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revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.715 by mlosch, Mon Aug 14 16:53:08 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 shelfice: add a simple boundary layer scheme to reduce noise
8  o moved ptracer ctrl index 17 -> 32  
9    checkpoint58n_post
10    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
11       local variable (not in common block).
12    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
13      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
14      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
15        to work with SingleCpuIO.
16    o add "_d 0" to real constant of pkg/cfc subroutines ;
17       update exp. cfc_exemple & tutorial_cfc_offline output files.
18    o multi-threading and IO:
19      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
20        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
21      - barrier before and after reading.
22      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
23      - avoid using MDS_WRITELOCAL for LAND pkg output.
24      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
25        common-block variables ; Allows multi-threading with master-thread IO.
26    o change default MAX_NO_THREADS from 32 to 4 ;
27      and stop cleanly when MAX_NO_THREADS is too small.
28    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
29    
30    checkpoint58m_post
31    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
32       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
33    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
34       keep global_ocean.90x40x15 (for AD testing) with former secondary test
35       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
36    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
37        add MITgcm_tutorials (= code + all the tutorials)
38    o ecco, option to compute cost for total ssh (mean+anom)
39    o consistent with addition of ptracer and ssh in pkg/profiles
40    o profiles: adding ptracer and ssh
41    o testreport: change multi-test output-file name
42      (from output.txt.{name} to output.{name}.txt)
43    o profiles: now ok for mutli-tiles case
44    o seaice: add 4 parameters for different advection schemes for area,
45      (effective) seaice thickness, enthalphy, and snow height. Their default
46      is the standard parameter SEAICEadvScheme
47    o calc_gw:
48     - add cosFacU in zonal viscous flux (harmonic.visc.).
49     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
50       of tutorial_plume_on_slope.
51    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
52    o calc_gw: true flux-form, account for horizontal grid spacing.
53      update rotating_tank results, but not plume_on_slope (affected at
54      truncation level, 11 digits).
55    
56    checkpoint58l_post
57    o calc_gw:
58     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
59     - remove side-drag for now (need to fix it); update plume_on_slope results.
60     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
61    o commit code to make SST/SSS weights spatially variable
62      (based on either variable in-situ or variable initial T/S weights)
63    o pkg/ecco:
64      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
65        now based on horizontally varying weights wthetaLev, wsaltLev
66      * cost_averagesflags now returns year indices in addition to day, month
67      * sflux balance is performed on annual basis
68        (sflxumm, sfluxmm2, bal_sfluxmm)
69      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
70        including separate counting and multipliers
71    o pkg/rbcs
72      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
73    
74    checkpoint58k_post
75    o testreport:
76     - always build in dir. "build" (if not there, mkdir build instead of building
77       & running in input)
78     - run in dir run (if it exists), in build otherwise.
79     - call prepare_run (if input/prepare_run exists)
80     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
81    o pkg/exf modifications to interpolation and rotation routines for more
82       reasonable treatment of North Pole singularity: for tracers North Pole
83       value is set to northernmost zonal-mean value, for zonal velocity it is
84       set to zero, and for meridional velocity it is set to northernmost value.
85    o pkg/exf/exf_check_range.F
86     - add tile index to diagnostics and move stop statement to the very
87       end of the routine.
88    o pkg/diagnostics: (diagnostics_main_init.F)
89      define title of isomorphic variables according to the current config.
90    o pkg/thsice with pkg/seaice dynamics:
91    - fix domain of computation (interior only, required for exf) and do exchanges
92    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
93    o towards a standard way of dealing with multi-threading in MONITOR
94      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
95    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
96       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
97    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
98    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
99    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
100       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
101    o tracer advection:
102     - clean-up and simplify calc_common_factors.F
103     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
104       advection subroutine (but still not used within DST advection S/R)
105    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
106    
107    checkpoint58j_post
108    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
109      from file (collects calls previously in FORWARD_STEP)
110    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
111    o adjoint store dir. adjusted accordingly
112    o genmake2
113      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
114    
115    checkpoint58i_post
116    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
117      on wind stress (SEAICEstressFactor defaults to 1.)
118    o Total number of Timers is finite (<=40): comment out 2 non-essential one
119      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
120    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
121      on CS-grid: no longer loosing mass.
122    o exf & curvilinear-grid: no longer modify longitude xC & xG.
123    o pkg/ggl90: fix sloppy output and fix a bug
124    o pkg/seaice: added SEAICEuseEVPpickup parameter
125      - Set to false in order to start EVP solver with
126        non-EVP pickup files when using SEAICEuseEVP
127      - fix sign error in diffusion in seaice_calc_rhs
128    
129    checkpoint58h_post
130    * Modifications for bottom topography control
131      o replace hFacC by _hFacC at various places
132      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
133      o add non-self-adjoint cg2d_nsa
134      o update autodiff support routines
135      o re-initialise hfac after ctrl_depth_ini
136      o works for 5x5 box, doesnt work for global_ocean.90x40x15
137    * Adding verification for 5x5 box (4-layer) bottom topography control
138    
139    checkpoint58g_post
140    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
141       used for mean seasonal cycle, mean diurnal cycle); add an example
142       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
143    o pkg/ggl90:
144      - add parameter (minimum surface kinetic energy)
145      - fix bug (avoiding division by zero)
146    o couple pkg/thsice to pkg/seaice:
147      - modify advection in seaice to accomodate new scalar fields to be advected
148      - only muliDimAdection scheme work with seaice/thsice
149      - mapping of thsice-variables to seaice-variables, back and forth
150      - does not break the verification experiments, but does not give the
151        desired results either
152    o pkg/seaice
153      - make (default) second order advection a bit less confusing?
154    
155    checkpoint58f_post
156    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
157      to pkg/seaice):
158      - new routines thsice_map_exf and thsice_get_exf provide the interface
159      - add an additional formal parameter to thsice_solve4temp
160    o pkg/exf:
161      - add new fields wspeed, snowprecip (to be able to couple to thsice)
162      - correct Stefan-Boltzmann constant
163      - new parameter for longwave surface emittance
164      - separate some stuff from exf_bulkformulae into new routines  
165        exf_radiation, exf_wind
166      - add new parameters and constants: longwave emissivity for ocean, ice
167        and snow, evaporation parameters over ice
168      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
169        either wind from stress or stress from wind
170    o pkg/thSIce:
171    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
172    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
173       and THSICE_CALC_THICKN
174    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
175    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
176      to make debugging easier.
177    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
178    o pkg/bulk_force:
179      - clean-up comments and parameters ;
180      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
181    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
182      generate new output for test-experiment: aim.5l_cs.thSI
183    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
184      testreport accordingly
185    
186    checkpoint58e_post
187    o SEAICE_CGRID adjoint done
188    o R_STAR adjoint implemented.
189      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
190      * need to sort out init. of h0facc, etc.
191    o Make pkg/profile fully independent of ecco,cost, etc. stuff
192      to be able to use it in pure forward.
193    
194    checkpoint58d_post
195    o upgrade simple test-experiment to tutorial example:
196     step.1: duplicate the experiment and (step.2) will remove the old copy.
197      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
198      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
199      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
200      tutorial_global_oce_biogeo    <- copy of dic_example
201      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
202      tutorial_plume_on_slope       <- copy of plume_on_slope
203      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
204      tutorial_global_oce_optim     <- empty for now (David ?)
205      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
206     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
207    o correct a sign problem in cost_scat.F
208    o obcs and ptracers: fix boundary conditions for advections schemes
209      with larger stencil
210    o thsice adjoint: start
211    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
212      completeness
213    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
214      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
215    o ptracers adjoint:
216      * avoid extensive recomputatations
217      * fix missing re-init. of gptr (missed by TAF)
218    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
219      me to turn off the excessive output to STDOUT that this package produces
220    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
221      and add those terms in Vector-Invariant formulation.
222    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
223      if the control period (xx_hfluxperiod etc) is 0
224    o in profiles pkg, clean routines and fix details
225    o in ecco pkg, reading ssh data:
226      fix problem in case the model does not start at iter0=0
227    o fix mnc-pickup/restart for ptracers
228    o new package prifiles:
229      code to compute profile-based cost by Gael Forget
230      (modifs in ecco, ctrl, autodiff)
231    o Benign bug fix in initialization (spotted by M. Mazloff) of
232      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
233    
234    checkpoint58c_post
235    o adjoint: finish NLFS adjoint and provide reference output in
236      verification/global_ocean.90x40x15/results_ad_nlfs
237    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
238      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
239      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
240      with SEAICE_CGRID defined.
241    o move calendarDumps from "data" to "data.cal" and clean-up the code
242      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
243    o add useEXF & useCAL flags (for now, set in hard-coded way)
244    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
245      (were missing in NH mode, and wrong in quasihydrostatic mode).
246      waiting for Chris updated version of calc_gw to add those CALLs.
247    o fix bug in quasihydrostatic S/R ;
248      add a test for this option: global_ocean.90x40x15.qshyd
249    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
250      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
251    o add on/off flag useOffLine for package OFFLINE
252    o seaice:
253      - modify advection so that it works also on the C-grid
254      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
255        problem in multi-tile runs with C-grid
256      - add flags for clipping ice velocities and/or masking solver forcing
257      - fix drag (ocean on ice) formulation and a bug that caused noise in the
258        C-grid solver
259      - added a few comments to seaice_diffusion.F
260      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
261        are now exclusive)
262      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
263        required re-ordering the code a little:
264       + make DAIRN global variable (defined in SEAICE)
265       + move computation of the viscosities eta and zeta into a new separate
266         routine (because I need to recompute them in seaice_ocean_stress.F)
267    
268    checkpoint58b_post
269    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
270      update output.txt of exp. aim.5l_cs.thSI
271    o various mnc cleanups and improvements:
272      + shrink lookup tables by factor of ~4
273      + better error reporting when running out of lookup space
274      + able to handle longer path/file names (up to 500 chars)
275    o adjoint:
276      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
277      - TBD: "hidden" mom_vecinv recomp. in dynamics
278    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
279     (allow to differentiate between forcing components using new integer flags:
280      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
281     and add new flag to put Dissipation tendency out of Adams-Bashforth.
282    o ecco
283      - enable trend removal from SSH anomaly obs.
284    o adjoint
285      - a fix for PmEpR when #undef EXACT_CONSERV
286      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
287      - try to fix "hidden" recomp. in forward_step for NLFS
288        (NLFS seems broken sometimes after I checked it in)
289    o seaice:
290     - add c-grid version of the dynamic solver:
291       + three new routines that are the c-grid substitute lsr, dynsolver
292         and ostres
293       + put a few fields that were local to dynsolver into global common
294         blocks, so that I can move the computation of stresses etc into
295         seaice_lsr (saves coding but may break the adjoint).
296     - replace more hardwired parameters by runtime parameters
297     - add ice masks that mask the rhs of the implicit solvers where there
298       is no ice (commented out in seaice_dynsolver, because i am not sure
299       if this works properly), eventually this should replace the clipping
300       of ice velocities in seaice_dynsolver to +/-40cm/s.
301    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
302      include it only where its needed
303    o move balancing of fluxes before the call of external_forcing_surf
304    o seaice:
305      - correct units of turning angles (now they are really in degrees)
306      - move computation of GWATX/Y out of main routine into dynsolver
307      - initialize GWATX/Y in seaice_init
308    o Apply mask on Fresh-Water flux (needed for SSH forcing).
309      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
310    o seaice: add runtime flags for turning angles (default to zero)
311    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
312      and trend from exf forcing and ctrl control adjustments
313    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
314      (since checkpoint57x_post)
315    o change the default rotation period to 86164.s = the Earth rotation
316    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
317      and based on a reference stratification. Tested within hs94.cs-32x32x5.
318    o seaice advection: add code for choosing between the default (2nd order
319      central differences) and multiDim advection schemes provided by
320      pkg/generic_advdiff
321    o seaice:
322      - removed all references to SEAICE_GRID.h fields from
323        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
324        (cubed-sphere configuration will change a little)
325      - grid computations in seaice_init are obsolete now.
326      - cleaned up code a little so that is easier to read (hopefully).
327      - added new (better?) discretizations of default advection and diffusion
328        (turn on with SEAICEuseFluxForm)
329      - replace 1 in 3d global fields by kSurface in growth.F
330      
331    checkpoint58a_post
332    o seaice:
333      - bug fix in advect.F
334    o shelfice:
335      - separate shelfice load anomaly from pload (breaks with time
336        dependent forcing), => introduce constant field shelficeLoadAnomaly.
337        Its default is 0., but it may be computed more cleverly from (unknown)
338        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
339        done offline. A good approximation of the pressure load anomaly is
340        necessary to avoid large initial adjustment processes underneath
341        deep-reaching shelfice.
342      - small fix in ISOMIP shelfice_thermodynamics
343      - add more sophisticated thermodynamics of Hellmer (1989), this is
344        now the default
345      - give a few constants more intuitive names
346    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
347      if bulk formulae are used in long integration (especially EmPmR). Turn
348      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
349      if balancePrintMean, the imbalance that is substracted is printed to
350      STDOUT.
351    o fix bug (typo) in obcs_apply_eta.F
352    o add a new package shelfice which enables us to model the circulation
353      underneath shelf-ice with draughts of hundreds of meters.
354     - works
355     - to do: + include improved thermodynamics
356              + check whether kSurfC (from model/inc/SURFACE.h) can be used
357                instead of new field kTopC
358              + can we use topoFile, Ro_surf and existing code in ini_depth.F
359                instead of new field R_shelfIce and new code in ini_depth.F
360                and ini_mask_etc.F?
361              + adjust vertical mixing schemes?
362    o seaice pkg:
363     - add a cpp-flag to include a simple formula for a salinity dependent
364       freezing point of sea water at the surface
365     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
366       meridional stresses are now different (and hopefully correct)
367    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
368       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
369       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
370    o pkg/diagnostics: add options and parameters for regional-statistics
371       diagnostics ; define regions by reading a region-mask from a file
372       (might add other options later)
373    o pkg/bulk_force:
374     - add option and parameters to use AIM surface-flux formulae.
375     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
376       others forcing fields (defined in PARM05, parameter file "data") are loaded
377       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
378     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
379     - use the right EXCH call for uwind,vwind (to work on CS-grid).
380     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
381       and parameters (note: calcWindStress replaces .NOT.readwindstress).
382     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
383    
384    checkpoint58
385    o add "--embed-source" option to genmake2 which, when the supporting
386      tools can be compiled (as determined by genmake2) will turn on the
387      embed_files package which then embeds the entire MITgcm source code
388      (*.[fFhc] + Makefile) used for the build within the executable
389      - requested by CNH but off by default
390      - adds a paltry <9MB to the mitgcmuv executable in most cases
391      - only writes the output when useEMBEDSRC in eedata is true
392    o clean up 3-dim. relaxation codes:
393      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
394      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
395      * Thanks to Tom Haine for testing!
396    
397    checkpoint57z_post
398    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
399      affects output (@ truncation level) of exp. plume_on_slope ; updated.
400    o fix the pickup behavior for obcs in combination with ptracers
401    o fix a bug in ptracers_external_fields_load
402    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
403      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
404    o transfered surface NH pressure to eta field (if exactConserv).
405    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
406         and update lab_sea output.txt file.
407    o completing 3-dim. relaxation code: additional term
408         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
409      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
410      * At compile time, in "EXF_OPTIONS.h" set
411          #define  ALLOW_CLIMTEMP_RELAXATION
412          #define  ALLOW_CLIMSALT_RELAXATION
413      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
414          tauThetaClimRelax3Dim = 15552000.0,
415          tauSaltClimRelax3Dim  = 15552000.0,
416      * 3 cases:
417          1) Use a constant-in-time 3-dim. field
418          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
419          3) Real-time relax. to time-evolving prescribed field
420    o Adding Laplacian-type smoothness constraint on
421      initial and boundary (forcing) controls (ic, bc)
422      * enable at compile-time via
423        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
424      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
425      * Absolute scale somewhat unclear so far
426      * no area weighting was included since no other cost term does so far
427    
428    checkpoint57y_post
429    First step for a NLFS adjoint
430    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
431    o new init. routines for calc_r_star, calc_surf_dr
432    o still need to deal with ini_masks_etc
433    o testreport seemed happy
434    checkpoint57y_pre
435    
436    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
437    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
438    o add new offset feature to offline pkg (plus minor cleanup)
439    o cfc fixes for final year of integration
440    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
441      be in GCHEM_OPTIONS).
442    
443    checkpoint57x_post
444    o fix testreport Pb in multiple test experiment.
445    o cleanup our namelist syntax in verification:
446      - make it more F95 standards compliant (some work still needed)
447      - allows the vast majority of our tests to work with gfortran
448    o Non-Hydrostatic:
449     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
450     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
451    o Allow to apply AB on T,S rather than on AB(gT,gS):
452     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
453     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
454       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
455     - need a "clever" read_pickup to restart from the other AB formulation
456    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
457    o remove some unused variables (reduces number of compiler warnings)
458    o adjoint
459      * Disable useVariableViscosity for adjoint for time being
460        (there are a number of extensive recomputations)
461      * Initialize certain variables needed for adjoint
462    
463    checkpoint57w_post
464    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
465                 fix the singleCpuIO RS version of MDSWRITEFIELD
466       and add a WARNING if using globalFiles=T with multi-processors.
467    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
468      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
469    o tracer advection scheme:
470      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
471       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
472       was not very convenient).
473      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
474       (further tests needed for the implicit DST & Flux-Limiter schemes).
475    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
476      and sRef for convenience, handy, when you want to initialize
477      ptracers in a large domain with a constant non-zero value. Also,
478      untangle ptracers_init.F a little.
479    
480    checkpoint57v_post
481    o change dome exp. to use variable viscosity in side-drag terms.
482    o remove all the files from the cfc_offline test since they are now
483      incorporated into tutorial_cfc_offline which has been producing
484      identical results for a few days of testing
485    o add new parameter: sideDragFactor to enable half-slip-side BC
486      and change side-drag S/R to use viscosity from mom_calc_visc
487      (can switch back by setting sideDragFactor=0.); affects results at
488      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
489       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
490    o vorticity & strain are now computed without masking, to account for
491      no-slip-side BC in variable viscosity calculation ; mask is applied
492      anyway later on, before computing advection/coriolis terms.
493    o modify exp4 to test new obcs support for reading from external files
494      and for passive tracers
495    o fix behavior of ptracers_monitor when monitor output is written to a
496      netcdf-file; still not independent of monitor.F (writes in the same
497      file).
498    o change default value of tRef (put a uniform, meaningful value for ocean
499      & atmos) and initialize sRef (was missing, as Martin mentioned).
500    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
501      to be proportional to enstrophy dissipation length.  Thus,
502       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
503      This is now consistent with Smagorinsky and with the manual.
504    
505    checkpoint57u_post
506    o OBCS and PTRACERS: add open boundary support for passive tracers
507      - either use homogenous (pseudo) v.Neumann conditions or prescribe
508        OB-values from file; this is not different from the way theta and salinity
509        are treated
510      - however, Orlanski-radiation conditions are not supported, and the model
511        will stop if you use pTracers and Orlanski at the same time.
512      - beefed up the rountine obcs_external_fields_load: now only those open
513        boundary values are overwritten with values from files for which there
514        are really files, otherwise the OB-fields remain untouched. This makes
515        it possible to use different OBs at different ends of the domain (as
516        with EXF)
517    o reduce number of exch calls in shap_filt (s2).
518    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
519      truncation level) 4/5 MLAdjust test results (11&12 digits match).
520    
521    checkpoint57t_post
522    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
523    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
524      same truncation, independent of the face number: affects affects several
525      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
526    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
527      note that biharmonic viscosity + no-slip was not tested in any experiment.
528    o fix bug in non-linear free-surf side-drag ; generate new output for
529      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
530    o make mnc honor the writeBinaryPrec flag for most kinds of output
531    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
532    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
533      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
534    o add brackets in multi-terms sum to get same truncation, independent of
535      the face number (manage to get exactly same value of gU,gV at the cs-edge)
536      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
537    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
538      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
539      a maximum grid-scale Reynolds number.  Also, changes all length calculations
540      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
541      Suggested values of viscosity parameters found in mom_calc_visc.
542      Many new viscosity diagnostics available.
543    
544    checkpoint57s_post
545    o Add clearing-house for viscosity calculations, mom_calc_visc and
546      correct numerous bugs in LeithD and Smagorinsky discretizations.  
547      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
548      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
549      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
550      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
551      The Strain-Tension form is now called with useStrainTensonVisc=.true.
552      ViscAhStrain and viscAhTension are now retired.
553    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
554    o In response to JMC's bug report, genmake2 now ignores any soft-links
555      that it finds in the *current* directory when searching for files.
556      Soft-links found in any other source directories will still work as
557      they did before.
558    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
559      a C routine to unlimit the stack size
560    o mnc-ify pkg/aim snapshot vars
561    o mnc-ify pkg/land as requested by Daniel
562    o various changes to mnc including:
563      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
564      - output can now be grouped so that all files within a group
565          change the ITER portion of their names in lock-step together
566      - can now read ("global") PER-FACE (in addition to PER-TILE) files
567          and works with both EXCH1 and EXCH2 (but needs more testing)
568      - writing works for all verification test cases w/ g77 on Linux
569    
570    checkpoint57r_post
571    o make MNC variable initialization happen earlier
572    o add diagnostics for (almost) each term of the momentum Eq.
573    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
574    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
575    o remove MINIMAL_TAVE_OUTPUT option ;
576      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
577    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
578      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
579    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
580    o add time-dependent SST, SSS control
581    o cost terms in ecco/ modularized (new cost_generic.F)
582    o cost_averages routines are modularized (new cost_averagesgeneric.F)
583    o new infrastructure for seaice model vs. obs misfits in seaice/
584      * driver from the_main_loop.F is seaice_cost_driver.F
585      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
586      * gradient check in Exp. 6a of natl_box_adjoint/
587    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
588      (see README file)
589    
590    checkpoint57q_post
591    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
592    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
593      - bug was reported by Jean-Michel and Ian Fenty
594    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
595      update exp. cpl_aim+ocn output.
596    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
597      Needed for high-res. runs with large global files
598      to be able to limit tapelev size
599    o Changed some tests for adjoint:
600      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
601      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
602      * global_ocean.90x40x15/ back to default 3-level checkpointing
603    o Modifications to enable scripted COMMON to MODULE conversion
604      * verification/OpenAD/code/ has necessary scripts and description;
605      * converts, compiles and runs successfully;
606    
607    checkpoint57p_post
608    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
609    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
610      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
611    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
612    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
613      (was already the case for dissipation with mom_vecinv,
614       and also the case for grad.PhiHyd when staggered-timeStep)
615      This will allow to put dissipation out-off the AB time-stepping.
616     Unfortunately, affects truncation error. Update output of exp. that "fails"
617      (cg2d matching number) and leave the others for later: front_relax(10),
618      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
619      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
620    
621    checkpoint57o_post
622    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
623      (2) its ready to be documented during the 20050801 DocFest
624    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
625      for ideal_2D_oce and lab_sea on linux_ia32_g77
626    o set to #undef CTRL_SET_OLD_MAXCVARS_30
627      in global1x1_tot/code_seaice_adj to access indices 32, 33
628      (worth another tag)
629    
630    checkpoint57n_post
631    o adding precip control xx_precip 32
632    o adding swflux control xx_swflux 33
633    o Replacing 10 forcing penalty cost routines by 1 generic.
634    o Implementing partitioning in time-mean and variable adjustment
635      for atmos. state.
636    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
637  o in natl_box_adjoint:  o in natl_box_adjoint:
638    * updated: results_bulk/    * updated exp 1 to 10
639    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
640    o updated global1x1/*_seaice_adj/
641      to incorporate latest changes
642    o enable useSingleCpuIO for mdsio vector routines
643      (applies in particular to tapelev I/O)
644    o removed inefficient K-loop in all active_file*control*.F
645    
646  checkpoint57m_post  checkpoint57m_post
647  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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