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revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.733 by jmc, Tue Oct 17 19:08:57 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 clean-up multi-threaded problems (reported by debugger tcheck on ACES);
8  o moved ptracer ctrl index 17 -> 32    add (in global_with_exf/code) a version of EXF_INTERP_READ without
9      dynamical allocation (seems to work in multi-threaded).
10    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
11      single CPU io) so that TAF does not have to see EESUPPORT.h
12    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
13    
14    checkpoint58p_post
15    o obcs: stop if obcs is used with useCDscheme = .true.
16    o shelfice:
17     - fix a sign error so that no slip at shelfice interface works
18     - remove stop for combination non-hydrostatic code and shelfice. That does
19       not mean, that the results are correct, but at least they are numerically
20       stable
21    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
22    o added adjoint exch routined for all exch*3d* routines
23      and updated flow directives
24    
25    checkpoint58o_post
26    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
27      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
28    o change controling S/R for writing pickup file (new S/R do_write_pickup)
29      and clean-up reading/writing of pickup files.
30    o fix local version of read/write pickup (NH part) in rotating_tank/code
31    o simplify EXCH interface:
32     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
33     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
34    o added the regrid package
35    o shelfice:
36     - add a simple boundary layer scheme to reduce noise
37     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
38    
39    checkpoint58n_post
40    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
41       local variable (not in common block).
42    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
43      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
44      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
45        to work with SingleCpuIO.
46    o add "_d 0" to real constant of pkg/cfc subroutines ;
47       update exp. cfc_exemple & tutorial_cfc_offline output files.
48    o multi-threading and IO:
49      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
50        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
51      - barrier before and after reading.
52      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
53      - avoid using MDS_WRITELOCAL for LAND pkg output.
54      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
55        common-block variables ; Allows multi-threading with master-thread IO.
56    o change default MAX_NO_THREADS from 32 to 4 ;
57      and stop cleanly when MAX_NO_THREADS is too small.
58    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
59    
60    checkpoint58m_post
61    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
62       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
63    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
64       keep global_ocean.90x40x15 (for AD testing) with former secondary test
65       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
66    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
67        add MITgcm_tutorials (= code + all the tutorials)
68    o ecco, option to compute cost for total ssh (mean+anom)
69    o consistent with addition of ptracer and ssh in pkg/profiles
70    o profiles: adding ptracer and ssh
71    o testreport: change multi-test output-file name
72      (from output.txt.{name} to output.{name}.txt)
73    o profiles: now ok for mutli-tiles case
74    o seaice: add 4 parameters for different advection schemes for area,
75      (effective) seaice thickness, enthalphy, and snow height. Their default
76      is the standard parameter SEAICEadvScheme
77    o calc_gw:
78     - add cosFacU in zonal viscous flux (harmonic.visc.).
79     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
80       of tutorial_plume_on_slope.
81    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
82    o calc_gw: true flux-form, account for horizontal grid spacing.
83      update rotating_tank results, but not plume_on_slope (affected at
84      truncation level, 11 digits).
85    
86    checkpoint58l_post
87    o calc_gw:
88     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
89     - remove side-drag for now (need to fix it); update plume_on_slope results.
90     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
91    o commit code to make SST/SSS weights spatially variable
92      (based on either variable in-situ or variable initial T/S weights)
93    o pkg/ecco:
94      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
95        now based on horizontally varying weights wthetaLev, wsaltLev
96      * cost_averagesflags now returns year indices in addition to day, month
97      * sflux balance is performed on annual basis
98        (sflxumm, sfluxmm2, bal_sfluxmm)
99      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
100        including separate counting and multipliers
101    o pkg/rbcs
102      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
103    
104    checkpoint58k_post
105    o testreport:
106     - always build in dir. "build" (if not there, mkdir build instead of building
107       & running in input)
108     - run in dir run (if it exists), in build otherwise.
109     - call prepare_run (if input/prepare_run exists)
110     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
111    o pkg/exf modifications to interpolation and rotation routines for more
112       reasonable treatment of North Pole singularity: for tracers North Pole
113       value is set to northernmost zonal-mean value, for zonal velocity it is
114       set to zero, and for meridional velocity it is set to northernmost value.
115    o pkg/exf/exf_check_range.F
116     - add tile index to diagnostics and move stop statement to the very
117       end of the routine.
118    o pkg/diagnostics: (diagnostics_main_init.F)
119      define title of isomorphic variables according to the current config.
120    o pkg/thsice with pkg/seaice dynamics:
121    - fix domain of computation (interior only, required for exf) and do exchanges
122    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
123    o towards a standard way of dealing with multi-threading in MONITOR
124      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
125    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
126       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
127    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
128    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
129    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
130       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
131    o tracer advection:
132     - clean-up and simplify calc_common_factors.F
133     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
134       advection subroutine (but still not used within DST advection S/R)
135    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
136    
137    checkpoint58j_post
138    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
139      from file (collects calls previously in FORWARD_STEP)
140    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
141    o adjoint store dir. adjusted accordingly
142    o genmake2
143      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
144    
145    checkpoint58i_post
146    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
147      on wind stress (SEAICEstressFactor defaults to 1.)
148    o Total number of Timers is finite (<=40): comment out 2 non-essential one
149      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
150    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
151      on CS-grid: no longer loosing mass.
152    o exf & curvilinear-grid: no longer modify longitude xC & xG.
153    o pkg/ggl90: fix sloppy output and fix a bug
154    o pkg/seaice: added SEAICEuseEVPpickup parameter
155      - Set to false in order to start EVP solver with
156        non-EVP pickup files when using SEAICEuseEVP
157      - fix sign error in diffusion in seaice_calc_rhs
158    
159    checkpoint58h_post
160    * Modifications for bottom topography control
161      o replace hFacC by _hFacC at various places
162      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
163      o add non-self-adjoint cg2d_nsa
164      o update autodiff support routines
165      o re-initialise hfac after ctrl_depth_ini
166      o works for 5x5 box, doesnt work for global_ocean.90x40x15
167    * Adding verification for 5x5 box (4-layer) bottom topography control
168    
169    checkpoint58g_post
170    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
171       used for mean seasonal cycle, mean diurnal cycle); add an example
172       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
173    o pkg/ggl90:
174      - add parameter (minimum surface kinetic energy)
175      - fix bug (avoiding division by zero)
176    o couple pkg/thsice to pkg/seaice:
177      - modify advection in seaice to accomodate new scalar fields to be advected
178      - only muliDimAdection scheme work with seaice/thsice
179      - mapping of thsice-variables to seaice-variables, back and forth
180      - does not break the verification experiments, but does not give the
181        desired results either
182    o pkg/seaice
183      - make (default) second order advection a bit less confusing?
184    
185    checkpoint58f_post
186    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
187      to pkg/seaice):
188      - new routines thsice_map_exf and thsice_get_exf provide the interface
189      - add an additional formal parameter to thsice_solve4temp
190    o pkg/exf:
191      - add new fields wspeed, snowprecip (to be able to couple to thsice)
192      - correct Stefan-Boltzmann constant
193      - new parameter for longwave surface emittance
194      - separate some stuff from exf_bulkformulae into new routines  
195        exf_radiation, exf_wind
196      - add new parameters and constants: longwave emissivity for ocean, ice
197        and snow, evaporation parameters over ice
198      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
199        either wind from stress or stress from wind
200    o pkg/thSIce:
201    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
202    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
203       and THSICE_CALC_THICKN
204    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
205    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
206      to make debugging easier.
207    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
208    o pkg/bulk_force:
209      - clean-up comments and parameters ;
210      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
211    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
212      generate new output for test-experiment: aim.5l_cs.thSI
213    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
214      testreport accordingly
215    
216    checkpoint58e_post
217    o SEAICE_CGRID adjoint done
218    o R_STAR adjoint implemented.
219      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
220      * need to sort out init. of h0facc, etc.
221    o Make pkg/profile fully independent of ecco,cost, etc. stuff
222      to be able to use it in pure forward.
223    
224    checkpoint58d_post
225    o upgrade simple test-experiment to tutorial example:
226     step.1: duplicate the experiment and (step.2) will remove the old copy.
227      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
228      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
229      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
230      tutorial_global_oce_biogeo    <- copy of dic_example
231      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
232      tutorial_plume_on_slope       <- copy of plume_on_slope
233      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
234      tutorial_global_oce_optim     <- empty for now (David ?)
235      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
236     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
237    o correct a sign problem in cost_scat.F
238    o obcs and ptracers: fix boundary conditions for advections schemes
239      with larger stencil
240    o thsice adjoint: start
241    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
242      completeness
243    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
244      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
245    o ptracers adjoint:
246      * avoid extensive recomputatations
247      * fix missing re-init. of gptr (missed by TAF)
248    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
249      me to turn off the excessive output to STDOUT that this package produces
250    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
251      and add those terms in Vector-Invariant formulation.
252    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
253      if the control period (xx_hfluxperiod etc) is 0
254    o in profiles pkg, clean routines and fix details
255    o in ecco pkg, reading ssh data:
256      fix problem in case the model does not start at iter0=0
257    o fix mnc-pickup/restart for ptracers
258    o new package prifiles:
259      code to compute profile-based cost by Gael Forget
260      (modifs in ecco, ctrl, autodiff)
261    o Benign bug fix in initialization (spotted by M. Mazloff) of
262      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
263    
264    checkpoint58c_post
265    o adjoint: finish NLFS adjoint and provide reference output in
266      verification/global_ocean.90x40x15/results_ad_nlfs
267    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
268      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
269      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
270      with SEAICE_CGRID defined.
271    o move calendarDumps from "data" to "data.cal" and clean-up the code
272      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
273    o add useEXF & useCAL flags (for now, set in hard-coded way)
274    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
275      (were missing in NH mode, and wrong in quasihydrostatic mode).
276      waiting for Chris updated version of calc_gw to add those CALLs.
277    o fix bug in quasihydrostatic S/R ;
278      add a test for this option: global_ocean.90x40x15.qshyd
279    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
280      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
281    o add on/off flag useOffLine for package OFFLINE
282    o seaice:
283      - modify advection so that it works also on the C-grid
284      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
285        problem in multi-tile runs with C-grid
286      - add flags for clipping ice velocities and/or masking solver forcing
287      - fix drag (ocean on ice) formulation and a bug that caused noise in the
288        C-grid solver
289      - added a few comments to seaice_diffusion.F
290      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
291        are now exclusive)
292      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
293        required re-ordering the code a little:
294       + make DAIRN global variable (defined in SEAICE)
295       + move computation of the viscosities eta and zeta into a new separate
296         routine (because I need to recompute them in seaice_ocean_stress.F)
297    
298    checkpoint58b_post
299    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
300      update output.txt of exp. aim.5l_cs.thSI
301    o various mnc cleanups and improvements:
302      + shrink lookup tables by factor of ~4
303      + better error reporting when running out of lookup space
304      + able to handle longer path/file names (up to 500 chars)
305    o adjoint:
306      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
307      - TBD: "hidden" mom_vecinv recomp. in dynamics
308    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
309     (allow to differentiate between forcing components using new integer flags:
310      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
311     and add new flag to put Dissipation tendency out of Adams-Bashforth.
312    o ecco
313      - enable trend removal from SSH anomaly obs.
314    o adjoint
315      - a fix for PmEpR when #undef EXACT_CONSERV
316      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
317      - try to fix "hidden" recomp. in forward_step for NLFS
318        (NLFS seems broken sometimes after I checked it in)
319    o seaice:
320     - add c-grid version of the dynamic solver:
321       + three new routines that are the c-grid substitute lsr, dynsolver
322         and ostres
323       + put a few fields that were local to dynsolver into global common
324         blocks, so that I can move the computation of stresses etc into
325         seaice_lsr (saves coding but may break the adjoint).
326     - replace more hardwired parameters by runtime parameters
327     - add ice masks that mask the rhs of the implicit solvers where there
328       is no ice (commented out in seaice_dynsolver, because i am not sure
329       if this works properly), eventually this should replace the clipping
330       of ice velocities in seaice_dynsolver to +/-40cm/s.
331    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
332      include it only where its needed
333    o move balancing of fluxes before the call of external_forcing_surf
334    o seaice:
335      - correct units of turning angles (now they are really in degrees)
336      - move computation of GWATX/Y out of main routine into dynsolver
337      - initialize GWATX/Y in seaice_init
338    o Apply mask on Fresh-Water flux (needed for SSH forcing).
339      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
340    o seaice: add runtime flags for turning angles (default to zero)
341    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
342      and trend from exf forcing and ctrl control adjustments
343    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
344      (since checkpoint57x_post)
345    o change the default rotation period to 86164.s = the Earth rotation
346    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
347      and based on a reference stratification. Tested within hs94.cs-32x32x5.
348    o seaice advection: add code for choosing between the default (2nd order
349      central differences) and multiDim advection schemes provided by
350      pkg/generic_advdiff
351    o seaice:
352      - removed all references to SEAICE_GRID.h fields from
353        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
354        (cubed-sphere configuration will change a little)
355      - grid computations in seaice_init are obsolete now.
356      - cleaned up code a little so that is easier to read (hopefully).
357      - added new (better?) discretizations of default advection and diffusion
358        (turn on with SEAICEuseFluxForm)
359      - replace 1 in 3d global fields by kSurface in growth.F
360      
361    checkpoint58a_post
362    o seaice:
363      - bug fix in advect.F
364    o shelfice:
365      - separate shelfice load anomaly from pload (breaks with time
366        dependent forcing), => introduce constant field shelficeLoadAnomaly.
367        Its default is 0., but it may be computed more cleverly from (unknown)
368        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
369        done offline. A good approximation of the pressure load anomaly is
370        necessary to avoid large initial adjustment processes underneath
371        deep-reaching shelfice.
372      - small fix in ISOMIP shelfice_thermodynamics
373      - add more sophisticated thermodynamics of Hellmer (1989), this is
374        now the default
375      - give a few constants more intuitive names
376    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
377      if bulk formulae are used in long integration (especially EmPmR). Turn
378      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
379      if balancePrintMean, the imbalance that is substracted is printed to
380      STDOUT.
381    o fix bug (typo) in obcs_apply_eta.F
382    o add a new package shelfice which enables us to model the circulation
383      underneath shelf-ice with draughts of hundreds of meters.
384     - works
385     - to do: + include improved thermodynamics
386              + check whether kSurfC (from model/inc/SURFACE.h) can be used
387                instead of new field kTopC
388              + can we use topoFile, Ro_surf and existing code in ini_depth.F
389                instead of new field R_shelfIce and new code in ini_depth.F
390                and ini_mask_etc.F?
391              + adjust vertical mixing schemes?
392    o seaice pkg:
393     - add a cpp-flag to include a simple formula for a salinity dependent
394       freezing point of sea water at the surface
395     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
396       meridional stresses are now different (and hopefully correct)
397    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
398       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
399       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
400    o pkg/diagnostics: add options and parameters for regional-statistics
401       diagnostics ; define regions by reading a region-mask from a file
402       (might add other options later)
403    o pkg/bulk_force:
404     - add option and parameters to use AIM surface-flux formulae.
405     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
406       others forcing fields (defined in PARM05, parameter file "data") are loaded
407       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
408     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
409     - use the right EXCH call for uwind,vwind (to work on CS-grid).
410     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
411       and parameters (note: calcWindStress replaces .NOT.readwindstress).
412     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
413    
414    checkpoint58
415    o add "--embed-source" option to genmake2 which, when the supporting
416      tools can be compiled (as determined by genmake2) will turn on the
417      embed_files package which then embeds the entire MITgcm source code
418      (*.[fFhc] + Makefile) used for the build within the executable
419      - requested by CNH but off by default
420      - adds a paltry <9MB to the mitgcmuv executable in most cases
421      - only writes the output when useEMBEDSRC in eedata is true
422    o clean up 3-dim. relaxation codes:
423      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
424      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
425      * Thanks to Tom Haine for testing!
426    
427    checkpoint57z_post
428    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
429      affects output (@ truncation level) of exp. plume_on_slope ; updated.
430    o fix the pickup behavior for obcs in combination with ptracers
431    o fix a bug in ptracers_external_fields_load
432    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
433      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
434    o transfered surface NH pressure to eta field (if exactConserv).
435    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
436         and update lab_sea output.txt file.
437    o completing 3-dim. relaxation code: additional term
438         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
439      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
440      * At compile time, in "EXF_OPTIONS.h" set
441          #define  ALLOW_CLIMTEMP_RELAXATION
442          #define  ALLOW_CLIMSALT_RELAXATION
443      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
444          tauThetaClimRelax3Dim = 15552000.0,
445          tauSaltClimRelax3Dim  = 15552000.0,
446      * 3 cases:
447          1) Use a constant-in-time 3-dim. field
448          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
449          3) Real-time relax. to time-evolving prescribed field
450    o Adding Laplacian-type smoothness constraint on
451      initial and boundary (forcing) controls (ic, bc)
452      * enable at compile-time via
453        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
454      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
455      * Absolute scale somewhat unclear so far
456      * no area weighting was included since no other cost term does so far
457    
458    checkpoint57y_post
459    First step for a NLFS adjoint
460    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
461    o new init. routines for calc_r_star, calc_surf_dr
462    o still need to deal with ini_masks_etc
463    o testreport seemed happy
464    checkpoint57y_pre
465    
466    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
467    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
468    o add new offset feature to offline pkg (plus minor cleanup)
469    o cfc fixes for final year of integration
470    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
471      be in GCHEM_OPTIONS).
472    
473    checkpoint57x_post
474    o fix testreport Pb in multiple test experiment.
475    o cleanup our namelist syntax in verification:
476      - make it more F95 standards compliant (some work still needed)
477      - allows the vast majority of our tests to work with gfortran
478    o Non-Hydrostatic:
479     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
480     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
481    o Allow to apply AB on T,S rather than on AB(gT,gS):
482     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
483     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
484       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
485     - need a "clever" read_pickup to restart from the other AB formulation
486    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
487    o remove some unused variables (reduces number of compiler warnings)
488    o adjoint
489      * Disable useVariableViscosity for adjoint for time being
490        (there are a number of extensive recomputations)
491      * Initialize certain variables needed for adjoint
492    
493    checkpoint57w_post
494    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
495                 fix the singleCpuIO RS version of MDSWRITEFIELD
496       and add a WARNING if using globalFiles=T with multi-processors.
497    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
498      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
499    o tracer advection scheme:
500      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
501       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
502       was not very convenient).
503      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
504       (further tests needed for the implicit DST & Flux-Limiter schemes).
505    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
506      and sRef for convenience, handy, when you want to initialize
507      ptracers in a large domain with a constant non-zero value. Also,
508      untangle ptracers_init.F a little.
509    
510    checkpoint57v_post
511    o change dome exp. to use variable viscosity in side-drag terms.
512    o remove all the files from the cfc_offline test since they are now
513      incorporated into tutorial_cfc_offline which has been producing
514      identical results for a few days of testing
515    o add new parameter: sideDragFactor to enable half-slip-side BC
516      and change side-drag S/R to use viscosity from mom_calc_visc
517      (can switch back by setting sideDragFactor=0.); affects results at
518      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
519       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
520    o vorticity & strain are now computed without masking, to account for
521      no-slip-side BC in variable viscosity calculation ; mask is applied
522      anyway later on, before computing advection/coriolis terms.
523    o modify exp4 to test new obcs support for reading from external files
524      and for passive tracers
525    o fix behavior of ptracers_monitor when monitor output is written to a
526      netcdf-file; still not independent of monitor.F (writes in the same
527      file).
528    o change default value of tRef (put a uniform, meaningful value for ocean
529      & atmos) and initialize sRef (was missing, as Martin mentioned).
530    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
531      to be proportional to enstrophy dissipation length.  Thus,
532       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
533      This is now consistent with Smagorinsky and with the manual.
534    
535    checkpoint57u_post
536    o OBCS and PTRACERS: add open boundary support for passive tracers
537      - either use homogenous (pseudo) v.Neumann conditions or prescribe
538        OB-values from file; this is not different from the way theta and salinity
539        are treated
540      - however, Orlanski-radiation conditions are not supported, and the model
541        will stop if you use pTracers and Orlanski at the same time.
542      - beefed up the rountine obcs_external_fields_load: now only those open
543        boundary values are overwritten with values from files for which there
544        are really files, otherwise the OB-fields remain untouched. This makes
545        it possible to use different OBs at different ends of the domain (as
546        with EXF)
547    o reduce number of exch calls in shap_filt (s2).
548    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
549      truncation level) 4/5 MLAdjust test results (11&12 digits match).
550    
551    checkpoint57t_post
552    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
553    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
554      same truncation, independent of the face number: affects affects several
555      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
556    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
557      note that biharmonic viscosity + no-slip was not tested in any experiment.
558    o fix bug in non-linear free-surf side-drag ; generate new output for
559      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
560    o make mnc honor the writeBinaryPrec flag for most kinds of output
561    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
562    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
563      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
564    o add brackets in multi-terms sum to get same truncation, independent of
565      the face number (manage to get exactly same value of gU,gV at the cs-edge)
566      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
567    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
568      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
569      a maximum grid-scale Reynolds number.  Also, changes all length calculations
570      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
571      Suggested values of viscosity parameters found in mom_calc_visc.
572      Many new viscosity diagnostics available.
573    
574    checkpoint57s_post
575    o Add clearing-house for viscosity calculations, mom_calc_visc and
576      correct numerous bugs in LeithD and Smagorinsky discretizations.  
577      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
578      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
579      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
580      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
581      The Strain-Tension form is now called with useStrainTensonVisc=.true.
582      ViscAhStrain and viscAhTension are now retired.
583    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
584    o In response to JMC's bug report, genmake2 now ignores any soft-links
585      that it finds in the *current* directory when searching for files.
586      Soft-links found in any other source directories will still work as
587      they did before.
588    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
589      a C routine to unlimit the stack size
590    o mnc-ify pkg/aim snapshot vars
591    o mnc-ify pkg/land as requested by Daniel
592    o various changes to mnc including:
593      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
594      - output can now be grouped so that all files within a group
595          change the ITER portion of their names in lock-step together
596      - can now read ("global") PER-FACE (in addition to PER-TILE) files
597          and works with both EXCH1 and EXCH2 (but needs more testing)
598      - writing works for all verification test cases w/ g77 on Linux
599    
600    checkpoint57r_post
601    o make MNC variable initialization happen earlier
602    o add diagnostics for (almost) each term of the momentum Eq.
603    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
604    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
605    o remove MINIMAL_TAVE_OUTPUT option ;
606      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
607    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
608      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
609    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
610    o add time-dependent SST, SSS control
611    o cost terms in ecco/ modularized (new cost_generic.F)
612    o cost_averages routines are modularized (new cost_averagesgeneric.F)
613    o new infrastructure for seaice model vs. obs misfits in seaice/
614      * driver from the_main_loop.F is seaice_cost_driver.F
615      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
616      * gradient check in Exp. 6a of natl_box_adjoint/
617    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
618      (see README file)
619    
620    checkpoint57q_post
621    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
622    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
623      - bug was reported by Jean-Michel and Ian Fenty
624    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
625      update exp. cpl_aim+ocn output.
626    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
627      Needed for high-res. runs with large global files
628      to be able to limit tapelev size
629    o Changed some tests for adjoint:
630      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
631      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
632      * global_ocean.90x40x15/ back to default 3-level checkpointing
633    o Modifications to enable scripted COMMON to MODULE conversion
634      * verification/OpenAD/code/ has necessary scripts and description;
635      * converts, compiles and runs successfully;
636    
637    checkpoint57p_post
638    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
639    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
640      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
641    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
642    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
643      (was already the case for dissipation with mom_vecinv,
644       and also the case for grad.PhiHyd when staggered-timeStep)
645      This will allow to put dissipation out-off the AB time-stepping.
646     Unfortunately, affects truncation error. Update output of exp. that "fails"
647      (cg2d matching number) and leave the others for later: front_relax(10),
648      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
649      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
650    
651    checkpoint57o_post
652    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
653      (2) its ready to be documented during the 20050801 DocFest
654    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
655      for ideal_2D_oce and lab_sea on linux_ia32_g77
656    o set to #undef CTRL_SET_OLD_MAXCVARS_30
657      in global1x1_tot/code_seaice_adj to access indices 32, 33
658      (worth another tag)
659    
660    checkpoint57n_post
661    o adding precip control xx_precip 32
662    o adding swflux control xx_swflux 33
663    o Replacing 10 forcing penalty cost routines by 1 generic.
664    o Implementing partitioning in time-mean and variable adjustment
665      for atmos. state.
666    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
667  o in natl_box_adjoint:  o in natl_box_adjoint:
668    * updated: results_bulk/    * updated exp 1 to 10
669    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
670    o updated global1x1/*_seaice_adj/
671      to incorporate latest changes
672    o enable useSingleCpuIO for mdsio vector routines
673      (applies in particular to tapelev I/O)
674    o removed inefficient K-loop in all active_file*control*.F
675    
676  checkpoint57m_post  checkpoint57m_post
677  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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