still need to deal with ini_masks_etc
342    o testreport seemed happy
343    checkpoint57y_pre
344    
345    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
346    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
347    o add new offset feature to offline pkg (plus minor cleanup)
348    o cfc fixes for final year of integration
349    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
350      be in GCHEM_OPTIONS).
351    
352    checkpoint57x_post
353    o fix testreport Pb in multiple test experiment.
354    o cleanup our namelist syntax in verification:
355      - make it more F95 standards compliant (some work still needed)
356      - allows the vast majority of our tests to work with gfortran
357    o Non-Hydrostatic:
358     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
359     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
360    o Allow to apply AB on T,S rather than on AB(gT,gS):
361     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
362     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
363       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
364     - need a "clever" read_pickup to restart from the other AB formulation
365    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
366    o remove some unused variables (reduces number of compiler warnings)
367    o adjoint
368      * Disable useVariableViscosity for adjoint for time being
369        (there are a number of extensive recomputations)
370      * Initialize certain variables needed for adjoint
371    
372    checkpoint57w_post
373    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
374                 fix the singleCpuIO RS version of MDSWRITEFIELD
375       and add a WARNING if using globalFiles=T with multi-processors.
376    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
377      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
378    o tracer advection scheme:
379      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
380       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
381       was not very convenient).
382      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
383       (further tests needed for the implicit DST & Flux-Limiter schemes).
384    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
385      and sRef for convenience, handy, when you want to initialize
386      ptracers in a large domain with a constant non-zero value. Also,
387      untangle ptracers_init.F a little.
388    
389    checkpoint57v_post
390    o change dome exp. to use variable viscosity in side-drag terms.
391    o remove all the files from the cfc_offline test since they are now
392      incorporated into tutorial_cfc_offline which has been producing
393      identical results for a few days of testing
394    o add new parameter: sideDragFactor to enable half-slip-side BC
395      and change side-drag S/R to use viscosity from mom_calc_visc
396      (can switch back by setting sideDragFactor=0.); affects results at
397      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
398       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
399    o vorticity & strain are now computed without masking, to account for
400      no-slip-side BC in variable viscosity calculation ; mask is applied
401      anyway later on, before computing advection/coriolis terms.
402    o modify exp4 to test new obcs support for reading from external files
403      and for passive tracers
404    o fix behavior of ptracers_monitor when monitor output is written to a
405      netcdf-file; still not independent of monitor.F (writes in the same
406      file).
407    o change default value of tRef (put a uniform, meaningful value for ocean
408      & atmos) and initialize sRef (was missing, as Martin mentioned).
409    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
410      to be proportional to enstrophy dissipation length.  Thus,
411       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
412      This is now consistent with Smagorinsky and with the manual.
413    
414    checkpoint57u_post
415    o OBCS and PTRACERS: add open boundary support for passive tracers
416      - either use homogenous (pseudo) v.Neumann conditions or prescribe
417        OB-values from file; this is not different from the way theta and salinity
418        are treated
419      - however, Orlanski-radiation conditions are not supported, and the model
420        will stop if you use pTracers and Orlanski at the same time.
421      - beefed up the rountine obcs_external_fields_load: now only those open
422        boundary values are overwritten with values from files for which there
423        are really files, otherwise the OB-fields remain untouched. This makes
424        it possible to use different OBs at different ends of the domain (as
425        with EXF)
426    o reduce number of exch calls in shap_filt (s2).
427    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
428      truncation level) 4/5 MLAdjust test results (11&12 digits match).
429    
430    checkpoint57t_post
431    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
432    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
433      same truncation, independent of the face number: affects affects several
434      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
435    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
436      note that biharmonic viscosity + no-slip was not tested in any experiment.
437    o fix bug in non-linear free-surf side-drag ; generate new output for
438      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
439    o make mnc honor the writeBinaryPrec flag for most kinds of output
440    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
441    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
442      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
443    o add brackets in multi-terms sum to get same truncation, independent of
444      the face number (manage to get exactly same value of gU,gV at the cs-edge)
445      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
446    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
447      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
448      a maximum grid-scale Reynolds number.  Also, changes all length calculations
449      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
450      Suggested values of viscosity parameters found in mom_calc_visc.
451      Many new viscosity diagnostics available.
452    
453    checkpoint57s_post
454    o Add clearing-house for viscosity calculations, mom_calc_visc and
455      correct numerous bugs in LeithD and Smagorinsky discretizations.  
456      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
457      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
458      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
459      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
460      The Strain-Tension form is now called with useStrainTensonVisc=.true.
461      ViscAhStrain and viscAhTension are now retired.
462    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
463    o In response to JMC's bug report, genmake2 now ignores any soft-links
464      that it finds in the *current* directory when searching for files.
465      Soft-links found in any other source directories will still work as
466      they did before.
467    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
468      a C routine to unlimit the stack size
469    o mnc-ify pkg/aim snapshot vars
470    o mnc-ify pkg/land as requested by Daniel
471    o various changes to mnc including:
472      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
473      - output can now be grouped so that all files within a group
474          change the ITER portion of their names in lock-step together
475      - can now read ("global") PER-FACE (in addition to PER-TILE) files
476          and works with both EXCH1 and EXCH2 (but needs more testing)
477      - writing works for all verification test cases w/ g77 on Linux
478    
479    checkpoint57r_post
480    o make MNC variable initialization happen earlier
481    o add diagnostics for (almost) each term of the momentum Eq.
482    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
483    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
484    o remove MINIMAL_TAVE_OUTPUT option ;
485      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
486    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
487      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
488    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
489    o add time-dependent SST, SSS control
490    o cost terms in ecco/ modularized (new cost_generic.F)
491    o cost_averages routines are modularized (new cost_averagesgeneric.F)
492    o new infrastructure for seaice model vs. obs misfits in seaice/
493      * driver from the_main_loop.F is seaice_cost_driver.F
494      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
495      * gradient check in Exp. 6a of natl_box_adjoint/
496    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
497      (see README file)
498    
499    checkpoint57q_post
500    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
501    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
502      - bug was reported by Jean-Michel and Ian Fenty
503    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
504      update exp. cpl_aim+ocn output.
505    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
506      Needed for high-res. runs with large global files
507      to be able to limit tapelev size
508    o Changed some tests for adjoint:
509      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
510      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
511      * global_ocean.90x40x15/ back to default 3-level checkpointing
512    o Modifications to enable scripted COMMON to MODULE conversion
513      * verification/OpenAD/code/ has necessary scripts and description;
514      * converts, compiles and runs successfully;
515    
516    checkpoint57p_post
517    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
518    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
519      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
520    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
521    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
522      (was already the case for dissipation with mom_vecinv,
523       and also the case for grad.PhiHyd when staggered-timeStep)
524      This will allow to put dissipation out-off the AB time-stepping.
525     Unfortunately, affects truncation error. Update output of exp. that "fails"
526      (cg2d matching number) and leave the others for later: front_relax(10),
527      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
528      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
529    
530    checkpoint57o_post
531    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
532      (2) its ready to be documented during the 20050801 DocFest
533    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
534      for ideal_2D_oce and lab_sea on linux_ia32_g77
535    o set to #undef CTRL_SET_OLD_MAXCVARS_30
536      in global1x1_tot/code_seaice_adj to access indices 32, 33
537      (worth another tag)
538    
539    checkpoint57n_post
540    o adding precip control xx_precip 32
541    o adding swflux control xx_swflux 33
542    o Replacing 10 forcing penalty cost routines by 1 generic.
543    o Implementing partitioning in time-mean and variable adjustment
544      for atmos. state.
545    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
546  o in natl_box_adjoint:  o in natl_box_adjoint:
547    * updated: results_bulk/    * updated exp 1 to 10
548    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
549    o updated global1x1/*_seaice_adj/
550      to incorporate latest changes
551    o enable useSingleCpuIO for mdsio vector routines
552      (applies in particular to tapelev I/O)
553    o removed inefficient K-loop in all active_file*control*.F
554    
555  checkpoint57m_post  checkpoint57m_post
556  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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