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revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.726 by mlosch, Wed Sep 27 11:32:31 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 obcs: stop if obcs is used with useCDscheme = .true.
9    o shelfice:
10     - fix a sign error so that no slip at shelfice interface works
11     - remove stop for combination non-hydrostatic code and shelfice. That does
12       not mean, that the results are correct, but at least they are numerically
13       stable
14    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
15    o added adjoint exch routined for all exch*3d* routines
16      and updated flow directives
17    
18    checkpoint58o_post
19    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
20      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
21    o change controling S/R for writing pickup file (new S/R do_write_pickup)
22      and clean-up reading/writing of pickup files.
23    o fix local version of read/write pickup (NH part) in rotating_tank/code
24    o simplify EXCH interface:
25     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
26     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
27    o added the regrid package
28    o shelfice:
29     - add a simple boundary layer scheme to reduce noise
30     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
31    
32    checkpoint58n_post
33    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
34       local variable (not in common block).
35    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
36      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
37      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
38        to work with SingleCpuIO.
39    o add "_d 0" to real constant of pkg/cfc subroutines ;
40       update exp. cfc_exemple & tutorial_cfc_offline output files.
41    o multi-threading and IO:
42      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
43        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
44      - barrier before and after reading.
45      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
46      - avoid using MDS_WRITELOCAL for LAND pkg output.
47      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
48        common-block variables ; Allows multi-threading with master-thread IO.
49    o change default MAX_NO_THREADS from 32 to 4 ;
50      and stop cleanly when MAX_NO_THREADS is too small.
51    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
52    
53    checkpoint58m_post
54    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
55       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
56    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
57       keep global_ocean.90x40x15 (for AD testing) with former secondary test
58       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
59    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
60        add MITgcm_tutorials (= code + all the tutorials)
61    o ecco, option to compute cost for total ssh (mean+anom)
62    o consistent with addition of ptracer and ssh in pkg/profiles
63    o profiles: adding ptracer and ssh
64    o testreport: change multi-test output-file name
65      (from output.txt.{name} to output.{name}.txt)
66    o profiles: now ok for mutli-tiles case
67    o seaice: add 4 parameters for different advection schemes for area,
68      (effective) seaice thickness, enthalphy, and snow height. Their default
69      is the standard parameter SEAICEadvScheme
70    o calc_gw:
71     - add cosFacU in zonal viscous flux (harmonic.visc.).
72     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
73       of tutorial_plume_on_slope.
74    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
75    o calc_gw: true flux-form, account for horizontal grid spacing.
76      update rotating_tank results, but not plume_on_slope (affected at
77      truncation level, 11 digits).
78    
79    checkpoint58l_post
80    o calc_gw:
81     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
82     - remove side-drag for now (need to fix it); update plume_on_slope results.
83     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
84    o commit code to make SST/SSS weights spatially variable
85      (based on either variable in-situ or variable initial T/S weights)
86    o pkg/ecco:
87      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
88        now based on horizontally varying weights wthetaLev, wsaltLev
89      * cost_averagesflags now returns year indices in addition to day, month
90      * sflux balance is performed on annual basis
91        (sflxumm, sfluxmm2, bal_sfluxmm)
92      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
93        including separate counting and multipliers
94    o pkg/rbcs
95      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
96    
97    checkpoint58k_post
98    o testreport:
99     - always build in dir. "build" (if not there, mkdir build instead of building
100       & running in input)
101     - run in dir run (if it exists), in build otherwise.
102     - call prepare_run (if input/prepare_run exists)
103     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
104    o pkg/exf modifications to interpolation and rotation routines for more
105       reasonable treatment of North Pole singularity: for tracers North Pole
106       value is set to northernmost zonal-mean value, for zonal velocity it is
107       set to zero, and for meridional velocity it is set to northernmost value.
108    o pkg/exf/exf_check_range.F
109     - add tile index to diagnostics and move stop statement to the very
110       end of the routine.
111    o pkg/diagnostics: (diagnostics_main_init.F)
112      define title of isomorphic variables according to the current config.
113    o pkg/thsice with pkg/seaice dynamics:
114    - fix domain of computation (interior only, required for exf) and do exchanges
115    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
116    o towards a standard way of dealing with multi-threading in MONITOR
117      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
118    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
119       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
120    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
121    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
122    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
123       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
124    o tracer advection:
125     - clean-up and simplify calc_common_factors.F
126     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
127       advection subroutine (but still not used within DST advection S/R)
128    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
129    
130    checkpoint58j_post
131    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
132      from file (collects calls previously in FORWARD_STEP)
133    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
134    o adjoint store dir. adjusted accordingly
135    o genmake2
136      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
137    
138    checkpoint58i_post
139    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
140      on wind stress (SEAICEstressFactor defaults to 1.)
141    o Total number of Timers is finite (<=40): comment out 2 non-essential one
142      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
143    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
144      on CS-grid: no longer loosing mass.
145    o exf & curvilinear-grid: no longer modify longitude xC & xG.
146    o pkg/ggl90: fix sloppy output and fix a bug
147    o pkg/seaice: added SEAICEuseEVPpickup parameter
148      - Set to false in order to start EVP solver with
149        non-EVP pickup files when using SEAICEuseEVP
150      - fix sign error in diffusion in seaice_calc_rhs
151    
152    checkpoint58h_post
153    * Modifications for bottom topography control
154      o replace hFacC by _hFacC at various places
155      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
156      o add non-self-adjoint cg2d_nsa
157      o update autodiff support routines
158      o re-initialise hfac after ctrl_depth_ini
159      o works for 5x5 box, doesnt work for global_ocean.90x40x15
160    * Adding verification for 5x5 box (4-layer) bottom topography control
161    
162    checkpoint58g_post
163    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
164       used for mean seasonal cycle, mean diurnal cycle); add an example
165       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
166    o pkg/ggl90:
167      - add parameter (minimum surface kinetic energy)
168      - fix bug (avoiding division by zero)
169    o couple pkg/thsice to pkg/seaice:
170      - modify advection in seaice to accomodate new scalar fields to be advected
171      - only muliDimAdection scheme work with seaice/thsice
172      - mapping of thsice-variables to seaice-variables, back and forth
173      - does not break the verification experiments, but does not give the
174        desired results either
175    o pkg/seaice
176      - make (default) second order advection a bit less confusing?
177    
178    checkpoint58f_post
179    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
180      to pkg/seaice):
181      - new routines thsice_map_exf and thsice_get_exf provide the interface
182      - add an additional formal parameter to thsice_solve4temp
183    o pkg/exf:
184      - add new fields wspeed, snowprecip (to be able to couple to thsice)
185      - correct Stefan-Boltzmann constant
186      - new parameter for longwave surface emittance
187      - separate some stuff from exf_bulkformulae into new routines  
188        exf_radiation, exf_wind
189      - add new parameters and constants: longwave emissivity for ocean, ice
190        and snow, evaporation parameters over ice
191      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
192        either wind from stress or stress from wind
193    o pkg/thSIce:
194    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
195    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
196       and THSICE_CALC_THICKN
197    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
198    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
199      to make debugging easier.
200    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
201    o pkg/bulk_force:
202      - clean-up comments and parameters ;
203      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
204    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
205      generate new output for test-experiment: aim.5l_cs.thSI
206    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
207      testreport accordingly
208    
209    checkpoint58e_post
210    o SEAICE_CGRID adjoint done
211    o R_STAR adjoint implemented.
212      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
213      * need to sort out init. of h0facc, etc.
214    o Make pkg/profile fully independent of ecco,cost, etc. stuff
215      to be able to use it in pure forward.
216    
217    checkpoint58d_post
218    o upgrade simple test-experiment to tutorial example:
219     step.1: duplicate the experiment and (step.2) will remove the old copy.
220      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
221      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
222      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
223      tutorial_global_oce_biogeo    <- copy of dic_example
224      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
225      tutorial_plume_on_slope       <- copy of plume_on_slope
226      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
227      tutorial_global_oce_optim     <- empty for now (David ?)
228      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
229     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
230    o correct a sign problem in cost_scat.F
231    o obcs and ptracers: fix boundary conditions for advections schemes
232      with larger stencil
233    o thsice adjoint: start
234    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
235      completeness
236    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
237      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
238    o ptracers adjoint:
239      * avoid extensive recomputatations
240      * fix missing re-init. of gptr (missed by TAF)
241    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
242      me to turn off the excessive output to STDOUT that this package produces
243    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
244      and add those terms in Vector-Invariant formulation.
245    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
246      if the control period (xx_hfluxperiod etc) is 0
247    o in profiles pkg, clean routines and fix details
248    o in ecco pkg, reading ssh data:
249      fix problem in case the model does not start at iter0=0
250    o fix mnc-pickup/restart for ptracers
251    o new package prifiles:
252      code to compute profile-based cost by Gael Forget
253      (modifs in ecco, ctrl, autodiff)
254    o Benign bug fix in initialization (spotted by M. Mazloff) of
255      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
256    
257    checkpoint58c_post
258    o adjoint: finish NLFS adjoint and provide reference output in
259      verification/global_ocean.90x40x15/results_ad_nlfs
260    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
261      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
262      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
263      with SEAICE_CGRID defined.
264    o move calendarDumps from "data" to "data.cal" and clean-up the code
265      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
266    o add useEXF & useCAL flags (for now, set in hard-coded way)
267    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
268      (were missing in NH mode, and wrong in quasihydrostatic mode).
269      waiting for Chris updated version of calc_gw to add those CALLs.
270    o fix bug in quasihydrostatic S/R ;
271      add a test for this option: global_ocean.90x40x15.qshyd
272    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
273      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
274    o add on/off flag useOffLine for package OFFLINE
275    o seaice:
276      - modify advection so that it works also on the C-grid
277      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
278        problem in multi-tile runs with C-grid
279      - add flags for clipping ice velocities and/or masking solver forcing
280      - fix drag (ocean on ice) formulation and a bug that caused noise in the
281        C-grid solver
282      - added a few comments to seaice_diffusion.F
283      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
284        are now exclusive)
285      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
286        required re-ordering the code a little:
287       + make DAIRN global variable (defined in SEAICE)
288       + move computation of the viscosities eta and zeta into a new separate
289         routine (because I need to recompute them in seaice_ocean_stress.F)
290    
291    checkpoint58b_post
292    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
293      update output.txt of exp. aim.5l_cs.thSI
294    o various mnc cleanups and improvements:
295      + shrink lookup tables by factor of ~4
296      + better error reporting when running out of lookup space
297      + able to handle longer path/file names (up to 500 chars)
298    o adjoint:
299      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
300      - TBD: "hidden" mom_vecinv recomp. in dynamics
301    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
302     (allow to differentiate between forcing components using new integer flags:
303      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
304     and add new flag to put Dissipation tendency out of Adams-Bashforth.
305    o ecco
306      - enable trend removal from SSH anomaly obs.
307    o adjoint
308      - a fix for PmEpR when #undef EXACT_CONSERV
309      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
310      - try to fix "hidden" recomp. in forward_step for NLFS
311        (NLFS seems broken sometimes after I checked it in)
312    o seaice:
313     - add c-grid version of the dynamic solver:
314       + three new routines that are the c-grid substitute lsr, dynsolver
315         and ostres
316       + put a few fields that were local to dynsolver into global common
317         blocks, so that I can move the computation of stresses etc into
318         seaice_lsr (saves coding but may break the adjoint).
319     - replace more hardwired parameters by runtime parameters
320     - add ice masks that mask the rhs of the implicit solvers where there
321       is no ice (commented out in seaice_dynsolver, because i am not sure
322       if this works properly), eventually this should replace the clipping
323       of ice velocities in seaice_dynsolver to +/-40cm/s.
324    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
325      include it only where its needed
326    o move balancing of fluxes before the call of external_forcing_surf
327    o seaice:
328      - correct units of turning angles (now they are really in degrees)
329      - move computation of GWATX/Y out of main routine into dynsolver
330      - initialize GWATX/Y in seaice_init
331    o Apply mask on Fresh-Water flux (needed for SSH forcing).
332      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
333    o seaice: add runtime flags for turning angles (default to zero)
334    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
335      and trend from exf forcing and ctrl control adjustments
336    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
337      (since checkpoint57x_post)
338    o change the default rotation period to 86164.s = the Earth rotation
339    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
340      and based on a reference stratification. Tested within hs94.cs-32x32x5.
341    o seaice advection: add code for choosing between the default (2nd order
342      central differences) and multiDim advection schemes provided by
343      pkg/generic_advdiff
344    o seaice:
345      - removed all references to SEAICE_GRID.h fields from
346        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
347        (cubed-sphere configuration will change a little)
348      - grid computations in seaice_init are obsolete now.
349      - cleaned up code a little so that is easier to read (hopefully).
350      - added new (better?) discretizations of default advection and diffusion
351        (turn on with SEAICEuseFluxForm)
352      - replace 1 in 3d global fields by kSurface in growth.F
353      
354    checkpoint58a_post
355    o seaice:
356      - bug fix in advect.F
357    o shelfice:
358      - separate shelfice load anomaly from pload (breaks with time
359        dependent forcing), => introduce constant field shelficeLoadAnomaly.
360        Its default is 0., but it may be computed more cleverly from (unknown)
361        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
362        done offline. A good approximation of the pressure load anomaly is
363        necessary to avoid large initial adjustment processes underneath
364        deep-reaching shelfice.
365      - small fix in ISOMIP shelfice_thermodynamics
366      - add more sophisticated thermodynamics of Hellmer (1989), this is
367        now the default
368      - give a few constants more intuitive names
369    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
370      if bulk formulae are used in long integration (especially EmPmR). Turn
371      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
372      if balancePrintMean, the imbalance that is substracted is printed to
373      STDOUT.
374    o fix bug (typo) in obcs_apply_eta.F
375    o add a new package shelfice which enables us to model the circulation
376      underneath shelf-ice with draughts of hundreds of meters.
377     - works
378     - to do: + include improved thermodynamics
379              + check whether kSurfC (from model/inc/SURFACE.h) can be used
380                instead of new field kTopC
381              + can we use topoFile, Ro_surf and existing code in ini_depth.F
382                instead of new field R_shelfIce and new code in ini_depth.F
383                and ini_mask_etc.F?
384              + adjust vertical mixing schemes?
385    o seaice pkg:
386     - add a cpp-flag to include a simple formula for a salinity dependent
387       freezing point of sea water at the surface
388     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
389       meridional stresses are now different (and hopefully correct)
390    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
391       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
392       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
393    o pkg/diagnostics: add options and parameters for regional-statistics
394       diagnostics ; define regions by reading a region-mask from a file
395       (might add other options later)
396    o pkg/bulk_force:
397     - add option and parameters to use AIM surface-flux formulae.
398     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
399       others forcing fields (defined in PARM05, parameter file "data") are loaded
400       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
401     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
402     - use the right EXCH call for uwind,vwind (to work on CS-grid).
403     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
404       and parameters (note: calcWindStress replaces .NOT.readwindstress).
405     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
406    
407    checkpoint58
408    o add "--embed-source" option to genmake2 which, when the supporting
409      tools can be compiled (as determined by genmake2) will turn on the
410      embed_files package which then embeds the entire MITgcm source code
411      (*.[fFhc] + Makefile) used for the build within the executable
412      - requested by CNH but off by default
413      - adds a paltry <9MB to the mitgcmuv executable in most cases
414      - only writes the output when useEMBEDSRC in eedata is true
415    o clean up 3-dim. relaxation codes:
416      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
417      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
418      * Thanks to Tom Haine for testing!
419    
420    checkpoint57z_post
421    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
422      affects output (@ truncation level) of exp. plume_on_slope ; updated.
423    o fix the pickup behavior for obcs in combination with ptracers
424    o fix a bug in ptracers_external_fields_load
425    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
426      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
427    o transfered surface NH pressure to eta field (if exactConserv).
428    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
429         and update lab_sea output.txt file.
430    o completing 3-dim. relaxation code: additional term
431         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
432      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
433      * At compile time, in "EXF_OPTIONS.h" set
434          #define  ALLOW_CLIMTEMP_RELAXATION
435          #define  ALLOW_CLIMSALT_RELAXATION
436      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
437          tauThetaClimRelax3Dim = 15552000.0,
438          tauSaltClimRelax3Dim  = 15552000.0,
439      * 3 cases:
440          1) Use a constant-in-time 3-dim. field
441          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
442          3) Real-time relax. to time-evolving prescribed field
443    o Adding Laplacian-type smoothness constraint on
444      initial and boundary (forcing) controls (ic, bc)
445      * enable at compile-time via
446        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
447      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
448      * Absolute scale somewhat unclear so far
449      * no area weighting was included since no other cost term does so far
450    
451    checkpoint57y_post
452    First step for a NLFS adjoint
453    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
454    o new init. routines for calc_r_star, calc_surf_dr
455    o still need to deal with ini_masks_etc
456    o testreport seemed happy
457    checkpoint57y_pre
458    
459    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
460    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
461    o add new offset feature to offline pkg (plus minor cleanup)
462    o cfc fixes for final year of integration
463    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
464      be in GCHEM_OPTIONS).
465    
466    checkpoint57x_post
467    o fix testreport Pb in multiple test experiment.
468    o cleanup our namelist syntax in verification:
469      - make it more F95 standards compliant (some work still needed)
470      - allows the vast majority of our tests to work with gfortran
471    o Non-Hydrostatic:
472     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
473     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
474    o Allow to apply AB on T,S rather than on AB(gT,gS):
475     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
476     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
477       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
478     - need a "clever" read_pickup to restart from the other AB formulation
479    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
480    o remove some unused variables (reduces number of compiler warnings)
481    o adjoint
482      * Disable useVariableViscosity for adjoint for time being
483        (there are a number of extensive recomputations)
484      * Initialize certain variables needed for adjoint
485    
486    checkpoint57w_post
487    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
488                 fix the singleCpuIO RS version of MDSWRITEFIELD
489       and add a WARNING if using globalFiles=T with multi-processors.
490    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
491      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
492    o tracer advection scheme:
493      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
494       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
495       was not very convenient).
496      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
497       (further tests needed for the implicit DST & Flux-Limiter schemes).
498    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
499      and sRef for convenience, handy, when you want to initialize
500      ptracers in a large domain with a constant non-zero value. Also,
501      untangle ptracers_init.F a little.
502    
503    checkpoint57v_post
504    o change dome exp. to use variable viscosity in side-drag terms.
505    o remove all the files from the cfc_offline test since they are now
506      incorporated into tutorial_cfc_offline which has been producing
507      identical results for a few days of testing
508    o add new parameter: sideDragFactor to enable half-slip-side BC
509      and change side-drag S/R to use viscosity from mom_calc_visc
510      (can switch back by setting sideDragFactor=0.); affects results at
511      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
512       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
513    o vorticity & strain are now computed without masking, to account for
514      no-slip-side BC in variable viscosity calculation ; mask is applied
515      anyway later on, before computing advection/coriolis terms.
516    o modify exp4 to test new obcs support for reading from external files
517      and for passive tracers
518    o fix behavior of ptracers_monitor when monitor output is written to a
519      netcdf-file; still not independent of monitor.F (writes in the same
520      file).
521    o change default value of tRef (put a uniform, meaningful value for ocean
522      & atmos) and initialize sRef (was missing, as Martin mentioned).
523    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
524      to be proportional to enstrophy dissipation length.  Thus,
525       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
526      This is now consistent with Smagorinsky and with the manual.
527    
528    checkpoint57u_post
529    o OBCS and PTRACERS: add open boundary support for passive tracers
530      - either use homogenous (pseudo) v.Neumann conditions or prescribe
531        OB-values from file; this is not different from the way theta and salinity
532        are treated
533      - however, Orlanski-radiation conditions are not supported, and the model
534        will stop if you use pTracers and Orlanski at the same time.
535      - beefed up the rountine obcs_external_fields_load: now only those open
536        boundary values are overwritten with values from files for which there
537        are really files, otherwise the OB-fields remain untouched. This makes
538        it possible to use different OBs at different ends of the domain (as
539        with EXF)
540    o reduce number of exch calls in shap_filt (s2).
541    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
542      truncation level) 4/5 MLAdjust test results (11&12 digits match).
543    
544    checkpoint57t_post
545    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
546    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
547      same truncation, independent of the face number: affects affects several
548      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
549    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
550      note that biharmonic viscosity + no-slip was not tested in any experiment.
551    o fix bug in non-linear free-surf side-drag ; generate new output for
552      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
553    o make mnc honor the writeBinaryPrec flag for most kinds of output
554    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
555    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
556      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
557    o add brackets in multi-terms sum to get same truncation, independent of
558      the face number (manage to get exactly same value of gU,gV at the cs-edge)
559      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
560    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
561      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
562      a maximum grid-scale Reynolds number.  Also, changes all length calculations
563      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
564      Suggested values of viscosity parameters found in mom_calc_visc.
565      Many new viscosity diagnostics available.
566    
567    checkpoint57s_post
568    o Add clearing-house for viscosity calculations, mom_calc_visc and
569      correct numerous bugs in LeithD and Smagorinsky discretizations.  
570      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
571      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
572      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
573      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
574      The Strain-Tension form is now called with useStrainTensonVisc=.true.
575      ViscAhStrain and viscAhTension are now retired.
576    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
577    o In response to JMC's bug report, genmake2 now ignores any soft-links
578      that it finds in the *current* directory when searching for files.
579      Soft-links found in any other source directories will still work as
580      they did before.
581    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
582      a C routine to unlimit the stack size
583    o mnc-ify pkg/aim snapshot vars
584    o mnc-ify pkg/land as requested by Daniel
585    o various changes to mnc including:
586      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
587      - output can now be grouped so that all files within a group
588          change the ITER portion of their names in lock-step together
589      - can now read ("global") PER-FACE (in addition to PER-TILE) files
590          and works with both EXCH1 and EXCH2 (but needs more testing)
591      - writing works for all verification test cases w/ g77 on Linux
592    
593    checkpoint57r_post
594    o make MNC variable initialization happen earlier
595    o add diagnostics for (almost) each term of the momentum Eq.
596    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
597    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
598    o remove MINIMAL_TAVE_OUTPUT option ;
599      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
600    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
601      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
602    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
603    o add time-dependent SST, SSS control
604    o cost terms in ecco/ modularized (new cost_generic.F)
605    o cost_averages routines are modularized (new cost_averagesgeneric.F)
606    o new infrastructure for seaice model vs. obs misfits in seaice/
607      * driver from the_main_loop.F is seaice_cost_driver.F
608      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
609      * gradient check in Exp. 6a of natl_box_adjoint/
610    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
611      (see README file)
612    
613    checkpoint57q_post
614    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
615    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
616      - bug was reported by Jean-Michel and Ian Fenty
617    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
618      update exp. cpl_aim+ocn output.
619    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
620      Needed for high-res. runs with large global files
621      to be able to limit tapelev size
622    o Changed some tests for adjoint:
623      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
624      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
625      * global_ocean.90x40x15/ back to default 3-level checkpointing
626    o Modifications to enable scripted COMMON to MODULE conversion
627      * verification/OpenAD/code/ has necessary scripts and description;
628      * converts, compiles and runs successfully;
629    
630    checkpoint57p_post
631    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
632    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
633      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
634    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
635    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
636      (was already the case for dissipation with mom_vecinv,
637       and also the case for grad.PhiHyd when staggered-timeStep)
638      This will allow to put dissipation out-off the AB time-stepping.
639     Unfortunately, affects truncation error. Update output of exp. that "fails"
640      (cg2d matching number) and leave the others for later: front_relax(10),
641      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
642      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
643    
644    checkpoint57o_post
645    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
646      (2) its ready to be documented during the 20050801 DocFest
647    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
648      for ideal_2D_oce and lab_sea on linux_ia32_g77
649    o set to #undef CTRL_SET_OLD_MAXCVARS_30
650      in global1x1_tot/code_seaice_adj to access indices 32, 33
651      (worth another tag)
652    
653    checkpoint57n_post
654    o adding precip control xx_precip 32
655    o adding swflux control xx_swflux 33
656    o Replacing 10 forcing penalty cost routines by 1 generic.
657    o Implementing partitioning in time-mean and variable adjustment
658      for atmos. state.
659    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
660  o in natl_box_adjoint:  o in natl_box_adjoint:
661    * updated: results_bulk/    * updated exp 1 to 10
662    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
663    o updated global1x1/*_seaice_adj/
664      to incorporate latest changes
665    o enable useSingleCpuIO for mdsio vector routines
666      (applies in particular to tapelev I/O)
667    o removed inefficient K-loop in all active_file*control*.F
668    
669  checkpoint57m_post  checkpoint57m_post
670  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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