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revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.725 by heimbach, Fri Sep 8 23:41:17 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  checkpoint58p_post
8  o moved ptracer ctrl index 17 -> 32  o shelfice:
9     - fix a sign error so that no slip at shelfice interface works
10     - remove stop for combination non-hydrostatic code and shelfice. That does
11       not mean, that the results are correct, but at least they are numerically
12       stable
13    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
14    o added adjoint exch routined for all exch*3d* routines
15      and updated flow directives
16    
17    checkpoint58o_post
18    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
19      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
20    o change controling S/R for writing pickup file (new S/R do_write_pickup)
21      and clean-up reading/writing of pickup files.
22    o fix local version of read/write pickup (NH part) in rotating_tank/code
23    o simplify EXCH interface:
24     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
25     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
26    o added the regrid package
27    o shelfice:
28     - add a simple boundary layer scheme to reduce noise
29     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
30    
31    checkpoint58n_post
32    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
33       local variable (not in common block).
34    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
35      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
36      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
37        to work with SingleCpuIO.
38    o add "_d 0" to real constant of pkg/cfc subroutines ;
39       update exp. cfc_exemple & tutorial_cfc_offline output files.
40    o multi-threading and IO:
41      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
42        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
43      - barrier before and after reading.
44      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
45      - avoid using MDS_WRITELOCAL for LAND pkg output.
46      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
47        common-block variables ; Allows multi-threading with master-thread IO.
48    o change default MAX_NO_THREADS from 32 to 4 ;
49      and stop cleanly when MAX_NO_THREADS is too small.
50    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
51    
52    checkpoint58m_post
53    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
54       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
55    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
56       keep global_ocean.90x40x15 (for AD testing) with former secondary test
57       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
58    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
59        add MITgcm_tutorials (= code + all the tutorials)
60    o ecco, option to compute cost for total ssh (mean+anom)
61    o consistent with addition of ptracer and ssh in pkg/profiles
62    o profiles: adding ptracer and ssh
63    o testreport: change multi-test output-file name
64      (from output.txt.{name} to output.{name}.txt)
65    o profiles: now ok for mutli-tiles case
66    o seaice: add 4 parameters for different advection schemes for area,
67      (effective) seaice thickness, enthalphy, and snow height. Their default
68      is the standard parameter SEAICEadvScheme
69    o calc_gw:
70     - add cosFacU in zonal viscous flux (harmonic.visc.).
71     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
72       of tutorial_plume_on_slope.
73    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
74    o calc_gw: true flux-form, account for horizontal grid spacing.
75      update rotating_tank results, but not plume_on_slope (affected at
76      truncation level, 11 digits).
77    
78    checkpoint58l_post
79    o calc_gw:
80     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
81     - remove side-drag for now (need to fix it); update plume_on_slope results.
82     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
83    o commit code to make SST/SSS weights spatially variable
84      (based on either variable in-situ or variable initial T/S weights)
85    o pkg/ecco:
86      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
87        now based on horizontally varying weights wthetaLev, wsaltLev
88      * cost_averagesflags now returns year indices in addition to day, month
89      * sflux balance is performed on annual basis
90        (sflxumm, sfluxmm2, bal_sfluxmm)
91      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
92        including separate counting and multipliers
93    o pkg/rbcs
94      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
95    
96    checkpoint58k_post
97    o testreport:
98     - always build in dir. "build" (if not there, mkdir build instead of building
99       & running in input)
100     - run in dir run (if it exists), in build otherwise.
101     - call prepare_run (if input/prepare_run exists)
102     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
103    o pkg/exf modifications to interpolation and rotation routines for more
104       reasonable treatment of North Pole singularity: for tracers North Pole
105       value is set to northernmost zonal-mean value, for zonal velocity it is
106       set to zero, and for meridional velocity it is set to northernmost value.
107    o pkg/exf/exf_check_range.F
108     - add tile index to diagnostics and move stop statement to the very
109       end of the routine.
110    o pkg/diagnostics: (diagnostics_main_init.F)
111      define title of isomorphic variables according to the current config.
112    o pkg/thsice with pkg/seaice dynamics:
113    - fix domain of computation (interior only, required for exf) and do exchanges
114    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
115    o towards a standard way of dealing with multi-threading in MONITOR
116      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
117    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
118       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
119    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
120    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
121    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
122       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
123    o tracer advection:
124     - clean-up and simplify calc_common_factors.F
125     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
126       advection subroutine (but still not used within DST advection S/R)
127    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
128    
129    checkpoint58j_post
130    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
131      from file (collects calls previously in FORWARD_STEP)
132    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
133    o adjoint store dir. adjusted accordingly
134    o genmake2
135      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
136    
137    checkpoint58i_post
138    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
139      on wind stress (SEAICEstressFactor defaults to 1.)
140    o Total number of Timers is finite (<=40): comment out 2 non-essential one
141      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
142    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
143      on CS-grid: no longer loosing mass.
144    o exf & curvilinear-grid: no longer modify longitude xC & xG.
145    o pkg/ggl90: fix sloppy output and fix a bug
146    o pkg/seaice: added SEAICEuseEVPpickup parameter
147      - Set to false in order to start EVP solver with
148        non-EVP pickup files when using SEAICEuseEVP
149      - fix sign error in diffusion in seaice_calc_rhs
150    
151    checkpoint58h_post
152    * Modifications for bottom topography control
153      o replace hFacC by _hFacC at various places
154      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
155      o add non-self-adjoint cg2d_nsa
156      o update autodiff support routines
157      o re-initialise hfac after ctrl_depth_ini
158      o works for 5x5 box, doesnt work for global_ocean.90x40x15
159    * Adding verification for 5x5 box (4-layer) bottom topography control
160    
161    checkpoint58g_post
162    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
163       used for mean seasonal cycle, mean diurnal cycle); add an example
164       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
165    o pkg/ggl90:
166      - add parameter (minimum surface kinetic energy)
167      - fix bug (avoiding division by zero)
168    o couple pkg/thsice to pkg/seaice:
169      - modify advection in seaice to accomodate new scalar fields to be advected
170      - only muliDimAdection scheme work with seaice/thsice
171      - mapping of thsice-variables to seaice-variables, back and forth
172      - does not break the verification experiments, but does not give the
173        desired results either
174    o pkg/seaice
175      - make (default) second order advection a bit less confusing?
176    
177    checkpoint58f_post
178    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
179      to pkg/seaice):
180      - new routines thsice_map_exf and thsice_get_exf provide the interface
181      - add an additional formal parameter to thsice_solve4temp
182    o pkg/exf:
183      - add new fields wspeed, snowprecip (to be able to couple to thsice)
184      - correct Stefan-Boltzmann constant
185      - new parameter for longwave surface emittance
186      - separate some stuff from exf_bulkformulae into new routines  
187        exf_radiation, exf_wind
188      - add new parameters and constants: longwave emissivity for ocean, ice
189        and snow, evaporation parameters over ice
190      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
191        either wind from stress or stress from wind
192    o pkg/thSIce:
193    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
194    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
195       and THSICE_CALC_THICKN
196    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
197    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
198      to make debugging easier.
199    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
200    o pkg/bulk_force:
201      - clean-up comments and parameters ;
202      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
203    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
204      generate new output for test-experiment: aim.5l_cs.thSI
205    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
206      testreport accordingly
207    
208    checkpoint58e_post
209    o SEAICE_CGRID adjoint done
210    o R_STAR adjoint implemented.
211      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
212      * need to sort out init. of h0facc, etc.
213    o Make pkg/profile fully independent of ecco,cost, etc. stuff
214      to be able to use it in pure forward.
215    
216    checkpoint58d_post
217    o upgrade simple test-experiment to tutorial example:
218     step.1: duplicate the experiment and (step.2) will remove the old copy.
219      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
220      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
221      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
222      tutorial_global_oce_biogeo    <- copy of dic_example
223      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
224      tutorial_plume_on_slope       <- copy of plume_on_slope
225      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
226      tutorial_global_oce_optim     <- empty for now (David ?)
227      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
228     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
229    o correct a sign problem in cost_scat.F
230    o obcs and ptracers: fix boundary conditions for advections schemes
231      with larger stencil
232    o thsice adjoint: start
233    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
234      completeness
235    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
236      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
237    o ptracers adjoint:
238      * avoid extensive recomputatations
239      * fix missing re-init. of gptr (missed by TAF)
240    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
241      me to turn off the excessive output to STDOUT that this package produces
242    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
243      and add those terms in Vector-Invariant formulation.
244    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
245      if the control period (xx_hfluxperiod etc) is 0
246    o in profiles pkg, clean routines and fix details
247    o in ecco pkg, reading ssh data:
248      fix problem in case the model does not start at iter0=0
249    o fix mnc-pickup/restart for ptracers
250    o new package prifiles:
251      code to compute profile-based cost by Gael Forget
252      (modifs in ecco, ctrl, autodiff)
253    o Benign bug fix in initialization (spotted by M. Mazloff) of
254      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
255    
256    checkpoint58c_post
257    o adjoint: finish NLFS adjoint and provide reference output in
258      verification/global_ocean.90x40x15/results_ad_nlfs
259    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
260      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
261      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
262      with SEAICE_CGRID defined.
263    o move calendarDumps from "data" to "data.cal" and clean-up the code
264      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
265    o add useEXF & useCAL flags (for now, set in hard-coded way)
266    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
267      (were missing in NH mode, and wrong in quasihydrostatic mode).
268      waiting for Chris updated version of calc_gw to add those CALLs.
269    o fix bug in quasihydrostatic S/R ;
270      add a test for this option: global_ocean.90x40x15.qshyd
271    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
272      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
273    o add on/off flag useOffLine for package OFFLINE
274    o seaice:
275      - modify advection so that it works also on the C-grid
276      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
277        problem in multi-tile runs with C-grid
278      - add flags for clipping ice velocities and/or masking solver forcing
279      - fix drag (ocean on ice) formulation and a bug that caused noise in the
280        C-grid solver
281      - added a few comments to seaice_diffusion.F
282      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
283        are now exclusive)
284      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
285        required re-ordering the code a little:
286       + make DAIRN global variable (defined in SEAICE)
287       + move computation of the viscosities eta and zeta into a new separate
288         routine (because I need to recompute them in seaice_ocean_stress.F)
289    
290    checkpoint58b_post
291    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
292      update output.txt of exp. aim.5l_cs.thSI
293    o various mnc cleanups and improvements:
294      + shrink lookup tables by factor of ~4
295      + better error reporting when running out of lookup space
296      + able to handle longer path/file names (up to 500 chars)
297    o adjoint:
298      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
299      - TBD: "hidden" mom_vecinv recomp. in dynamics
300    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
301     (allow to differentiate between forcing components using new integer flags:
302      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
303     and add new flag to put Dissipation tendency out of Adams-Bashforth.
304    o ecco
305      - enable trend removal from SSH anomaly obs.
306    o adjoint
307      - a fix for PmEpR when #undef EXACT_CONSERV
308      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
309      - try to fix "hidden" recomp. in forward_step for NLFS
310        (NLFS seems broken sometimes after I checked it in)
311    o seaice:
312     - add c-grid version of the dynamic solver:
313       + three new routines that are the c-grid substitute lsr, dynsolver
314         and ostres
315       + put a few fields that were local to dynsolver into global common
316         blocks, so that I can move the computation of stresses etc into
317         seaice_lsr (saves coding but may break the adjoint).
318     - replace more hardwired parameters by runtime parameters
319     - add ice masks that mask the rhs of the implicit solvers where there
320       is no ice (commented out in seaice_dynsolver, because i am not sure
321       if this works properly), eventually this should replace the clipping
322       of ice velocities in seaice_dynsolver to +/-40cm/s.
323    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
324      include it only where its needed
325    o move balancing of fluxes before the call of external_forcing_surf
326    o seaice:
327      - correct units of turning angles (now they are really in degrees)
328      - move computation of GWATX/Y out of main routine into dynsolver
329      - initialize GWATX/Y in seaice_init
330    o Apply mask on Fresh-Water flux (needed for SSH forcing).
331      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
332    o seaice: add runtime flags for turning angles (default to zero)
333    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
334      and trend from exf forcing and ctrl control adjustments
335    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
336      (since checkpoint57x_post)
337    o change the default rotation period to 86164.s = the Earth rotation
338    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
339      and based on a reference stratification. Tested within hs94.cs-32x32x5.
340    o seaice advection: add code for choosing between the default (2nd order
341      central differences) and multiDim advection schemes provided by
342      pkg/generic_advdiff
343    o seaice:
344      - removed all references to SEAICE_GRID.h fields from
345        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
346        (cubed-sphere configuration will change a little)
347      - grid computations in seaice_init are obsolete now.
348      - cleaned up code a little so that is easier to read (hopefully).
349      - added new (better?) discretizations of default advection and diffusion
350        (turn on with SEAICEuseFluxForm)
351      - replace 1 in 3d global fields by kSurface in growth.F
352      
353    checkpoint58a_post
354    o seaice:
355      - bug fix in advect.F
356    o shelfice:
357      - separate shelfice load anomaly from pload (breaks with time
358        dependent forcing), => introduce constant field shelficeLoadAnomaly.
359        Its default is 0., but it may be computed more cleverly from (unknown)
360        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
361        done offline. A good approximation of the pressure load anomaly is
362        necessary to avoid large initial adjustment processes underneath
363        deep-reaching shelfice.
364      - small fix in ISOMIP shelfice_thermodynamics
365      - add more sophisticated thermodynamics of Hellmer (1989), this is
366        now the default
367      - give a few constants more intuitive names
368    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
369      if bulk formulae are used in long integration (especially EmPmR). Turn
370      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
371      if balancePrintMean, the imbalance that is substracted is printed to
372      STDOUT.
373    o fix bug (typo) in obcs_apply_eta.F
374    o add a new package shelfice which enables us to model the circulation
375      underneath shelf-ice with draughts of hundreds of meters.
376     - works
377     - to do: + include improved thermodynamics
378              + check whether kSurfC (from model/inc/SURFACE.h) can be used
379                instead of new field kTopC
380              + can we use topoFile, Ro_surf and existing code in ini_depth.F
381                instead of new field R_shelfIce and new code in ini_depth.F
382                and ini_mask_etc.F?
383              + adjust vertical mixing schemes?
384    o seaice pkg:
385     - add a cpp-flag to include a simple formula for a salinity dependent
386       freezing point of sea water at the surface
387     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
388       meridional stresses are now different (and hopefully correct)
389    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
390       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
391       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
392    o pkg/diagnostics: add options and parameters for regional-statistics
393       diagnostics ; define regions by reading a region-mask from a file
394       (might add other options later)
395    o pkg/bulk_force:
396     - add option and parameters to use AIM surface-flux formulae.
397     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
398       others forcing fields (defined in PARM05, parameter file "data") are loaded
399       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
400     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
401     - use the right EXCH call for uwind,vwind (to work on CS-grid).
402     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
403       and parameters (note: calcWindStress replaces .NOT.readwindstress).
404     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
405    
406    checkpoint58
407    o add "--embed-source" option to genmake2 which, when the supporting
408      tools can be compiled (as determined by genmake2) will turn on the
409      embed_files package which then embeds the entire MITgcm source code
410      (*.[fFhc] + Makefile) used for the build within the executable
411      - requested by CNH but off by default
412      - adds a paltry <9MB to the mitgcmuv executable in most cases
413      - only writes the output when useEMBEDSRC in eedata is true
414    o clean up 3-dim. relaxation codes:
415      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
416      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
417      * Thanks to Tom Haine for testing!
418    
419    checkpoint57z_post
420    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
421      affects output (@ truncation level) of exp. plume_on_slope ; updated.
422    o fix the pickup behavior for obcs in combination with ptracers
423    o fix a bug in ptracers_external_fields_load
424    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
425      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
426    o transfered surface NH pressure to eta field (if exactConserv).
427    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
428         and update lab_sea output.txt file.
429    o completing 3-dim. relaxation code: additional term
430         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
431      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
432      * At compile time, in "EXF_OPTIONS.h" set
433          #define  ALLOW_CLIMTEMP_RELAXATION
434          #define  ALLOW_CLIMSALT_RELAXATION
435      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
436          tauThetaClimRelax3Dim = 15552000.0,
437          tauSaltClimRelax3Dim  = 15552000.0,
438      * 3 cases:
439          1) Use a constant-in-time 3-dim. field
440          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
441          3) Real-time relax. to time-evolving prescribed field
442    o Adding Laplacian-type smoothness constraint on
443      initial and boundary (forcing) controls (ic, bc)
444      * enable at compile-time via
445        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
446      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
447      * Absolute scale somewhat unclear so far
448      * no area weighting was included since no other cost term does so far
449    
450    checkpoint57y_post
451    First step for a NLFS adjoint
452    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
453    o new init. routines for calc_r_star, calc_surf_dr
454    o still need to deal with ini_masks_etc
455    o testreport seemed happy
456    checkpoint57y_pre
457    
458    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
459    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
460    o add new offset feature to offline pkg (plus minor cleanup)
461    o cfc fixes for final year of integration
462    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
463      be in GCHEM_OPTIONS).
464    
465    checkpoint57x_post
466    o fix testreport Pb in multiple test experiment.
467    o cleanup our namelist syntax in verification:
468      - make it more F95 standards compliant (some work still needed)
469      - allows the vast majority of our tests to work with gfortran
470    o Non-Hydrostatic:
471     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
472     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
473    o Allow to apply AB on T,S rather than on AB(gT,gS):
474     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
475     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
476       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
477     - need a "clever" read_pickup to restart from the other AB formulation
478    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
479    o remove some unused variables (reduces number of compiler warnings)
480    o adjoint
481      * Disable useVariableViscosity for adjoint for time being
482        (there are a number of extensive recomputations)
483      * Initialize certain variables needed for adjoint
484    
485    checkpoint57w_post
486    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
487                 fix the singleCpuIO RS version of MDSWRITEFIELD
488       and add a WARNING if using globalFiles=T with multi-processors.
489    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
490      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
491    o tracer advection scheme:
492      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
493       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
494       was not very convenient).
495      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
496       (further tests needed for the implicit DST & Flux-Limiter schemes).
497    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
498      and sRef for convenience, handy, when you want to initialize
499      ptracers in a large domain with a constant non-zero value. Also,
500      untangle ptracers_init.F a little.
501    
502    checkpoint57v_post
503    o change dome exp. to use variable viscosity in side-drag terms.
504    o remove all the files from the cfc_offline test since they are now
505      incorporated into tutorial_cfc_offline which has been producing
506      identical results for a few days of testing
507    o add new parameter: sideDragFactor to enable half-slip-side BC
508      and change side-drag S/R to use viscosity from mom_calc_visc
509      (can switch back by setting sideDragFactor=0.); affects results at
510      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
511       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
512    o vorticity & strain are now computed without masking, to account for
513      no-slip-side BC in variable viscosity calculation ; mask is applied
514      anyway later on, before computing advection/coriolis terms.
515    o modify exp4 to test new obcs support for reading from external files
516      and for passive tracers
517    o fix behavior of ptracers_monitor when monitor output is written to a
518      netcdf-file; still not independent of monitor.F (writes in the same
519      file).
520    o change default value of tRef (put a uniform, meaningful value for ocean
521      & atmos) and initialize sRef (was missing, as Martin mentioned).
522    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
523      to be proportional to enstrophy dissipation length.  Thus,
524       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
525      This is now consistent with Smagorinsky and with the manual.
526    
527    checkpoint57u_post
528    o OBCS and PTRACERS: add open boundary support for passive tracers
529      - either use homogenous (pseudo) v.Neumann conditions or prescribe
530        OB-values from file; this is not different from the way theta and salinity
531        are treated
532      - however, Orlanski-radiation conditions are not supported, and the model
533        will stop if you use pTracers and Orlanski at the same time.
534      - beefed up the rountine obcs_external_fields_load: now only those open
535        boundary values are overwritten with values from files for which there
536        are really files, otherwise the OB-fields remain untouched. This makes
537        it possible to use different OBs at different ends of the domain (as
538        with EXF)
539    o reduce number of exch calls in shap_filt (s2).
540    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
541      truncation level) 4/5 MLAdjust test results (11&12 digits match).
542    
543    checkpoint57t_post
544    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
545    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
546      same truncation, independent of the face number: affects affects several
547      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
548    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
549      note that biharmonic viscosity + no-slip was not tested in any experiment.
550    o fix bug in non-linear free-surf side-drag ; generate new output for
551      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
552    o make mnc honor the writeBinaryPrec flag for most kinds of output
553    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
554    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
555      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
556    o add brackets in multi-terms sum to get same truncation, independent of
557      the face number (manage to get exactly same value of gU,gV at the cs-edge)
558      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
559    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
560      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
561      a maximum grid-scale Reynolds number.  Also, changes all length calculations
562      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
563      Suggested values of viscosity parameters found in mom_calc_visc.
564      Many new viscosity diagnostics available.
565    
566    checkpoint57s_post
567    o Add clearing-house for viscosity calculations, mom_calc_visc and
568      correct numerous bugs in LeithD and Smagorinsky discretizations.  
569      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
570      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
571      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
572      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
573      The Strain-Tension form is now called with useStrainTensonVisc=.true.
574      ViscAhStrain and viscAhTension are now retired.
575    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
576    o In response to JMC's bug report, genmake2 now ignores any soft-links
577      that it finds in the *current* directory when searching for files.
578      Soft-links found in any other source directories will still work as
579      they did before.
580    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
581      a C routine to unlimit the stack size
582    o mnc-ify pkg/aim snapshot vars
583    o mnc-ify pkg/land as requested by Daniel
584    o various changes to mnc including:
585      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
586      - output can now be grouped so that all files within a group
587          change the ITER portion of their names in lock-step together
588      - can now read ("global") PER-FACE (in addition to PER-TILE) files
589          and works with both EXCH1 and EXCH2 (but needs more testing)
590      - writing works for all verification test cases w/ g77 on Linux
591    
592    checkpoint57r_post
593    o make MNC variable initialization happen earlier
594    o add diagnostics for (almost) each term of the momentum Eq.
595    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
596    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
597    o remove MINIMAL_TAVE_OUTPUT option ;
598      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
599    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
600      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
601    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
602    o add time-dependent SST, SSS control
603    o cost terms in ecco/ modularized (new cost_generic.F)
604    o cost_averages routines are modularized (new cost_averagesgeneric.F)
605    o new infrastructure for seaice model vs. obs misfits in seaice/
606      * driver from the_main_loop.F is seaice_cost_driver.F
607      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
608      * gradient check in Exp. 6a of natl_box_adjoint/
609    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
610      (see README file)
611    
612    checkpoint57q_post
613    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
614    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
615      - bug was reported by Jean-Michel and Ian Fenty
616    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
617      update exp. cpl_aim+ocn output.
618    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
619      Needed for high-res. runs with large global files
620      to be able to limit tapelev size
621    o Changed some tests for adjoint:
622      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
623      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
624      * global_ocean.90x40x15/ back to default 3-level checkpointing
625    o Modifications to enable scripted COMMON to MODULE conversion
626      * verification/OpenAD/code/ has necessary scripts and description;
627      * converts, compiles and runs successfully;
628    
629    checkpoint57p_post
630    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
631    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
632      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
633    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
634    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
635      (was already the case for dissipation with mom_vecinv,
636       and also the case for grad.PhiHyd when staggered-timeStep)
637      This will allow to put dissipation out-off the AB time-stepping.
638     Unfortunately, affects truncation error. Update output of exp. that "fails"
639      (cg2d matching number) and leave the others for later: front_relax(10),
640      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
641      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
642    
643    checkpoint57o_post
644    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
645      (2) its ready to be documented during the 20050801 DocFest
646    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
647      for ideal_2D_oce and lab_sea on linux_ia32_g77
648    o set to #undef CTRL_SET_OLD_MAXCVARS_30
649      in global1x1_tot/code_seaice_adj to access indices 32, 33
650      (worth another tag)
651    
652    checkpoint57n_post
653    o adding precip control xx_precip 32
654    o adding swflux control xx_swflux 33
655    o Replacing 10 forcing penalty cost routines by 1 generic.
656    o Implementing partitioning in time-mean and variable adjustment
657      for atmos. state.
658    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
659  o in natl_box_adjoint:  o in natl_box_adjoint:
660    * updated: results_bulk/    * updated exp 1 to 10
661    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
662    o updated global1x1/*_seaice_adj/
663      to incorporate latest changes
664    o enable useSingleCpuIO for mdsio vector routines
665      (applies in particular to tapelev I/O)
666    o removed inefficient K-loop in all active_file*control*.F
667    
668  checkpoint57m_post  checkpoint57m_post
669  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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