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revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.717 by edhill, Tue Aug 15 04:30:53 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 added the regrid package
8  o moved ptracer ctrl index 17 -> 32  o shelfice:
9     - add a simple boundary layer scheme to reduce noise
10     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
11    checkpoint58n_post
12    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
13       local variable (not in common block).
14    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
15      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
16      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
17        to work with SingleCpuIO.
18    o add "_d 0" to real constant of pkg/cfc subroutines ;
19       update exp. cfc_exemple & tutorial_cfc_offline output files.
20    o multi-threading and IO:
21      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
22        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
23      - barrier before and after reading.
24      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
25      - avoid using MDS_WRITELOCAL for LAND pkg output.
26      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
27        common-block variables ; Allows multi-threading with master-thread IO.
28    o change default MAX_NO_THREADS from 32 to 4 ;
29      and stop cleanly when MAX_NO_THREADS is too small.
30    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
31    
32    checkpoint58m_post
33    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
34       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
35    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
36       keep global_ocean.90x40x15 (for AD testing) with former secondary test
37       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
38    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
39        add MITgcm_tutorials (= code + all the tutorials)
40    o ecco, option to compute cost for total ssh (mean+anom)
41    o consistent with addition of ptracer and ssh in pkg/profiles
42    o profiles: adding ptracer and ssh
43    o testreport: change multi-test output-file name
44      (from output.txt.{name} to output.{name}.txt)
45    o profiles: now ok for mutli-tiles case
46    o seaice: add 4 parameters for different advection schemes for area,
47      (effective) seaice thickness, enthalphy, and snow height. Their default
48      is the standard parameter SEAICEadvScheme
49    o calc_gw:
50     - add cosFacU in zonal viscous flux (harmonic.visc.).
51     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
52       of tutorial_plume_on_slope.
53    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
54    o calc_gw: true flux-form, account for horizontal grid spacing.
55      update rotating_tank results, but not plume_on_slope (affected at
56      truncation level, 11 digits).
57    
58    checkpoint58l_post
59    o calc_gw:
60     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
61     - remove side-drag for now (need to fix it); update plume_on_slope results.
62     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
63    o commit code to make SST/SSS weights spatially variable
64      (based on either variable in-situ or variable initial T/S weights)
65    o pkg/ecco:
66      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
67        now based on horizontally varying weights wthetaLev, wsaltLev
68      * cost_averagesflags now returns year indices in addition to day, month
69      * sflux balance is performed on annual basis
70        (sflxumm, sfluxmm2, bal_sfluxmm)
71      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
72        including separate counting and multipliers
73    o pkg/rbcs
74      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
75    
76    checkpoint58k_post
77    o testreport:
78     - always build in dir. "build" (if not there, mkdir build instead of building
79       & running in input)
80     - run in dir run (if it exists), in build otherwise.
81     - call prepare_run (if input/prepare_run exists)
82     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
83    o pkg/exf modifications to interpolation and rotation routines for more
84       reasonable treatment of North Pole singularity: for tracers North Pole
85       value is set to northernmost zonal-mean value, for zonal velocity it is
86       set to zero, and for meridional velocity it is set to northernmost value.
87    o pkg/exf/exf_check_range.F
88     - add tile index to diagnostics and move stop statement to the very
89       end of the routine.
90    o pkg/diagnostics: (diagnostics_main_init.F)
91      define title of isomorphic variables according to the current config.
92    o pkg/thsice with pkg/seaice dynamics:
93    - fix domain of computation (interior only, required for exf) and do exchanges
94    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
95    o towards a standard way of dealing with multi-threading in MONITOR
96      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
97    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
98       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
99    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
100    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
101    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
102       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
103    o tracer advection:
104     - clean-up and simplify calc_common_factors.F
105     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
106       advection subroutine (but still not used within DST advection S/R)
107    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
108    
109    checkpoint58j_post
110    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
111      from file (collects calls previously in FORWARD_STEP)
112    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
113    o adjoint store dir. adjusted accordingly
114    o genmake2
115      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
116    
117    checkpoint58i_post
118    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
119      on wind stress (SEAICEstressFactor defaults to 1.)
120    o Total number of Timers is finite (<=40): comment out 2 non-essential one
121      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
122    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
123      on CS-grid: no longer loosing mass.
124    o exf & curvilinear-grid: no longer modify longitude xC & xG.
125    o pkg/ggl90: fix sloppy output and fix a bug
126    o pkg/seaice: added SEAICEuseEVPpickup parameter
127      - Set to false in order to start EVP solver with
128        non-EVP pickup files when using SEAICEuseEVP
129      - fix sign error in diffusion in seaice_calc_rhs
130    
131    checkpoint58h_post
132    * Modifications for bottom topography control
133      o replace hFacC by _hFacC at various places
134      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
135      o add non-self-adjoint cg2d_nsa
136      o update autodiff support routines
137      o re-initialise hfac after ctrl_depth_ini
138      o works for 5x5 box, doesnt work for global_ocean.90x40x15
139    * Adding verification for 5x5 box (4-layer) bottom topography control
140    
141    checkpoint58g_post
142    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
143       used for mean seasonal cycle, mean diurnal cycle); add an example
144       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
145    o pkg/ggl90:
146      - add parameter (minimum surface kinetic energy)
147      - fix bug (avoiding division by zero)
148    o couple pkg/thsice to pkg/seaice:
149      - modify advection in seaice to accomodate new scalar fields to be advected
150      - only muliDimAdection scheme work with seaice/thsice
151      - mapping of thsice-variables to seaice-variables, back and forth
152      - does not break the verification experiments, but does not give the
153        desired results either
154    o pkg/seaice
155      - make (default) second order advection a bit less confusing?
156    
157    checkpoint58f_post
158    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
159      to pkg/seaice):
160      - new routines thsice_map_exf and thsice_get_exf provide the interface
161      - add an additional formal parameter to thsice_solve4temp
162    o pkg/exf:
163      - add new fields wspeed, snowprecip (to be able to couple to thsice)
164      - correct Stefan-Boltzmann constant
165      - new parameter for longwave surface emittance
166      - separate some stuff from exf_bulkformulae into new routines  
167        exf_radiation, exf_wind
168      - add new parameters and constants: longwave emissivity for ocean, ice
169        and snow, evaporation parameters over ice
170      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
171        either wind from stress or stress from wind
172    o pkg/thSIce:
173    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
174    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
175       and THSICE_CALC_THICKN
176    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
177    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
178      to make debugging easier.
179    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
180    o pkg/bulk_force:
181      - clean-up comments and parameters ;
182      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
183    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
184      generate new output for test-experiment: aim.5l_cs.thSI
185    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
186      testreport accordingly
187    
188    checkpoint58e_post
189    o SEAICE_CGRID adjoint done
190    o R_STAR adjoint implemented.
191      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
192      * need to sort out init. of h0facc, etc.
193    o Make pkg/profile fully independent of ecco,cost, etc. stuff
194      to be able to use it in pure forward.
195    
196    checkpoint58d_post
197    o upgrade simple test-experiment to tutorial example:
198     step.1: duplicate the experiment and (step.2) will remove the old copy.
199      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
200      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
201      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
202      tutorial_global_oce_biogeo    <- copy of dic_example
203      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
204      tutorial_plume_on_slope       <- copy of plume_on_slope
205      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
206      tutorial_global_oce_optim     <- empty for now (David ?)
207      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
208     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
209    o correct a sign problem in cost_scat.F
210    o obcs and ptracers: fix boundary conditions for advections schemes
211      with larger stencil
212    o thsice adjoint: start
213    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
214      completeness
215    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
216      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
217    o ptracers adjoint:
218      * avoid extensive recomputatations
219      * fix missing re-init. of gptr (missed by TAF)
220    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
221      me to turn off the excessive output to STDOUT that this package produces
222    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
223      and add those terms in Vector-Invariant formulation.
224    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
225      if the control period (xx_hfluxperiod etc) is 0
226    o in profiles pkg, clean routines and fix details
227    o in ecco pkg, reading ssh data:
228      fix problem in case the model does not start at iter0=0
229    o fix mnc-pickup/restart for ptracers
230    o new package prifiles:
231      code to compute profile-based cost by Gael Forget
232      (modifs in ecco, ctrl, autodiff)
233    o Benign bug fix in initialization (spotted by M. Mazloff) of
234      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
235    
236    checkpoint58c_post
237    o adjoint: finish NLFS adjoint and provide reference output in
238      verification/global_ocean.90x40x15/results_ad_nlfs
239    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
240      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
241      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
242      with SEAICE_CGRID defined.
243    o move calendarDumps from "data" to "data.cal" and clean-up the code
244      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
245    o add useEXF & useCAL flags (for now, set in hard-coded way)
246    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
247      (were missing in NH mode, and wrong in quasihydrostatic mode).
248      waiting for Chris updated version of calc_gw to add those CALLs.
249    o fix bug in quasihydrostatic S/R ;
250      add a test for this option: global_ocean.90x40x15.qshyd
251    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
252      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
253    o add on/off flag useOffLine for package OFFLINE
254    o seaice:
255      - modify advection so that it works also on the C-grid
256      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
257        problem in multi-tile runs with C-grid
258      - add flags for clipping ice velocities and/or masking solver forcing
259      - fix drag (ocean on ice) formulation and a bug that caused noise in the
260        C-grid solver
261      - added a few comments to seaice_diffusion.F
262      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
263        are now exclusive)
264      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
265        required re-ordering the code a little:
266       + make DAIRN global variable (defined in SEAICE)
267       + move computation of the viscosities eta and zeta into a new separate
268         routine (because I need to recompute them in seaice_ocean_stress.F)
269    
270    checkpoint58b_post
271    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
272      update output.txt of exp. aim.5l_cs.thSI
273    o various mnc cleanups and improvements:
274      + shrink lookup tables by factor of ~4
275      + better error reporting when running out of lookup space
276      + able to handle longer path/file names (up to 500 chars)
277    o adjoint:
278      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
279      - TBD: "hidden" mom_vecinv recomp. in dynamics
280    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
281     (allow to differentiate between forcing components using new integer flags:
282      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
283     and add new flag to put Dissipation tendency out of Adams-Bashforth.
284    o ecco
285      - enable trend removal from SSH anomaly obs.
286    o adjoint
287      - a fix for PmEpR when #undef EXACT_CONSERV
288      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
289      - try to fix "hidden" recomp. in forward_step for NLFS
290        (NLFS seems broken sometimes after I checked it in)
291    o seaice:
292     - add c-grid version of the dynamic solver:
293       + three new routines that are the c-grid substitute lsr, dynsolver
294         and ostres
295       + put a few fields that were local to dynsolver into global common
296         blocks, so that I can move the computation of stresses etc into
297         seaice_lsr (saves coding but may break the adjoint).
298     - replace more hardwired parameters by runtime parameters
299     - add ice masks that mask the rhs of the implicit solvers where there
300       is no ice (commented out in seaice_dynsolver, because i am not sure
301       if this works properly), eventually this should replace the clipping
302       of ice velocities in seaice_dynsolver to +/-40cm/s.
303    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
304      include it only where its needed
305    o move balancing of fluxes before the call of external_forcing_surf
306    o seaice:
307      - correct units of turning angles (now they are really in degrees)
308      - move computation of GWATX/Y out of main routine into dynsolver
309      - initialize GWATX/Y in seaice_init
310    o Apply mask on Fresh-Water flux (needed for SSH forcing).
311      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
312    o seaice: add runtime flags for turning angles (default to zero)
313    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
314      and trend from exf forcing and ctrl control adjustments
315    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
316      (since checkpoint57x_post)
317    o change the default rotation period to 86164.s = the Earth rotation
318    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
319      and based on a reference stratification. Tested within hs94.cs-32x32x5.
320    o seaice advection: add code for choosing between the default (2nd order
321      central differences) and multiDim advection schemes provided by
322      pkg/generic_advdiff
323    o seaice:
324      - removed all references to SEAICE_GRID.h fields from
325        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
326        (cubed-sphere configuration will change a little)
327      - grid computations in seaice_init are obsolete now.
328      - cleaned up code a little so that is easier to read (hopefully).
329      - added new (better?) discretizations of default advection and diffusion
330        (turn on with SEAICEuseFluxForm)
331      - replace 1 in 3d global fields by kSurface in growth.F
332      
333    checkpoint58a_post
334    o seaice:
335      - bug fix in advect.F
336    o shelfice:
337      - separate shelfice load anomaly from pload (breaks with time
338        dependent forcing), => introduce constant field shelficeLoadAnomaly.
339        Its default is 0., but it may be computed more cleverly from (unknown)
340        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
341        done offline. A good approximation of the pressure load anomaly is
342        necessary to avoid large initial adjustment processes underneath
343        deep-reaching shelfice.
344      - small fix in ISOMIP shelfice_thermodynamics
345      - add more sophisticated thermodynamics of Hellmer (1989), this is
346        now the default
347      - give a few constants more intuitive names
348    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
349      if bulk formulae are used in long integration (especially EmPmR). Turn
350      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
351      if balancePrintMean, the imbalance that is substracted is printed to
352      STDOUT.
353    o fix bug (typo) in obcs_apply_eta.F
354    o add a new package shelfice which enables us to model the circulation
355      underneath shelf-ice with draughts of hundreds of meters.
356     - works
357     - to do: + include improved thermodynamics
358              + check whether kSurfC (from model/inc/SURFACE.h) can be used
359                instead of new field kTopC
360              + can we use topoFile, Ro_surf and existing code in ini_depth.F
361                instead of new field R_shelfIce and new code in ini_depth.F
362                and ini_mask_etc.F?
363              + adjust vertical mixing schemes?
364    o seaice pkg:
365     - add a cpp-flag to include a simple formula for a salinity dependent
366       freezing point of sea water at the surface
367     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
368       meridional stresses are now different (and hopefully correct)
369    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
370       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
371       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
372    o pkg/diagnostics: add options and parameters for regional-statistics
373       diagnostics ; define regions by reading a region-mask from a file
374       (might add other options later)
375    o pkg/bulk_force:
376     - add option and parameters to use AIM surface-flux formulae.
377     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
378       others forcing fields (defined in PARM05, parameter file "data") are loaded
379       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
380     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
381     - use the right EXCH call for uwind,vwind (to work on CS-grid).
382     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
383       and parameters (note: calcWindStress replaces .NOT.readwindstress).
384     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
385    
386    checkpoint58
387    o add "--embed-source" option to genmake2 which, when the supporting
388      tools can be compiled (as determined by genmake2) will turn on the
389      embed_files package which then embeds the entire MITgcm source code
390      (*.[fFhc] + Makefile) used for the build within the executable
391      - requested by CNH but off by default
392      - adds a paltry <9MB to the mitgcmuv executable in most cases
393      - only writes the output when useEMBEDSRC in eedata is true
394    o clean up 3-dim. relaxation codes:
395      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
396      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
397      * Thanks to Tom Haine for testing!
398    
399    checkpoint57z_post
400    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
401      affects output (@ truncation level) of exp. plume_on_slope ; updated.
402    o fix the pickup behavior for obcs in combination with ptracers
403    o fix a bug in ptracers_external_fields_load
404    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
405      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
406    o transfered surface NH pressure to eta field (if exactConserv).
407    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
408         and update lab_sea output.txt file.
409    o completing 3-dim. relaxation code: additional term
410         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
411      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
412      * At compile time, in "EXF_OPTIONS.h" set
413          #define  ALLOW_CLIMTEMP_RELAXATION
414          #define  ALLOW_CLIMSALT_RELAXATION
415      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
416          tauThetaClimRelax3Dim = 15552000.0,
417          tauSaltClimRelax3Dim  = 15552000.0,
418      * 3 cases:
419          1) Use a constant-in-time 3-dim. field
420          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
421          3) Real-time relax. to time-evolving prescribed field
422    o Adding Laplacian-type smoothness constraint on
423      initial and boundary (forcing) controls (ic, bc)
424      * enable at compile-time via
425        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
426      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
427      * Absolute scale somewhat unclear so far
428      * no area weighting was included since no other cost term does so far
429    
430    checkpoint57y_post
431    First step for a NLFS adjoint
432    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
433    o new init. routines for calc_r_star, calc_surf_dr
434    o still need to deal with ini_masks_etc
435    o testreport seemed happy
436    checkpoint57y_pre
437    
438    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
439    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
440    o add new offset feature to offline pkg (plus minor cleanup)
441    o cfc fixes for final year of integration
442    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
443      be in GCHEM_OPTIONS).
444    
445    checkpoint57x_post
446    o fix testreport Pb in multiple test experiment.
447    o cleanup our namelist syntax in verification:
448      - make it more F95 standards compliant (some work still needed)
449      - allows the vast majority of our tests to work with gfortran
450    o Non-Hydrostatic:
451     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
452     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
453    o Allow to apply AB on T,S rather than on AB(gT,gS):
454     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
455     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
456       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
457     - need a "clever" read_pickup to restart from the other AB formulation
458    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
459    o remove some unused variables (reduces number of compiler warnings)
460    o adjoint
461      * Disable useVariableViscosity for adjoint for time being
462        (there are a number of extensive recomputations)
463      * Initialize certain variables needed for adjoint
464    
465    checkpoint57w_post
466    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
467                 fix the singleCpuIO RS version of MDSWRITEFIELD
468       and add a WARNING if using globalFiles=T with multi-processors.
469    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
470      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
471    o tracer advection scheme:
472      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
473       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
474       was not very convenient).
475      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
476       (further tests needed for the implicit DST & Flux-Limiter schemes).
477    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
478      and sRef for convenience, handy, when you want to initialize
479      ptracers in a large domain with a constant non-zero value. Also,
480      untangle ptracers_init.F a little.
481    
482    checkpoint57v_post
483    o change dome exp. to use variable viscosity in side-drag terms.
484    o remove all the files from the cfc_offline test since they are now
485      incorporated into tutorial_cfc_offline which has been producing
486      identical results for a few days of testing
487    o add new parameter: sideDragFactor to enable half-slip-side BC
488      and change side-drag S/R to use viscosity from mom_calc_visc
489      (can switch back by setting sideDragFactor=0.); affects results at
490      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
491       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
492    o vorticity & strain are now computed without masking, to account for
493      no-slip-side BC in variable viscosity calculation ; mask is applied
494      anyway later on, before computing advection/coriolis terms.
495    o modify exp4 to test new obcs support for reading from external files
496      and for passive tracers
497    o fix behavior of ptracers_monitor when monitor output is written to a
498      netcdf-file; still not independent of monitor.F (writes in the same
499      file).
500    o change default value of tRef (put a uniform, meaningful value for ocean
501      & atmos) and initialize sRef (was missing, as Martin mentioned).
502    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
503      to be proportional to enstrophy dissipation length.  Thus,
504       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
505      This is now consistent with Smagorinsky and with the manual.
506    
507    checkpoint57u_post
508    o OBCS and PTRACERS: add open boundary support for passive tracers
509      - either use homogenous (pseudo) v.Neumann conditions or prescribe
510        OB-values from file; this is not different from the way theta and salinity
511        are treated
512      - however, Orlanski-radiation conditions are not supported, and the model
513        will stop if you use pTracers and Orlanski at the same time.
514      - beefed up the rountine obcs_external_fields_load: now only those open
515        boundary values are overwritten with values from files for which there
516        are really files, otherwise the OB-fields remain untouched. This makes
517        it possible to use different OBs at different ends of the domain (as
518        with EXF)
519    o reduce number of exch calls in shap_filt (s2).
520    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
521      truncation level) 4/5 MLAdjust test results (11&12 digits match).
522    
523    checkpoint57t_post
524    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
525    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
526      same truncation, independent of the face number: affects affects several
527      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
528    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
529      note that biharmonic viscosity + no-slip was not tested in any experiment.
530    o fix bug in non-linear free-surf side-drag ; generate new output for
531      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
532    o make mnc honor the writeBinaryPrec flag for most kinds of output
533    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
534    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
535      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
536    o add brackets in multi-terms sum to get same truncation, independent of
537      the face number (manage to get exactly same value of gU,gV at the cs-edge)
538      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
539    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
540      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
541      a maximum grid-scale Reynolds number.  Also, changes all length calculations
542      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
543      Suggested values of viscosity parameters found in mom_calc_visc.
544      Many new viscosity diagnostics available.
545    
546    checkpoint57s_post
547    o Add clearing-house for viscosity calculations, mom_calc_visc and
548      correct numerous bugs in LeithD and Smagorinsky discretizations.  
549      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
550      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
551      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
552      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
553      The Strain-Tension form is now called with useStrainTensonVisc=.true.
554      ViscAhStrain and viscAhTension are now retired.
555    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
556    o In response to JMC's bug report, genmake2 now ignores any soft-links
557      that it finds in the *current* directory when searching for files.
558      Soft-links found in any other source directories will still work as
559      they did before.
560    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
561      a C routine to unlimit the stack size
562    o mnc-ify pkg/aim snapshot vars
563    o mnc-ify pkg/land as requested by Daniel
564    o various changes to mnc including:
565      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
566      - output can now be grouped so that all files within a group
567          change the ITER portion of their names in lock-step together
568      - can now read ("global") PER-FACE (in addition to PER-TILE) files
569          and works with both EXCH1 and EXCH2 (but needs more testing)
570      - writing works for all verification test cases w/ g77 on Linux
571    
572    checkpoint57r_post
573    o make MNC variable initialization happen earlier
574    o add diagnostics for (almost) each term of the momentum Eq.
575    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
576    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
577    o remove MINIMAL_TAVE_OUTPUT option ;
578      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
579    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
580      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
581    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
582    o add time-dependent SST, SSS control
583    o cost terms in ecco/ modularized (new cost_generic.F)
584    o cost_averages routines are modularized (new cost_averagesgeneric.F)
585    o new infrastructure for seaice model vs. obs misfits in seaice/
586      * driver from the_main_loop.F is seaice_cost_driver.F
587      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
588      * gradient check in Exp. 6a of natl_box_adjoint/
589    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
590      (see README file)
591    
592    checkpoint57q_post
593    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
594    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
595      - bug was reported by Jean-Michel and Ian Fenty
596    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
597      update exp. cpl_aim+ocn output.
598    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
599      Needed for high-res. runs with large global files
600      to be able to limit tapelev size
601    o Changed some tests for adjoint:
602      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
603      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
604      * global_ocean.90x40x15/ back to default 3-level checkpointing
605    o Modifications to enable scripted COMMON to MODULE conversion
606      * verification/OpenAD/code/ has necessary scripts and description;
607      * converts, compiles and runs successfully;
608    
609    checkpoint57p_post
610    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
611    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
612      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
613    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
614    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
615      (was already the case for dissipation with mom_vecinv,
616       and also the case for grad.PhiHyd when staggered-timeStep)
617      This will allow to put dissipation out-off the AB time-stepping.
618     Unfortunately, affects truncation error. Update output of exp. that "fails"
619      (cg2d matching number) and leave the others for later: front_relax(10),
620      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
621      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
622    
623    checkpoint57o_post
624    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
625      (2) its ready to be documented during the 20050801 DocFest
626    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
627      for ideal_2D_oce and lab_sea on linux_ia32_g77
628    o set to #undef CTRL_SET_OLD_MAXCVARS_30
629      in global1x1_tot/code_seaice_adj to access indices 32, 33
630      (worth another tag)
631    
632    checkpoint57n_post
633    o adding precip control xx_precip 32
634    o adding swflux control xx_swflux 33
635    o Replacing 10 forcing penalty cost routines by 1 generic.
636    o Implementing partitioning in time-mean and variable adjustment
637      for atmos. state.
638    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
639  o in natl_box_adjoint:  o in natl_box_adjoint:
640    * updated: results_bulk/    * updated exp 1 to 10
641    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
642    o updated global1x1/*_seaice_adj/
643      to incorporate latest changes
644    o enable useSingleCpuIO for mdsio vector routines
645      (applies in particular to tapelev I/O)
646    o removed inefficient K-loop in all active_file*control*.F
647    
648  checkpoint57m_post  checkpoint57m_post
649  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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