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revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.669 by heimbach, Wed Jun 7 02:02:52 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  checkpoint58h_post
8  o moved ptracer ctrl index 17 -> 32  * Modifications for bottom topography control
9      o replace hFacC by _hFacC at various places
10      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
11      o add non-self-adjoint cg2d_nsa
12      o update autodiff support routines
13      o re-initialise hfac after ctrl_depth_ini
14      o works for 5x5 box, doesnt work for global_ocean.90x40x15
15    * Adding verification for 5x5 box (4-layer) bottom topography control
16    
17    checkpoint58g_post
18    o pkg/ggl90:
19      - add parameter (minimum surface kinetic energy)
20      - fix bug (avoiding division by zero)
21    o couple pkg/thsice to pkg/seaice:
22      - modify advection in seaice to accomodate new scalar fields to be advected
23      - only muliDimAdection scheme work with seaice/thsice
24      - mapping of thsice-variables to seaice-variables, back and forth
25      - does not break the verification experiments, but does not give the
26        desired results either
27    o pkg/seaice
28      - make (default) second order advection a bit less confusing?
29    
30    checkpoint58f_post
31    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
32      to pkg/seaice):
33      - new routines thsice_map_exf and thsice_get_exf provide the interface
34      - add an additional formal parameter to thsice_solve4temp
35    o pkg/exf:
36      - add new fields wspeed, snowprecip (to be able to couple to thsice)
37      - correct Stefan-Boltzmann constant
38      - new parameter for longwave surface emittance
39      - separate some stuff from exf_bulkformulae into new routines  
40        exf_radiation, exf_wind
41      - add new parameters and constants: longwave emissivity for ocean, ice
42        and snow, evaporation parameters over ice
43      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
44        either wind from stress or stress from wind
45    o pkg/thSIce:
46    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
47    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
48       and THSICE_CALC_THICKN
49    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
50    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
51      to make debugging easier.
52    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
53    o pkg/bulk_force:
54      - clean-up comments and parameters ;
55      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
56    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
57      generate new output for test-experiment: aim.5l_cs.thSI
58    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
59      testreport accordingly
60    
61    checkpoint58e_post
62    o SEAICE_CGRID adjoint done
63    o R_STAR adjoint implemented.
64      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
65      * need to sort out init. of h0facc, etc.
66    o Make pkg/profile fully independent of ecco,cost, etc. stuff
67      to be able to use it in pure forward.
68    
69    checkpoint58d_post
70    o upgrade simple test-experiment to tutorial example:
71     step.1: duplicate the experiment and (step.2) will remove the old copy.
72      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
73      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
74      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
75      tutorial_global_oce_biogeo    <- copy of dic_example
76      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
77      tutorial_plume_on_slope       <- copy of plume_on_slope
78      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
79      tutorial_global_oce_optim     <- empty for now (David ?)
80      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
81     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
82    o correct a sign problem in cost_scat.F
83    o obcs and ptracers: fix boundary conditions for advections schemes
84      with larger stencil
85    o thsice adjoint: start
86    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
87      completeness
88    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
89      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
90    o ptracers adjoint:
91      * avoid extensive recomputatations
92      * fix missing re-init. of gptr (missed by TAF)
93    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
94      me to turn off the excessive output to STDOUT that this package produces
95    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
96      and add those terms in Vector-Invariant formulation.
97    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
98      if the control period (xx_hfluxperiod etc) is 0
99    o in profiles pkg, clean routines and fix details
100    o in ecco pkg, reading ssh data:
101      fix problem in case the model does not start at iter0=0
102    o fix mnc-pickup/restart for ptracers
103    o new package prifiles:
104      code to compute profile-based cost by Gael Forget
105      (modifs in ecco, ctrl, autodiff)
106    o Benign bug fix in initialization (spotted by M. Mazloff) of
107      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
108    
109    checkpoint58c_post
110    o adjoint: finish NLFS adjoint and provide reference output in
111      verification/global_ocean.90x40x15/results_ad_nlfs
112    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
113      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
114      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
115      with SEAICE_CGRID defined.
116    o move calendarDumps from "data" to "data.cal" and clean-up the code
117      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
118    o add useEXF & useCAL flags (for now, set in hard-coded way)
119    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
120      (were missing in NH mode, and wrong in quasihydrostatic mode).
121      waiting for Chris updated version of calc_gw to add those CALLs.
122    o fix bug in quasihydrostatic S/R ;
123      add a test for this option: global_ocean.90x40x15.qshyd
124    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
125      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
126    o add on/off flag useOffLine for package OFFLINE
127    o seaice:
128      - modify advection so that it works also on the C-grid
129      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
130        problem in multi-tile runs with C-grid
131      - add flags for clipping ice velocities and/or masking solver forcing
132      - fix drag (ocean on ice) formulation and a bug that caused noise in the
133        C-grid solver
134      - added a few comments to seaice_diffusion.F
135      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
136        are now exclusive)
137      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
138        required re-ordering the code a little:
139       + make DAIRN global variable (defined in SEAICE)
140       + move computation of the viscosities eta and zeta into a new separate
141         routine (because I need to recompute them in seaice_ocean_stress.F)
142    
143    checkpoint58b_post
144    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
145      update output.txt of exp. aim.5l_cs.thSI
146    o various mnc cleanups and improvements:
147      + shrink lookup tables by factor of ~4
148      + better error reporting when running out of lookup space
149      + able to handle longer path/file names (up to 500 chars)
150    o adjoint:
151      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
152      - TBD: "hidden" mom_vecinv recomp. in dynamics
153    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
154     (allow to differentiate between forcing components using new integer flags:
155      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
156     and add new flag to put Dissipation tendency out of Adams-Bashforth.
157    o ecco
158      - enable trend removal from SSH anomaly obs.
159    o adjoint
160      - a fix for PmEpR when #undef EXACT_CONSERV
161      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
162      - try to fix "hidden" recomp. in forward_step for NLFS
163        (NLFS seems broken sometimes after I checked it in)
164    o seaice:
165     - add c-grid version of the dynamic solver:
166       + three new routines that are the c-grid substitute lsr, dynsolver
167         and ostres
168       + put a few fields that were local to dynsolver into global common
169         blocks, so that I can move the computation of stresses etc into
170         seaice_lsr (saves coding but may break the adjoint).
171     - replace more hardwired parameters by runtime parameters
172     - add ice masks that mask the rhs of the implicit solvers where there
173       is no ice (commented out in seaice_dynsolver, because i am not sure
174       if this works properly), eventually this should replace the clipping
175       of ice velocities in seaice_dynsolver to +/-40cm/s.
176    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
177      include it only where its needed
178    o move balancing of fluxes before the call of external_forcing_surf
179    o seaice:
180      - correct units of turning angles (now they are really in degrees)
181      - move computation of GWATX/Y out of main routine into dynsolver
182      - initialize GWATX/Y in seaice_init
183    o Apply mask on Fresh-Water flux (needed for SSH forcing).
184      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
185    o seaice: add runtime flags for turning angles (default to zero)
186    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
187      and trend from exf forcing and ctrl control adjustments
188    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
189      (since checkpoint57x_post)
190    o change the default rotation period to 86164.s = the Earth rotation
191    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
192      and based on a reference stratification. Tested within hs94.cs-32x32x5.
193    o seaice advection: add code for choosing between the default (2nd order
194      central differences) and multiDim advection schemes provided by
195      pkg/generic_advdiff
196    o seaice:
197      - removed all references to SEAICE_GRID.h fields from
198        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
199        (cubed-sphere configuration will change a little)
200      - grid computations in seaice_init are obsolete now.
201      - cleaned up code a little so that is easier to read (hopefully).
202      - added new (better?) discretizations of default advection and diffusion
203        (turn on with SEAICEuseFluxForm)
204      - replace 1 in 3d global fields by kSurface in growth.F
205      
206    checkpoint58a_post
207    o seaice:
208      - bug fix in advect.F
209    o shelfice:
210      - separate shelfice load anomaly from pload (breaks with time
211        dependent forcing), => introduce constant field shelficeLoadAnomaly.
212        Its default is 0., but it may be computed more cleverly from (unknown)
213        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
214        done offline. A good approximation of the pressure load anomaly is
215        necessary to avoid large initial adjustment processes underneath
216        deep-reaching shelfice.
217      - small fix in ISOMIP shelfice_thermodynamics
218      - add more sophisticated thermodynamics of Hellmer (1989), this is
219        now the default
220      - give a few constants more intuitive names
221    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
222      if bulk formulae are used in long integration (especially EmPmR). Turn
223      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
224      if balancePrintMean, the imbalance that is substracted is printed to
225      STDOUT.
226    o fix bug (typo) in obcs_apply_eta.F
227    o add a new package shelfice which enables us to model the circulation
228      underneath shelf-ice with draughts of hundreds of meters.
229     - works
230     - to do: + include improved thermodynamics
231              + check whether kSurfC (from model/inc/SURFACE.h) can be used
232                instead of new field kTopC
233              + can we use topoFile, Ro_surf and existing code in ini_depth.F
234                instead of new field R_shelfIce and new code in ini_depth.F
235                and ini_mask_etc.F?
236              + adjust vertical mixing schemes?
237    o seaice pkg:
238     - add a cpp-flag to include a simple formula for a salinity dependent
239       freezing point of sea water at the surface
240     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
241       meridional stresses are now different (and hopefully correct)
242    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
243       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
244       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
245    o pkg/diagnostics: add options and parameters for regional-statistics
246       diagnostics ; define regions by reading a region-mask from a file
247       (might add other options later)
248    o pkg/bulk_force:
249     - add option and parameters to use AIM surface-flux formulae.
250     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
251       others forcing fields (defined in PARM05, parameter file "data") are loaded
252       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
253     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
254     - use the right EXCH call for uwind,vwind (to work on CS-grid).
255     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
256       and parameters (note: calcWindStress replaces .NOT.readwindstress).
257     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
258    
259    checkpoint58
260    o add "--embed-source" option to genmake2 which, when the supporting
261      tools can be compiled (as determined by genmake2) will turn on the
262      embed_files package which then embeds the entire MITgcm source code
263      (*.[fFhc] + Makefile) used for the build within the executable
264      - requested by CNH but off by default
265      - adds a paltry <9MB to the mitgcmuv executable in most cases
266      - only writes the output when useEMBEDSRC in eedata is true
267    o clean up 3-dim. relaxation codes:
268      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
269      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
270      * Thanks to Tom Haine for testing!
271    
272    checkpoint57z_post
273    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
274      affects output (@ truncation level) of exp. plume_on_slope ; updated.
275    o fix the pickup behavior for obcs in combination with ptracers
276    o fix a bug in ptracers_external_fields_load
277    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
278      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
279    o transfered surface NH pressure to eta field (if exactConserv).
280    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
281         and update lab_sea output.txt file.
282    o completing 3-dim. relaxation code: additional term
283         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
284      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
285      * At compile time, in "EXF_OPTIONS.h" set
286          #define  ALLOW_CLIMTEMP_RELAXATION
287          #define  ALLOW_CLIMSALT_RELAXATION
288      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
289          tauThetaClimRelax3Dim = 15552000.0,
290          tauSaltClimRelax3Dim  = 15552000.0,
291      * 3 cases:
292          1) Use a constant-in-time 3-dim. field
293          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
294          3) Real-time relax. to time-evolving prescribed field
295    o Adding Laplacian-type smoothness constraint on
296      initial and boundary (forcing) controls (ic, bc)
297      * enable at compile-time via
298        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
299      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
300      * Absolute scale somewhat unclear so far
301      * no area weighting was included since no other cost term does so far
302    
303    checkpoint57y_post
304    First step for a NLFS adjoint
305    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
306    o new init. routines for calc_r_star, calc_surf_dr
307    o still need to deal with ini_masks_etc
308    o testreport seemed happy
309    checkpoint57y_pre
310    
311    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
312    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
313    o add new offset feature to offline pkg (plus minor cleanup)
314    o cfc fixes for final year of integration
315    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
316      be in GCHEM_OPTIONS).
317    
318    checkpoint57x_post
319    o fix testreport Pb in multiple test experiment.
320    o cleanup our namelist syntax in verification:
321      - make it more F95 standards compliant (some work still needed)
322      - allows the vast majority of our tests to work with gfortran
323    o Non-Hydrostatic:
324     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
325     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
326    o Allow to apply AB on T,S rather than on AB(gT,gS):
327     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
328     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
329       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
330     - need a "clever" read_pickup to restart from the other AB formulation
331    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
332    o remove some unused variables (reduces number of compiler warnings)
333    o adjoint
334      * Disable useVariableViscosity for adjoint for time being
335        (there are a number of extensive recomputations)
336      * Initialize certain variables needed for adjoint
337    
338    checkpoint57w_post
339    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
340                 fix the singleCpuIO RS version of MDSWRITEFIELD
341       and add a WARNING if using globalFiles=T with multi-processors.
342    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
343      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
344    o tracer advection scheme:
345      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
346       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
347       was not very convenient).
348      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
349       (further tests needed for the implicit DST & Flux-Limiter schemes).
350    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
351      and sRef for convenience, handy, when you want to initialize
352      ptracers in a large domain with a constant non-zero value. Also,
353      untangle ptracers_init.F a little.
354    
355    checkpoint57v_post
356    o change dome exp. to use variable viscosity in side-drag terms.
357    o remove all the files from the cfc_offline test since they are now
358      incorporated into tutorial_cfc_offline which has been producing
359      identical results for a few days of testing
360    o add new parameter: sideDragFactor to enable half-slip-side BC
361      and change side-drag S/R to use viscosity from mom_calc_visc
362      (can switch back by setting sideDragFactor=0.); affects results at
363      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
364       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
365    o vorticity & strain are now computed without masking, to account for
366      no-slip-side BC in variable viscosity calculation ; mask is applied
367      anyway later on, before computing advection/coriolis terms.
368    o modify exp4 to test new obcs support for reading from external files
369      and for passive tracers
370    o fix behavior of ptracers_monitor when monitor output is written to a
371      netcdf-file; still not independent of monitor.F (writes in the same
372      file).
373    o change default value of tRef (put a uniform, meaningful value for ocean
374      & atmos) and initialize sRef (was missing, as Martin mentioned).
375    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
376      to be proportional to enstrophy dissipation length.  Thus,
377       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
378      This is now consistent with Smagorinsky and with the manual.
379    
380    checkpoint57u_post
381    o OBCS and PTRACERS: add open boundary support for passive tracers
382      - either use homogenous (pseudo) v.Neumann conditions or prescribe
383        OB-values from file; this is not different from the way theta and salinity
384        are treated
385      - however, Orlanski-radiation conditions are not supported, and the model
386        will stop if you use pTracers and Orlanski at the same time.
387      - beefed up the rountine obcs_external_fields_load: now only those open
388        boundary values are overwritten with values from files for which there
389        are really files, otherwise the OB-fields remain untouched. This makes
390        it possible to use different OBs at different ends of the domain (as
391        with EXF)
392    o reduce number of exch calls in shap_filt (s2).
393    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
394      truncation level) 4/5 MLAdjust test results (11&12 digits match).
395    
396    checkpoint57t_post
397    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
398    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
399      same truncation, independent of the face number: affects affects several
400      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
401    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
402      note that biharmonic viscosity + no-slip was not tested in any experiment.
403    o fix bug in non-linear free-surf side-drag ; generate new output for
404      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
405    o make mnc honor the writeBinaryPrec flag for most kinds of output
406    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
407    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
408      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
409    o add brackets in multi-terms sum to get same truncation, independent of
410      the face number (manage to get exactly same value of gU,gV at the cs-edge)
411      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
412    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
413      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
414      a maximum grid-scale Reynolds number.  Also, changes all length calculations
415      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
416      Suggested values of viscosity parameters found in mom_calc_visc.
417      Many new viscosity diagnostics available.
418    
419    checkpoint57s_post
420    o Add clearing-house for viscosity calculations, mom_calc_visc and
421      correct numerous bugs in LeithD and Smagorinsky discretizations.  
422      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
423      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
424      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
425      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
426      The Strain-Tension form is now called with useStrainTensonVisc=.true.
427      ViscAhStrain and viscAhTension are now retired.
428    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
429    o In response to JMC's bug report, genmake2 now ignores any soft-links
430      that it finds in the *current* directory when searching for files.
431      Soft-links found in any other source directories will still work as
432      they did before.
433    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
434      a C routine to unlimit the stack size
435    o mnc-ify pkg/aim snapshot vars
436    o mnc-ify pkg/land as requested by Daniel
437    o various changes to mnc including:
438      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
439      - output can now be grouped so that all files within a group
440          change the ITER portion of their names in lock-step together
441      - can now read ("global") PER-FACE (in addition to PER-TILE) files
442          and works with both EXCH1 and EXCH2 (but needs more testing)
443      - writing works for all verification test cases w/ g77 on Linux
444    
445    checkpoint57r_post
446    o make MNC variable initialization happen earlier
447    o add diagnostics for (almost) each term of the momentum Eq.
448    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
449    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
450    o remove MINIMAL_TAVE_OUTPUT option ;
451      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
452    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
453      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
454    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
455    o add time-dependent SST, SSS control
456    o cost terms in ecco/ modularized (new cost_generic.F)
457    o cost_averages routines are modularized (new cost_averagesgeneric.F)
458    o new infrastructure for seaice model vs. obs misfits in seaice/
459      * driver from the_main_loop.F is seaice_cost_driver.F
460      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
461      * gradient check in Exp. 6a of natl_box_adjoint/
462    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
463      (see README file)
464    
465    checkpoint57q_post
466    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
467    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
468      - bug was reported by Jean-Michel and Ian Fenty
469    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
470      update exp. cpl_aim+ocn output.
471    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
472      Needed for high-res. runs with large global files
473      to be able to limit tapelev size
474    o Changed some tests for adjoint:
475      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
476      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
477      * global_ocean.90x40x15/ back to default 3-level checkpointing
478    o Modifications to enable scripted COMMON to MODULE conversion
479      * verification/OpenAD/code/ has necessary scripts and description;
480      * converts, compiles and runs successfully;
481    
482    checkpoint57p_post
483    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
484    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
485      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
486    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
487    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
488      (was already the case for dissipation with mom_vecinv,
489       and also the case for grad.PhiHyd when staggered-timeStep)
490      This will allow to put dissipation out-off the AB time-stepping.
491     Unfortunately, affects truncation error. Update output of exp. that "fails"
492      (cg2d matching number) and leave the others for later: front_relax(10),
493      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
494      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
495    
496    checkpoint57o_post
497    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
498      (2) its ready to be documented during the 20050801 DocFest
499    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
500      for ideal_2D_oce and lab_sea on linux_ia32_g77
501    o set to #undef CTRL_SET_OLD_MAXCVARS_30
502      in global1x1_tot/code_seaice_adj to access indices 32, 33
503      (worth another tag)
504    
505    checkpoint57n_post
506    o adding precip control xx_precip 32
507    o adding swflux control xx_swflux 33
508    o Replacing 10 forcing penalty cost routines by 1 generic.
509    o Implementing partitioning in time-mean and variable adjustment
510      for atmos. state.
511    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
512  o in natl_box_adjoint:  o in natl_box_adjoint:
513    * updated: results_bulk/    * updated exp 1 to 10
514    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
515    o updated global1x1/*_seaice_adj/
516      to incorporate latest changes
517    o enable useSingleCpuIO for mdsio vector routines
518      (applies in particular to tapelev I/O)
519    o removed inefficient K-loop in all active_file*control*.F
520    
521  checkpoint57m_post  checkpoint57m_post
522  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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