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revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.744 by dimitri, Mon Nov 6 20:37:25 2006 UTC
# Line 3  $Name$ Line 3  $Name$
3    
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    o modifications to pkg/seaice/growth.F, which change results of
7      lab_sea experiment: fixes pertain to melting snow over open water, to
8      masking EVAP under sea ice, and to using the correct AREA variable for
9      computations of EVAP, PRECIP, HSNOW, and GHEFF
10    o add ability to read bathy, salt, and theta using MNC (off by def)
11    o add flooding algorithm and advection of HSNOW for pkg/seaice;
12      both are turned off by default and do no change any results
13    o seaice advection with pkg/thsice: a step toward the use of non-linear
14      advection scheme, but #ifdef or commented out for now (requires more EXCH).
15    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
16      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
17      in natl_box (affects results @ truncation level: update output.txt)
18    o multi-threading and IO:
19      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
20      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
21        (needed to work with SingleCpuIO): tested in all verif. exp.
22    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
23      affects the results (but none of the verification test uses this scheme).
24    o Adding some pkg/diagnostics capability to pkg/seaice
25      (will certainly be subject to changes)
26    o ctrl: adding new control variables:
27      lwflux, lwdown, evap, snowprecip, apressure, runoff
28    
29  o adding precip control xx_precip  checkpoint58q_post
30  o moved ptracer ctrl index 17 -> 32  o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
31      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
32      high_res_cube configuration by 4% on Columbia.
33    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
34      add (in global_with_exf/code) a version of EXF_INTERP_READ without
35      dynamical allocation (seems to work in multi-threaded).
36    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
37      single CPU io) so that TAF does not have to see EESUPPORT.h
38    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
39    
40    checkpoint58p_post
41    o obcs: stop if obcs is used with useCDscheme = .true.
42    o shelfice:
43     - fix a sign error so that no slip at shelfice interface works
44     - remove stop for combination non-hydrostatic code and shelfice. That does
45       not mean, that the results are correct, but at least they are numerically
46       stable
47    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
48    o added adjoint exch routined for all exch*3d* routines
49      and updated flow directives
50    
51    checkpoint58o_post
52    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
53      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
54    o change controling S/R for writing pickup file (new S/R do_write_pickup)
55      and clean-up reading/writing of pickup files.
56    o fix local version of read/write pickup (NH part) in rotating_tank/code
57    o simplify EXCH interface:
58     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
59     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
60    o added the regrid package
61    o shelfice:
62     - add a simple boundary layer scheme to reduce noise
63     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
64    
65    checkpoint58n_post
66    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
67       local variable (not in common block).
68    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
69      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
70      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
71        to work with SingleCpuIO.
72    o add "_d 0" to real constant of pkg/cfc subroutines ;
73       update exp. cfc_exemple & tutorial_cfc_offline output files.
74    o multi-threading and IO:
75      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
76        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
77      - barrier before and after reading.
78      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
79      - avoid using MDS_WRITELOCAL for LAND pkg output.
80      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
81        common-block variables ; Allows multi-threading with master-thread IO.
82    o change default MAX_NO_THREADS from 32 to 4 ;
83      and stop cleanly when MAX_NO_THREADS is too small.
84    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
85    
86    checkpoint58m_post
87    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
88       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
89    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
90       keep global_ocean.90x40x15 (for AD testing) with former secondary test
91       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
92    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
93        add MITgcm_tutorials (= code + all the tutorials)
94    o ecco, option to compute cost for total ssh (mean+anom)
95    o consistent with addition of ptracer and ssh in pkg/profiles
96    o profiles: adding ptracer and ssh
97    o testreport: change multi-test output-file name
98      (from output.txt.{name} to output.{name}.txt)
99    o profiles: now ok for mutli-tiles case
100    o seaice: add 4 parameters for different advection schemes for area,
101      (effective) seaice thickness, enthalphy, and snow height. Their default
102      is the standard parameter SEAICEadvScheme
103    o calc_gw:
104     - add cosFacU in zonal viscous flux (harmonic.visc.).
105     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
106       of tutorial_plume_on_slope.
107    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
108    o calc_gw: true flux-form, account for horizontal grid spacing.
109      update rotating_tank results, but not plume_on_slope (affected at
110      truncation level, 11 digits).
111    
112    checkpoint58l_post
113    o calc_gw:
114     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
115     - remove side-drag for now (need to fix it); update plume_on_slope results.
116     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
117    o commit code to make SST/SSS weights spatially variable
118      (based on either variable in-situ or variable initial T/S weights)
119    o pkg/ecco:
120      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
121        now based on horizontally varying weights wthetaLev, wsaltLev
122      * cost_averagesflags now returns year indices in addition to day, month
123      * sflux balance is performed on annual basis
124        (sflxumm, sfluxmm2, bal_sfluxmm)
125      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
126        including separate counting and multipliers
127    o pkg/rbcs
128      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
129    
130    checkpoint58k_post
131    o testreport:
132     - always build in dir. "build" (if not there, mkdir build instead of building
133       & running in input)
134     - run in dir run (if it exists), in build otherwise.
135     - call prepare_run (if input/prepare_run exists)
136     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
137    o pkg/exf modifications to interpolation and rotation routines for more
138       reasonable treatment of North Pole singularity: for tracers North Pole
139       value is set to northernmost zonal-mean value, for zonal velocity it is
140       set to zero, and for meridional velocity it is set to northernmost value.
141    o pkg/exf/exf_check_range.F
142     - add tile index to diagnostics and move stop statement to the very
143       end of the routine.
144    o pkg/diagnostics: (diagnostics_main_init.F)
145      define title of isomorphic variables according to the current config.
146    o pkg/thsice with pkg/seaice dynamics:
147    - fix domain of computation (interior only, required for exf) and do exchanges
148    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
149    o towards a standard way of dealing with multi-threading in MONITOR
150      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
151    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
152       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
153    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
154    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
155    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
156       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
157    o tracer advection:
158     - clean-up and simplify calc_common_factors.F
159     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
160       advection subroutine (but still not used within DST advection S/R)
161    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
162    
163    checkpoint58j_post
164    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
165      from file (collects calls previously in FORWARD_STEP)
166    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
167    o adjoint store dir. adjusted accordingly
168    o genmake2
169      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
170    
171    checkpoint58i_post
172    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
173      on wind stress (SEAICEstressFactor defaults to 1.)
174    o Total number of Timers is finite (<=40): comment out 2 non-essential one
175      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
176    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
177      on CS-grid: no longer loosing mass.
178    o exf & curvilinear-grid: no longer modify longitude xC & xG.
179    o pkg/ggl90: fix sloppy output and fix a bug
180    o pkg/seaice: added SEAICEuseEVPpickup parameter
181      - Set to false in order to start EVP solver with
182        non-EVP pickup files when using SEAICEuseEVP
183      - fix sign error in diffusion in seaice_calc_rhs
184    
185    checkpoint58h_post
186    * Modifications for bottom topography control
187      o replace hFacC by _hFacC at various places
188      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
189      o add non-self-adjoint cg2d_nsa
190      o update autodiff support routines
191      o re-initialise hfac after ctrl_depth_ini
192      o works for 5x5 box, doesnt work for global_ocean.90x40x15
193    * Adding verification for 5x5 box (4-layer) bottom topography control
194    
195    checkpoint58g_post
196    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
197       used for mean seasonal cycle, mean diurnal cycle); add an example
198       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
199    o pkg/ggl90:
200      - add parameter (minimum surface kinetic energy)
201      - fix bug (avoiding division by zero)
202    o couple pkg/thsice to pkg/seaice:
203      - modify advection in seaice to accomodate new scalar fields to be advected
204      - only muliDimAdection scheme work with seaice/thsice
205      - mapping of thsice-variables to seaice-variables, back and forth
206      - does not break the verification experiments, but does not give the
207        desired results either
208    o pkg/seaice
209      - make (default) second order advection a bit less confusing?
210    
211    checkpoint58f_post
212    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
213      to pkg/seaice):
214      - new routines thsice_map_exf and thsice_get_exf provide the interface
215      - add an additional formal parameter to thsice_solve4temp
216    o pkg/exf:
217      - add new fields wspeed, snowprecip (to be able to couple to thsice)
218      - correct Stefan-Boltzmann constant
219      - new parameter for longwave surface emittance
220      - separate some stuff from exf_bulkformulae into new routines  
221        exf_radiation, exf_wind
222      - add new parameters and constants: longwave emissivity for ocean, ice
223        and snow, evaporation parameters over ice
224      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
225        either wind from stress or stress from wind
226    o pkg/thSIce:
227    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
228    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
229       and THSICE_CALC_THICKN
230    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
231    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
232      to make debugging easier.
233    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
234    o pkg/bulk_force:
235      - clean-up comments and parameters ;
236      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
237    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
238      generate new output for test-experiment: aim.5l_cs.thSI
239    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
240      testreport accordingly
241    
242    checkpoint58e_post
243    o SEAICE_CGRID adjoint done
244    o R_STAR adjoint implemented.
245      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
246      * need to sort out init. of h0facc, etc.
247    o Make pkg/profile fully independent of ecco,cost, etc. stuff
248      to be able to use it in pure forward.
249    
250    checkpoint58d_post
251    o upgrade simple test-experiment to tutorial example:
252     step.1: duplicate the experiment and (step.2) will remove the old copy.
253      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
254      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
255      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
256      tutorial_global_oce_biogeo    <- copy of dic_example
257      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
258      tutorial_plume_on_slope       <- copy of plume_on_slope
259      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
260      tutorial_global_oce_optim     <- empty for now (David ?)
261      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
262     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
263    o correct a sign problem in cost_scat.F
264    o obcs and ptracers: fix boundary conditions for advections schemes
265      with larger stencil
266    o thsice adjoint: start
267    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
268      completeness
269    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
270      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
271    o ptracers adjoint:
272      * avoid extensive recomputatations
273      * fix missing re-init. of gptr (missed by TAF)
274    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
275      me to turn off the excessive output to STDOUT that this package produces
276    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
277      and add those terms in Vector-Invariant formulation.
278    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
279      if the control period (xx_hfluxperiod etc) is 0
280    o in profiles pkg, clean routines and fix details
281    o in ecco pkg, reading ssh data:
282      fix problem in case the model does not start at iter0=0
283    o fix mnc-pickup/restart for ptracers
284    o new package prifiles:
285      code to compute profile-based cost by Gael Forget
286      (modifs in ecco, ctrl, autodiff)
287    o Benign bug fix in initialization (spotted by M. Mazloff) of
288      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
289    
290    checkpoint58c_post
291    o adjoint: finish NLFS adjoint and provide reference output in
292      verification/global_ocean.90x40x15/results_ad_nlfs
293    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
294      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
295      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
296      with SEAICE_CGRID defined.
297    o move calendarDumps from "data" to "data.cal" and clean-up the code
298      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
299    o add useEXF & useCAL flags (for now, set in hard-coded way)
300    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
301      (were missing in NH mode, and wrong in quasihydrostatic mode).
302      waiting for Chris updated version of calc_gw to add those CALLs.
303    o fix bug in quasihydrostatic S/R ;
304      add a test for this option: global_ocean.90x40x15.qshyd
305    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
306      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
307    o add on/off flag useOffLine for package OFFLINE
308    o seaice:
309      - modify advection so that it works also on the C-grid
310      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
311        problem in multi-tile runs with C-grid
312      - add flags for clipping ice velocities and/or masking solver forcing
313      - fix drag (ocean on ice) formulation and a bug that caused noise in the
314        C-grid solver
315      - added a few comments to seaice_diffusion.F
316      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
317        are now exclusive)
318      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
319        required re-ordering the code a little:
320       + make DAIRN global variable (defined in SEAICE)
321       + move computation of the viscosities eta and zeta into a new separate
322         routine (because I need to recompute them in seaice_ocean_stress.F)
323    
324    checkpoint58b_post
325    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
326      update output.txt of exp. aim.5l_cs.thSI
327    o various mnc cleanups and improvements:
328      + shrink lookup tables by factor of ~4
329      + better error reporting when running out of lookup space
330      + able to handle longer path/file names (up to 500 chars)
331    o adjoint:
332      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
333      - TBD: "hidden" mom_vecinv recomp. in dynamics
334    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
335     (allow to differentiate between forcing components using new integer flags:
336      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
337     and add new flag to put Dissipation tendency out of Adams-Bashforth.
338    o ecco
339      - enable trend removal from SSH anomaly obs.
340    o adjoint
341      - a fix for PmEpR when #undef EXACT_CONSERV
342      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
343      - try to fix "hidden" recomp. in forward_step for NLFS
344        (NLFS seems broken sometimes after I checked it in)
345    o seaice:
346     - add c-grid version of the dynamic solver:
347       + three new routines that are the c-grid substitute lsr, dynsolver
348         and ostres
349       + put a few fields that were local to dynsolver into global common
350         blocks, so that I can move the computation of stresses etc into
351         seaice_lsr (saves coding but may break the adjoint).
352     - replace more hardwired parameters by runtime parameters
353     - add ice masks that mask the rhs of the implicit solvers where there
354       is no ice (commented out in seaice_dynsolver, because i am not sure
355       if this works properly), eventually this should replace the clipping
356       of ice velocities in seaice_dynsolver to +/-40cm/s.
357    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
358      include it only where its needed
359    o move balancing of fluxes before the call of external_forcing_surf
360    o seaice:
361      - correct units of turning angles (now they are really in degrees)
362      - move computation of GWATX/Y out of main routine into dynsolver
363      - initialize GWATX/Y in seaice_init
364    o Apply mask on Fresh-Water flux (needed for SSH forcing).
365      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
366    o seaice: add runtime flags for turning angles (default to zero)
367    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
368      and trend from exf forcing and ctrl control adjustments
369    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
370      (since checkpoint57x_post)
371    o change the default rotation period to 86164.s = the Earth rotation
372    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
373      and based on a reference stratification. Tested within hs94.cs-32x32x5.
374    o seaice advection: add code for choosing between the default (2nd order
375      central differences) and multiDim advection schemes provided by
376      pkg/generic_advdiff
377    o seaice:
378      - removed all references to SEAICE_GRID.h fields from
379        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
380        (cubed-sphere configuration will change a little)
381      - grid computations in seaice_init are obsolete now.
382      - cleaned up code a little so that is easier to read (hopefully).
383      - added new (better?) discretizations of default advection and diffusion
384        (turn on with SEAICEuseFluxForm)
385      - replace 1 in 3d global fields by kSurface in growth.F
386      
387    checkpoint58a_post
388    o seaice:
389      - bug fix in advect.F
390    o shelfice:
391      - separate shelfice load anomaly from pload (breaks with time
392        dependent forcing), => introduce constant field shelficeLoadAnomaly.
393        Its default is 0., but it may be computed more cleverly from (unknown)
394        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
395        done offline. A good approximation of the pressure load anomaly is
396        necessary to avoid large initial adjustment processes underneath
397        deep-reaching shelfice.
398      - small fix in ISOMIP shelfice_thermodynamics
399      - add more sophisticated thermodynamics of Hellmer (1989), this is
400        now the default
401      - give a few constants more intuitive names
402    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
403      if bulk formulae are used in long integration (especially EmPmR). Turn
404      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
405      if balancePrintMean, the imbalance that is substracted is printed to
406      STDOUT.
407    o fix bug (typo) in obcs_apply_eta.F
408    o add a new package shelfice which enables us to model the circulation
409      underneath shelf-ice with draughts of hundreds of meters.
410     - works
411     - to do: + include improved thermodynamics
412              + check whether kSurfC (from model/inc/SURFACE.h) can be used
413                instead of new field kTopC
414              + can we use topoFile, Ro_surf and existing code in ini_depth.F
415                instead of new field R_shelfIce and new code in ini_depth.F
416                and ini_mask_etc.F?
417              + adjust vertical mixing schemes?
418    o seaice pkg:
419     - add a cpp-flag to include a simple formula for a salinity dependent
420       freezing point of sea water at the surface
421     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
422       meridional stresses are now different (and hopefully correct)
423    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
424       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
425       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
426    o pkg/diagnostics: add options and parameters for regional-statistics
427       diagnostics ; define regions by reading a region-mask from a file
428       (might add other options later)
429    o pkg/bulk_force:
430     - add option and parameters to use AIM surface-flux formulae.
431     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
432       others forcing fields (defined in PARM05, parameter file "data") are loaded
433       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
434     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
435     - use the right EXCH call for uwind,vwind (to work on CS-grid).
436     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
437       and parameters (note: calcWindStress replaces .NOT.readwindstress).
438     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
439    
440    checkpoint58
441    o add "--embed-source" option to genmake2 which, when the supporting
442      tools can be compiled (as determined by genmake2) will turn on the
443      embed_files package which then embeds the entire MITgcm source code
444      (*.[fFhc] + Makefile) used for the build within the executable
445      - requested by CNH but off by default
446      - adds a paltry <9MB to the mitgcmuv executable in most cases
447      - only writes the output when useEMBEDSRC in eedata is true
448    o clean up 3-dim. relaxation codes:
449      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
450      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
451      * Thanks to Tom Haine for testing!
452    
453    checkpoint57z_post
454    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
455      affects output (@ truncation level) of exp. plume_on_slope ; updated.
456    o fix the pickup behavior for obcs in combination with ptracers
457    o fix a bug in ptracers_external_fields_load
458    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
459      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
460    o transfered surface NH pressure to eta field (if exactConserv).
461    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
462         and update lab_sea output.txt file.
463    o completing 3-dim. relaxation code: additional term
464         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
465      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
466      * At compile time, in "EXF_OPTIONS.h" set
467          #define  ALLOW_CLIMTEMP_RELAXATION
468          #define  ALLOW_CLIMSALT_RELAXATION
469      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
470          tauThetaClimRelax3Dim = 15552000.0,
471          tauSaltClimRelax3Dim  = 15552000.0,
472      * 3 cases:
473          1) Use a constant-in-time 3-dim. field
474          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
475          3) Real-time relax. to time-evolving prescribed field
476    o Adding Laplacian-type smoothness constraint on
477      initial and boundary (forcing) controls (ic, bc)
478      * enable at compile-time via
479        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
480      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
481      * Absolute scale somewhat unclear so far
482      * no area weighting was included since no other cost term does so far
483    
484    checkpoint57y_post
485    First step for a NLFS adjoint
486    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
487    o new init. routines for calc_r_star, calc_surf_dr
488    o still need to deal with ini_masks_etc
489    o testreport seemed happy
490    checkpoint57y_pre
491    
492    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
493    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
494    o add new offset feature to offline pkg (plus minor cleanup)
495    o cfc fixes for final year of integration
496    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
497      be in GCHEM_OPTIONS).
498    
499    checkpoint57x_post
500    o fix testreport Pb in multiple test experiment.
501    o cleanup our namelist syntax in verification:
502      - make it more F95 standards compliant (some work still needed)
503      - allows the vast majority of our tests to work with gfortran
504    o Non-Hydrostatic:
505     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
506     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
507    o Allow to apply AB on T,S rather than on AB(gT,gS):
508     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
509     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
510       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
511     - need a "clever" read_pickup to restart from the other AB formulation
512    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
513    o remove some unused variables (reduces number of compiler warnings)
514    o adjoint
515      * Disable useVariableViscosity for adjoint for time being
516        (there are a number of extensive recomputations)
517      * Initialize certain variables needed for adjoint
518    
519    checkpoint57w_post
520    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
521                 fix the singleCpuIO RS version of MDSWRITEFIELD
522       and add a WARNING if using globalFiles=T with multi-processors.
523    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
524      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
525    o tracer advection scheme:
526      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
527       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
528       was not very convenient).
529      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
530       (further tests needed for the implicit DST & Flux-Limiter schemes).
531    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
532      and sRef for convenience, handy, when you want to initialize
533      ptracers in a large domain with a constant non-zero value. Also,
534      untangle ptracers_init.F a little.
535    
536    checkpoint57v_post
537    o change dome exp. to use variable viscosity in side-drag terms.
538    o remove all the files from the cfc_offline test since they are now
539      incorporated into tutorial_cfc_offline which has been producing
540      identical results for a few days of testing
541    o add new parameter: sideDragFactor to enable half-slip-side BC
542      and change side-drag S/R to use viscosity from mom_calc_visc
543      (can switch back by setting sideDragFactor=0.); affects results at
544      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
545       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
546    o vorticity & strain are now computed without masking, to account for
547      no-slip-side BC in variable viscosity calculation ; mask is applied
548      anyway later on, before computing advection/coriolis terms.
549    o modify exp4 to test new obcs support for reading from external files
550      and for passive tracers
551    o fix behavior of ptracers_monitor when monitor output is written to a
552      netcdf-file; still not independent of monitor.F (writes in the same
553      file).
554    o change default value of tRef (put a uniform, meaningful value for ocean
555      & atmos) and initialize sRef (was missing, as Martin mentioned).
556    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
557      to be proportional to enstrophy dissipation length.  Thus,
558       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
559      This is now consistent with Smagorinsky and with the manual.
560    
561    checkpoint57u_post
562    o OBCS and PTRACERS: add open boundary support for passive tracers
563      - either use homogenous (pseudo) v.Neumann conditions or prescribe
564        OB-values from file; this is not different from the way theta and salinity
565        are treated
566      - however, Orlanski-radiation conditions are not supported, and the model
567        will stop if you use pTracers and Orlanski at the same time.
568      - beefed up the rountine obcs_external_fields_load: now only those open
569        boundary values are overwritten with values from files for which there
570        are really files, otherwise the OB-fields remain untouched. This makes
571        it possible to use different OBs at different ends of the domain (as
572        with EXF)
573    o reduce number of exch calls in shap_filt (s2).
574    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
575      truncation level) 4/5 MLAdjust test results (11&12 digits match).
576    
577    checkpoint57t_post
578    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
579    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
580      same truncation, independent of the face number: affects affects several
581      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
582    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
583      note that biharmonic viscosity + no-slip was not tested in any experiment.
584    o fix bug in non-linear free-surf side-drag ; generate new output for
585      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
586    o make mnc honor the writeBinaryPrec flag for most kinds of output
587    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
588    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
589      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
590    o add brackets in multi-terms sum to get same truncation, independent of
591      the face number (manage to get exactly same value of gU,gV at the cs-edge)
592      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
593    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
594      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
595      a maximum grid-scale Reynolds number.  Also, changes all length calculations
596      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
597      Suggested values of viscosity parameters found in mom_calc_visc.
598      Many new viscosity diagnostics available.
599    
600    checkpoint57s_post
601    o Add clearing-house for viscosity calculations, mom_calc_visc and
602      correct numerous bugs in LeithD and Smagorinsky discretizations.  
603      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
604      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
605      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
606      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
607      The Strain-Tension form is now called with useStrainTensonVisc=.true.
608      ViscAhStrain and viscAhTension are now retired.
609    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
610    o In response to JMC's bug report, genmake2 now ignores any soft-links
611      that it finds in the *current* directory when searching for files.
612      Soft-links found in any other source directories will still work as
613      they did before.
614    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
615      a C routine to unlimit the stack size
616    o mnc-ify pkg/aim snapshot vars
617    o mnc-ify pkg/land as requested by Daniel
618    o various changes to mnc including:
619      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
620      - output can now be grouped so that all files within a group
621          change the ITER portion of their names in lock-step together
622      - can now read ("global") PER-FACE (in addition to PER-TILE) files
623          and works with both EXCH1 and EXCH2 (but needs more testing)
624      - writing works for all verification test cases w/ g77 on Linux
625    
626    checkpoint57r_post
627    o make MNC variable initialization happen earlier
628    o add diagnostics for (almost) each term of the momentum Eq.
629    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
630    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
631    o remove MINIMAL_TAVE_OUTPUT option ;
632      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
633    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
634      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
635    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
636    o add time-dependent SST, SSS control
637    o cost terms in ecco/ modularized (new cost_generic.F)
638    o cost_averages routines are modularized (new cost_averagesgeneric.F)
639    o new infrastructure for seaice model vs. obs misfits in seaice/
640      * driver from the_main_loop.F is seaice_cost_driver.F
641      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
642      * gradient check in Exp. 6a of natl_box_adjoint/
643    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
644      (see README file)
645    
646    checkpoint57q_post
647    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
648    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
649      - bug was reported by Jean-Michel and Ian Fenty
650    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
651      update exp. cpl_aim+ocn output.
652    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
653      Needed for high-res. runs with large global files
654      to be able to limit tapelev size
655    o Changed some tests for adjoint:
656      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
657      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
658      * global_ocean.90x40x15/ back to default 3-level checkpointing
659    o Modifications to enable scripted COMMON to MODULE conversion
660      * verification/OpenAD/code/ has necessary scripts and description;
661      * converts, compiles and runs successfully;
662    
663    checkpoint57p_post
664    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
665    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
666      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
667    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
668    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
669      (was already the case for dissipation with mom_vecinv,
670       and also the case for grad.PhiHyd when staggered-timeStep)
671      This will allow to put dissipation out-off the AB time-stepping.
672     Unfortunately, affects truncation error. Update output of exp. that "fails"
673      (cg2d matching number) and leave the others for later: front_relax(10),
674      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
675      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
676    
677    checkpoint57o_post
678    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
679      (2) its ready to be documented during the 20050801 DocFest
680    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
681      for ideal_2D_oce and lab_sea on linux_ia32_g77
682    o set to #undef CTRL_SET_OLD_MAXCVARS_30
683      in global1x1_tot/code_seaice_adj to access indices 32, 33
684      (worth another tag)
685    
686    checkpoint57n_post
687    o adding precip control xx_precip 32
688    o adding swflux control xx_swflux 33
689    o Replacing 10 forcing penalty cost routines by 1 generic.
690    o Implementing partitioning in time-mean and variable adjustment
691      for atmos. state.
692    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
693  o in natl_box_adjoint:  o in natl_box_adjoint:
694    * updated: results_bulk/    * updated exp 1 to 10
695    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
696    o updated global1x1/*_seaice_adj/
697      to incorporate latest changes
698    o enable useSingleCpuIO for mdsio vector routines
699      (applies in particular to tapelev I/O)
700    o removed inefficient K-loop in all active_file*control*.F
701    
702  checkpoint57m_post  checkpoint57m_post
703  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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