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revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.691 by dimitri, Fri Jun 30 12:05:42 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/exf modifications to interpolation and rotation routines for more
8  o moved ptracer ctrl index 17 -> 32     reasonable treatment of North Pole singularity: for tracers North Pole
9       value is set to northernmost zonal-mean value, for zonal velocity it is
10       set to zero, and for meridional velocity it is set to northernmost value.
11    o pkg/exf/exf_check_range.F
12     - add tile index to diagnostics and move stop statement to the very
13       end of the routine.
14    o pkg/diagnostics: (diagnostics_main_init.F)
15      define title of isomorphic variables according to the current config.
16    o pkg/thsice with pkg/seaice dynamics:
17    - fix domain of computation (interior only, required for exf) and do exchanges
18    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
19    o towards a standard way of dealing with multi-threading in MONITOR
20      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
21    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
22       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
23    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
24    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
25    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
26       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
27    o tracer advection:
28     - clean-up and simplify calc_common_factors.F
29     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
30       advection subroutine (but still not used within DST advection S/R)
31    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
32    
33    checkpoint58j_post
34    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
35      from file (collects calls previously in FORWARD_STEP)
36    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
37    o adjoint store dir. adjusted accordingly
38    o genmake2
39      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
40    
41    checkpoint58i_post
42    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
43      on wind stress (SEAICEstressFactor defaults to 1.)
44    o Total number of Timers is finite (<=40): comment out 2 non-essential one
45      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
46    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
47      on CS-grid: no longer loosing mass.
48    o exf & curvilinear-grid: no longer modify longitude xC & xG.
49    o pkg/ggl90: fix sloppy output and fix a bug
50    o pkg/seaice: added SEAICEuseEVPpickup parameter
51      - Set to false in order to start EVP solver with
52        non-EVP pickup files when using SEAICEuseEVP
53      - fix sign error in diffusion in seaice_calc_rhs
54    
55    checkpoint58h_post
56    * Modifications for bottom topography control
57      o replace hFacC by _hFacC at various places
58      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
59      o add non-self-adjoint cg2d_nsa
60      o update autodiff support routines
61      o re-initialise hfac after ctrl_depth_ini
62      o works for 5x5 box, doesnt work for global_ocean.90x40x15
63    * Adding verification for 5x5 box (4-layer) bottom topography control
64    
65    checkpoint58g_post
66    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
67       used for mean seasonal cycle, mean diurnal cycle); add an example
68       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
69    o pkg/ggl90:
70      - add parameter (minimum surface kinetic energy)
71      - fix bug (avoiding division by zero)
72    o couple pkg/thsice to pkg/seaice:
73      - modify advection in seaice to accomodate new scalar fields to be advected
74      - only muliDimAdection scheme work with seaice/thsice
75      - mapping of thsice-variables to seaice-variables, back and forth
76      - does not break the verification experiments, but does not give the
77        desired results either
78    o pkg/seaice
79      - make (default) second order advection a bit less confusing?
80    
81    checkpoint58f_post
82    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
83      to pkg/seaice):
84      - new routines thsice_map_exf and thsice_get_exf provide the interface
85      - add an additional formal parameter to thsice_solve4temp
86    o pkg/exf:
87      - add new fields wspeed, snowprecip (to be able to couple to thsice)
88      - correct Stefan-Boltzmann constant
89      - new parameter for longwave surface emittance
90      - separate some stuff from exf_bulkformulae into new routines  
91        exf_radiation, exf_wind
92      - add new parameters and constants: longwave emissivity for ocean, ice
93        and snow, evaporation parameters over ice
94      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
95        either wind from stress or stress from wind
96    o pkg/thSIce:
97    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
98    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
99       and THSICE_CALC_THICKN
100    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
101    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
102      to make debugging easier.
103    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
104    o pkg/bulk_force:
105      - clean-up comments and parameters ;
106      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
107    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
108      generate new output for test-experiment: aim.5l_cs.thSI
109    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
110      testreport accordingly
111    
112    checkpoint58e_post
113    o SEAICE_CGRID adjoint done
114    o R_STAR adjoint implemented.
115      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
116      * need to sort out init. of h0facc, etc.
117    o Make pkg/profile fully independent of ecco,cost, etc. stuff
118      to be able to use it in pure forward.
119    
120    checkpoint58d_post
121    o upgrade simple test-experiment to tutorial example:
122     step.1: duplicate the experiment and (step.2) will remove the old copy.
123      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
124      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
125      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
126      tutorial_global_oce_biogeo    <- copy of dic_example
127      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
128      tutorial_plume_on_slope       <- copy of plume_on_slope
129      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
130      tutorial_global_oce_optim     <- empty for now (David ?)
131      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
132     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
133    o correct a sign problem in cost_scat.F
134    o obcs and ptracers: fix boundary conditions for advections schemes
135      with larger stencil
136    o thsice adjoint: start
137    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
138      completeness
139    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
140      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
141    o ptracers adjoint:
142      * avoid extensive recomputatations
143      * fix missing re-init. of gptr (missed by TAF)
144    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
145      me to turn off the excessive output to STDOUT that this package produces
146    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
147      and add those terms in Vector-Invariant formulation.
148    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
149      if the control period (xx_hfluxperiod etc) is 0
150    o in profiles pkg, clean routines and fix details
151    o in ecco pkg, reading ssh data:
152      fix problem in case the model does not start at iter0=0
153    o fix mnc-pickup/restart for ptracers
154    o new package prifiles:
155      code to compute profile-based cost by Gael Forget
156      (modifs in ecco, ctrl, autodiff)
157    o Benign bug fix in initialization (spotted by M. Mazloff) of
158      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
159    
160    checkpoint58c_post
161    o adjoint: finish NLFS adjoint and provide reference output in
162      verification/global_ocean.90x40x15/results_ad_nlfs
163    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
164      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
165      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
166      with SEAICE_CGRID defined.
167    o move calendarDumps from "data" to "data.cal" and clean-up the code
168      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
169    o add useEXF & useCAL flags (for now, set in hard-coded way)
170    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
171      (were missing in NH mode, and wrong in quasihydrostatic mode).
172      waiting for Chris updated version of calc_gw to add those CALLs.
173    o fix bug in quasihydrostatic S/R ;
174      add a test for this option: global_ocean.90x40x15.qshyd
175    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
176      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
177    o add on/off flag useOffLine for package OFFLINE
178    o seaice:
179      - modify advection so that it works also on the C-grid
180      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
181        problem in multi-tile runs with C-grid
182      - add flags for clipping ice velocities and/or masking solver forcing
183      - fix drag (ocean on ice) formulation and a bug that caused noise in the
184        C-grid solver
185      - added a few comments to seaice_diffusion.F
186      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
187        are now exclusive)
188      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
189        required re-ordering the code a little:
190       + make DAIRN global variable (defined in SEAICE)
191       + move computation of the viscosities eta and zeta into a new separate
192         routine (because I need to recompute them in seaice_ocean_stress.F)
193    
194    checkpoint58b_post
195    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
196      update output.txt of exp. aim.5l_cs.thSI
197    o various mnc cleanups and improvements:
198      + shrink lookup tables by factor of ~4
199      + better error reporting when running out of lookup space
200      + able to handle longer path/file names (up to 500 chars)
201    o adjoint:
202      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
203      - TBD: "hidden" mom_vecinv recomp. in dynamics
204    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
205     (allow to differentiate between forcing components using new integer flags:
206      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
207     and add new flag to put Dissipation tendency out of Adams-Bashforth.
208    o ecco
209      - enable trend removal from SSH anomaly obs.
210    o adjoint
211      - a fix for PmEpR when #undef EXACT_CONSERV
212      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
213      - try to fix "hidden" recomp. in forward_step for NLFS
214        (NLFS seems broken sometimes after I checked it in)
215    o seaice:
216     - add c-grid version of the dynamic solver:
217       + three new routines that are the c-grid substitute lsr, dynsolver
218         and ostres
219       + put a few fields that were local to dynsolver into global common
220         blocks, so that I can move the computation of stresses etc into
221         seaice_lsr (saves coding but may break the adjoint).
222     - replace more hardwired parameters by runtime parameters
223     - add ice masks that mask the rhs of the implicit solvers where there
224       is no ice (commented out in seaice_dynsolver, because i am not sure
225       if this works properly), eventually this should replace the clipping
226       of ice velocities in seaice_dynsolver to +/-40cm/s.
227    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
228      include it only where its needed
229    o move balancing of fluxes before the call of external_forcing_surf
230    o seaice:
231      - correct units of turning angles (now they are really in degrees)
232      - move computation of GWATX/Y out of main routine into dynsolver
233      - initialize GWATX/Y in seaice_init
234    o Apply mask on Fresh-Water flux (needed for SSH forcing).
235      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
236    o seaice: add runtime flags for turning angles (default to zero)
237    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
238      and trend from exf forcing and ctrl control adjustments
239    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
240      (since checkpoint57x_post)
241    o change the default rotation period to 86164.s = the Earth rotation
242    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
243      and based on a reference stratification. Tested within hs94.cs-32x32x5.
244    o seaice advection: add code for choosing between the default (2nd order
245      central differences) and multiDim advection schemes provided by
246      pkg/generic_advdiff
247    o seaice:
248      - removed all references to SEAICE_GRID.h fields from
249        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
250        (cubed-sphere configuration will change a little)
251      - grid computations in seaice_init are obsolete now.
252      - cleaned up code a little so that is easier to read (hopefully).
253      - added new (better?) discretizations of default advection and diffusion
254        (turn on with SEAICEuseFluxForm)
255      - replace 1 in 3d global fields by kSurface in growth.F
256      
257    checkpoint58a_post
258    o seaice:
259      - bug fix in advect.F
260    o shelfice:
261      - separate shelfice load anomaly from pload (breaks with time
262        dependent forcing), => introduce constant field shelficeLoadAnomaly.
263        Its default is 0., but it may be computed more cleverly from (unknown)
264        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
265        done offline. A good approximation of the pressure load anomaly is
266        necessary to avoid large initial adjustment processes underneath
267        deep-reaching shelfice.
268      - small fix in ISOMIP shelfice_thermodynamics
269      - add more sophisticated thermodynamics of Hellmer (1989), this is
270        now the default
271      - give a few constants more intuitive names
272    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
273      if bulk formulae are used in long integration (especially EmPmR). Turn
274      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
275      if balancePrintMean, the imbalance that is substracted is printed to
276      STDOUT.
277    o fix bug (typo) in obcs_apply_eta.F
278    o add a new package shelfice which enables us to model the circulation
279      underneath shelf-ice with draughts of hundreds of meters.
280     - works
281     - to do: + include improved thermodynamics
282              + check whether kSurfC (from model/inc/SURFACE.h) can be used
283                instead of new field kTopC
284              + can we use topoFile, Ro_surf and existing code in ini_depth.F
285                instead of new field R_shelfIce and new code in ini_depth.F
286                and ini_mask_etc.F?
287              + adjust vertical mixing schemes?
288    o seaice pkg:
289     - add a cpp-flag to include a simple formula for a salinity dependent
290       freezing point of sea water at the surface
291     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
292       meridional stresses are now different (and hopefully correct)
293    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
294       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
295       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
296    o pkg/diagnostics: add options and parameters for regional-statistics
297       diagnostics ; define regions by reading a region-mask from a file
298       (might add other options later)
299    o pkg/bulk_force:
300     - add option and parameters to use AIM surface-flux formulae.
301     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
302       others forcing fields (defined in PARM05, parameter file "data") are loaded
303       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
304     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
305     - use the right EXCH call for uwind,vwind (to work on CS-grid).
306     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
307       and parameters (note: calcWindStress replaces .NOT.readwindstress).
308     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
309    
310    checkpoint58
311    o add "--embed-source" option to genmake2 which, when the supporting
312      tools can be compiled (as determined by genmake2) will turn on the
313      embed_files package which then embeds the entire MITgcm source code
314      (*.[fFhc] + Makefile) used for the build within the executable
315      - requested by CNH but off by default
316      - adds a paltry <9MB to the mitgcmuv executable in most cases
317      - only writes the output when useEMBEDSRC in eedata is true
318    o clean up 3-dim. relaxation codes:
319      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
320      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
321      * Thanks to Tom Haine for testing!
322    
323    checkpoint57z_post
324    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
325      affects output (@ truncation level) of exp. plume_on_slope ; updated.
326    o fix the pickup behavior for obcs in combination with ptracers
327    o fix a bug in ptracers_external_fields_load
328    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
329      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
330    o transfered surface NH pressure to eta field (if exactConserv).
331    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
332         and update lab_sea output.txt file.
333    o completing 3-dim. relaxation code: additional term
334         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
335      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
336      * At compile time, in "EXF_OPTIONS.h" set
337          #define  ALLOW_CLIMTEMP_RELAXATION
338          #define  ALLOW_CLIMSALT_RELAXATION
339      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
340          tauThetaClimRelax3Dim = 15552000.0,
341          tauSaltClimRelax3Dim  = 15552000.0,
342      * 3 cases:
343          1) Use a constant-in-time 3-dim. field
344          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
345          3) Real-time relax. to time-evolving prescribed field
346    o Adding Laplacian-type smoothness constraint on
347      initial and boundary (forcing) controls (ic, bc)
348      * enable at compile-time via
349        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
350      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
351      * Absolute scale somewhat unclear so far
352      * no area weighting was included since no other cost term does so far
353    
354    checkpoint57y_post
355    First step for a NLFS adjoint
356    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
357    o new init. routines for calc_r_star, calc_surf_dr
358    o still need to deal with ini_masks_etc
359    o testreport seemed happy
360    checkpoint57y_pre
361    
362    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
363    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
364    o add new offset feature to offline pkg (plus minor cleanup)
365    o cfc fixes for final year of integration
366    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
367      be in GCHEM_OPTIONS).
368    
369    checkpoint57x_post
370    o fix testreport Pb in multiple test experiment.
371    o cleanup our namelist syntax in verification:
372      - make it more F95 standards compliant (some work still needed)
373      - allows the vast majority of our tests to work with gfortran
374    o Non-Hydrostatic:
375     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
376     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
377    o Allow to apply AB on T,S rather than on AB(gT,gS):
378     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
379     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
380       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
381     - need a "clever" read_pickup to restart from the other AB formulation
382    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
383    o remove some unused variables (reduces number of compiler warnings)
384    o adjoint
385      * Disable useVariableViscosity for adjoint for time being
386        (there are a number of extensive recomputations)
387      * Initialize certain variables needed for adjoint
388    
389    checkpoint57w_post
390    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
391                 fix the singleCpuIO RS version of MDSWRITEFIELD
392       and add a WARNING if using globalFiles=T with multi-processors.
393    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
394      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
395    o tracer advection scheme:
396      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
397       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
398       was not very convenient).
399      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
400       (further tests needed for the implicit DST & Flux-Limiter schemes).
401    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
402      and sRef for convenience, handy, when you want to initialize
403      ptracers in a large domain with a constant non-zero value. Also,
404      untangle ptracers_init.F a little.
405    
406    checkpoint57v_post
407    o change dome exp. to use variable viscosity in side-drag terms.
408    o remove all the files from the cfc_offline test since they are now
409      incorporated into tutorial_cfc_offline which has been producing
410      identical results for a few days of testing
411    o add new parameter: sideDragFactor to enable half-slip-side BC
412      and change side-drag S/R to use viscosity from mom_calc_visc
413      (can switch back by setting sideDragFactor=0.); affects results at
414      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
415       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
416    o vorticity & strain are now computed without masking, to account for
417      no-slip-side BC in variable viscosity calculation ; mask is applied
418      anyway later on, before computing advection/coriolis terms.
419    o modify exp4 to test new obcs support for reading from external files
420      and for passive tracers
421    o fix behavior of ptracers_monitor when monitor output is written to a
422      netcdf-file; still not independent of monitor.F (writes in the same
423      file).
424    o change default value of tRef (put a uniform, meaningful value for ocean
425      & atmos) and initialize sRef (was missing, as Martin mentioned).
426    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
427      to be proportional to enstrophy dissipation length.  Thus,
428       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
429      This is now consistent with Smagorinsky and with the manual.
430    
431    checkpoint57u_post
432    o OBCS and PTRACERS: add open boundary support for passive tracers
433      - either use homogenous (pseudo) v.Neumann conditions or prescribe
434        OB-values from file; this is not different from the way theta and salinity
435        are treated
436      - however, Orlanski-radiation conditions are not supported, and the model
437        will stop if you use pTracers and Orlanski at the same time.
438      - beefed up the rountine obcs_external_fields_load: now only those open
439        boundary values are overwritten with values from files for which there
440        are really files, otherwise the OB-fields remain untouched. This makes
441        it possible to use different OBs at different ends of the domain (as
442        with EXF)
443    o reduce number of exch calls in shap_filt (s2).
444    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
445      truncation level) 4/5 MLAdjust test results (11&12 digits match).
446    
447    checkpoint57t_post
448    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
449    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
450      same truncation, independent of the face number: affects affects several
451      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
452    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
453      note that biharmonic viscosity + no-slip was not tested in any experiment.
454    o fix bug in non-linear free-surf side-drag ; generate new output for
455      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
456    o make mnc honor the writeBinaryPrec flag for most kinds of output
457    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
458    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
459      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
460    o add brackets in multi-terms sum to get same truncation, independent of
461      the face number (manage to get exactly same value of gU,gV at the cs-edge)
462      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
463    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
464      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
465      a maximum grid-scale Reynolds number.  Also, changes all length calculations
466      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
467      Suggested values of viscosity parameters found in mom_calc_visc.
468      Many new viscosity diagnostics available.
469    
470    checkpoint57s_post
471    o Add clearing-house for viscosity calculations, mom_calc_visc and
472      correct numerous bugs in LeithD and Smagorinsky discretizations.  
473      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
474      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
475      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
476      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
477      The Strain-Tension form is now called with useStrainTensonVisc=.true.
478      ViscAhStrain and viscAhTension are now retired.
479    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
480    o In response to JMC's bug report, genmake2 now ignores any soft-links
481      that it finds in the *current* directory when searching for files.
482      Soft-links found in any other source directories will still work as
483      they did before.
484    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
485      a C routine to unlimit the stack size
486    o mnc-ify pkg/aim snapshot vars
487    o mnc-ify pkg/land as requested by Daniel
488    o various changes to mnc including:
489      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
490      - output can now be grouped so that all files within a group
491          change the ITER portion of their names in lock-step together
492      - can now read ("global") PER-FACE (in addition to PER-TILE) files
493          and works with both EXCH1 and EXCH2 (but needs more testing)
494      - writing works for all verification test cases w/ g77 on Linux
495    
496    checkpoint57r_post
497    o make MNC variable initialization happen earlier
498    o add diagnostics for (almost) each term of the momentum Eq.
499    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
500    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
501    o remove MINIMAL_TAVE_OUTPUT option ;
502      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
503    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
504      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
505    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
506    o add time-dependent SST, SSS control
507    o cost terms in ecco/ modularized (new cost_generic.F)
508    o cost_averages routines are modularized (new cost_averagesgeneric.F)
509    o new infrastructure for seaice model vs. obs misfits in seaice/
510      * driver from the_main_loop.F is seaice_cost_driver.F
511      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
512      * gradient check in Exp. 6a of natl_box_adjoint/
513    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
514      (see README file)
515    
516    checkpoint57q_post
517    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
518    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
519      - bug was reported by Jean-Michel and Ian Fenty
520    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
521      update exp. cpl_aim+ocn output.
522    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
523      Needed for high-res. runs with large global files
524      to be able to limit tapelev size
525    o Changed some tests for adjoint:
526      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
527      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
528      * global_ocean.90x40x15/ back to default 3-level checkpointing
529    o Modifications to enable scripted COMMON to MODULE conversion
530      * verification/OpenAD/code/ has necessary scripts and description;
531      * converts, compiles and runs successfully;
532    
533    checkpoint57p_post
534    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
535    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
536      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
537    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
538    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
539      (was already the case for dissipation with mom_vecinv,
540       and also the case for grad.PhiHyd when staggered-timeStep)
541      This will allow to put dissipation out-off the AB time-stepping.
542     Unfortunately, affects truncation error. Update output of exp. that "fails"
543      (cg2d matching number) and leave the others for later: front_relax(10),
544      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
545      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
546    
547    checkpoint57o_post
548    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
549      (2) its ready to be documented during the 20050801 DocFest
550    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
551      for ideal_2D_oce and lab_sea on linux_ia32_g77
552    o set to #undef CTRL_SET_OLD_MAXCVARS_30
553      in global1x1_tot/code_seaice_adj to access indices 32, 33
554      (worth another tag)
555    
556    checkpoint57n_post
557    o adding precip control xx_precip 32
558    o adding swflux control xx_swflux 33
559    o Replacing 10 forcing penalty cost routines by 1 generic.
560    o Implementing partitioning in time-mean and variable adjustment
561      for atmos. state.
562    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
563  o in natl_box_adjoint:  o in natl_box_adjoint:
564    * updated: results_bulk/    * updated exp 1 to 10
565    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
566    o updated global1x1/*_seaice_adj/
567      to incorporate latest changes
568    o enable useSingleCpuIO for mdsio vector routines
569      (applies in particular to tapelev I/O)
570    o removed inefficient K-loop in all active_file*control*.F
571    
572  checkpoint57m_post  checkpoint57m_post
573  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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