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revision 1.323 by jmc, Wed Jul 7 02:12:08 2004 UTC revision 1.716 by mlosch, Mon Aug 14 17:29:53 2006 UTC
# Line 1  Line 1 
1  $Header$  $Header$
2    $Name$
3    
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o shelfice:
8     - add a simple boundary layer scheme to reduce noise
9     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
10    checkpoint58n_post
11    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
12       local variable (not in common block).
13    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
14      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
15      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
16        to work with SingleCpuIO.
17    o add "_d 0" to real constant of pkg/cfc subroutines ;
18       update exp. cfc_exemple & tutorial_cfc_offline output files.
19    o multi-threading and IO:
20      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
21        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
22      - barrier before and after reading.
23      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
24      - avoid using MDS_WRITELOCAL for LAND pkg output.
25      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
26        common-block variables ; Allows multi-threading with master-thread IO.
27    o change default MAX_NO_THREADS from 32 to 4 ;
28      and stop cleanly when MAX_NO_THREADS is too small.
29    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
30    
31    checkpoint58m_post
32    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
33       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
34    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
35       keep global_ocean.90x40x15 (for AD testing) with former secondary test
36       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
37    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
38        add MITgcm_tutorials (= code + all the tutorials)
39    o ecco, option to compute cost for total ssh (mean+anom)
40    o consistent with addition of ptracer and ssh in pkg/profiles
41    o profiles: adding ptracer and ssh
42    o testreport: change multi-test output-file name
43      (from output.txt.{name} to output.{name}.txt)
44    o profiles: now ok for mutli-tiles case
45    o seaice: add 4 parameters for different advection schemes for area,
46      (effective) seaice thickness, enthalphy, and snow height. Their default
47      is the standard parameter SEAICEadvScheme
48    o calc_gw:
49     - add cosFacU in zonal viscous flux (harmonic.visc.).
50     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
51       of tutorial_plume_on_slope.
52    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
53    o calc_gw: true flux-form, account for horizontal grid spacing.
54      update rotating_tank results, but not plume_on_slope (affected at
55      truncation level, 11 digits).
56    
57    checkpoint58l_post
58    o calc_gw:
59     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
60     - remove side-drag for now (need to fix it); update plume_on_slope results.
61     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
62    o commit code to make SST/SSS weights spatially variable
63      (based on either variable in-situ or variable initial T/S weights)
64    o pkg/ecco:
65      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
66        now based on horizontally varying weights wthetaLev, wsaltLev
67      * cost_averagesflags now returns year indices in addition to day, month
68      * sflux balance is performed on annual basis
69        (sflxumm, sfluxmm2, bal_sfluxmm)
70      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
71        including separate counting and multipliers
72    o pkg/rbcs
73      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
74    
75    checkpoint58k_post
76    o testreport:
77     - always build in dir. "build" (if not there, mkdir build instead of building
78       & running in input)
79     - run in dir run (if it exists), in build otherwise.
80     - call prepare_run (if input/prepare_run exists)
81     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
82    o pkg/exf modifications to interpolation and rotation routines for more
83       reasonable treatment of North Pole singularity: for tracers North Pole
84       value is set to northernmost zonal-mean value, for zonal velocity it is
85       set to zero, and for meridional velocity it is set to northernmost value.
86    o pkg/exf/exf_check_range.F
87     - add tile index to diagnostics and move stop statement to the very
88       end of the routine.
89    o pkg/diagnostics: (diagnostics_main_init.F)
90      define title of isomorphic variables according to the current config.
91    o pkg/thsice with pkg/seaice dynamics:
92    - fix domain of computation (interior only, required for exf) and do exchanges
93    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
94    o towards a standard way of dealing with multi-threading in MONITOR
95      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
96    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
97       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
98    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
99    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
100    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
101       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
102    o tracer advection:
103     - clean-up and simplify calc_common_factors.F
104     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
105       advection subroutine (but still not used within DST advection S/R)
106    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
107    
108    checkpoint58j_post
109    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
110      from file (collects calls previously in FORWARD_STEP)
111    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
112    o adjoint store dir. adjusted accordingly
113    o genmake2
114      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
115    
116    checkpoint58i_post
117    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
118      on wind stress (SEAICEstressFactor defaults to 1.)
119    o Total number of Timers is finite (<=40): comment out 2 non-essential one
120      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
121    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
122      on CS-grid: no longer loosing mass.
123    o exf & curvilinear-grid: no longer modify longitude xC & xG.
124    o pkg/ggl90: fix sloppy output and fix a bug
125    o pkg/seaice: added SEAICEuseEVPpickup parameter
126      - Set to false in order to start EVP solver with
127        non-EVP pickup files when using SEAICEuseEVP
128      - fix sign error in diffusion in seaice_calc_rhs
129    
130    checkpoint58h_post
131    * Modifications for bottom topography control
132      o replace hFacC by _hFacC at various places
133      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
134      o add non-self-adjoint cg2d_nsa
135      o update autodiff support routines
136      o re-initialise hfac after ctrl_depth_ini
137      o works for 5x5 box, doesnt work for global_ocean.90x40x15
138    * Adding verification for 5x5 box (4-layer) bottom topography control
139    
140    checkpoint58g_post
141    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
142       used for mean seasonal cycle, mean diurnal cycle); add an example
143       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
144    o pkg/ggl90:
145      - add parameter (minimum surface kinetic energy)
146      - fix bug (avoiding division by zero)
147    o couple pkg/thsice to pkg/seaice:
148      - modify advection in seaice to accomodate new scalar fields to be advected
149      - only muliDimAdection scheme work with seaice/thsice
150      - mapping of thsice-variables to seaice-variables, back and forth
151      - does not break the verification experiments, but does not give the
152        desired results either
153    o pkg/seaice
154      - make (default) second order advection a bit less confusing?
155    
156    checkpoint58f_post
157    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
158      to pkg/seaice):
159      - new routines thsice_map_exf and thsice_get_exf provide the interface
160      - add an additional formal parameter to thsice_solve4temp
161    o pkg/exf:
162      - add new fields wspeed, snowprecip (to be able to couple to thsice)
163      - correct Stefan-Boltzmann constant
164      - new parameter for longwave surface emittance
165      - separate some stuff from exf_bulkformulae into new routines  
166        exf_radiation, exf_wind
167      - add new parameters and constants: longwave emissivity for ocean, ice
168        and snow, evaporation parameters over ice
169      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
170        either wind from stress or stress from wind
171    o pkg/thSIce:
172    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
173    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
174       and THSICE_CALC_THICKN
175    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
176    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
177      to make debugging easier.
178    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
179    o pkg/bulk_force:
180      - clean-up comments and parameters ;
181      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
182    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
183      generate new output for test-experiment: aim.5l_cs.thSI
184    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
185      testreport accordingly
186    
187    checkpoint58e_post
188    o SEAICE_CGRID adjoint done
189    o R_STAR adjoint implemented.
190      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
191      * need to sort out init. of h0facc, etc.
192    o Make pkg/profile fully independent of ecco,cost, etc. stuff
193      to be able to use it in pure forward.
194    
195    checkpoint58d_post
196    o upgrade simple test-experiment to tutorial example:
197     step.1: duplicate the experiment and (step.2) will remove the old copy.
198      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
199      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
200      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
201      tutorial_global_oce_biogeo    <- copy of dic_example
202      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
203      tutorial_plume_on_slope       <- copy of plume_on_slope
204      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
205      tutorial_global_oce_optim     <- empty for now (David ?)
206      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
207     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
208    o correct a sign problem in cost_scat.F
209    o obcs and ptracers: fix boundary conditions for advections schemes
210      with larger stencil
211    o thsice adjoint: start
212    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
213      completeness
214    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
215      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
216    o ptracers adjoint:
217      * avoid extensive recomputatations
218      * fix missing re-init. of gptr (missed by TAF)
219    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
220      me to turn off the excessive output to STDOUT that this package produces
221    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
222      and add those terms in Vector-Invariant formulation.
223    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
224      if the control period (xx_hfluxperiod etc) is 0
225    o in profiles pkg, clean routines and fix details
226    o in ecco pkg, reading ssh data:
227      fix problem in case the model does not start at iter0=0
228    o fix mnc-pickup/restart for ptracers
229    o new package prifiles:
230      code to compute profile-based cost by Gael Forget
231      (modifs in ecco, ctrl, autodiff)
232    o Benign bug fix in initialization (spotted by M. Mazloff) of
233      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
234    
235    checkpoint58c_post
236    o adjoint: finish NLFS adjoint and provide reference output in
237      verification/global_ocean.90x40x15/results_ad_nlfs
238    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
239      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
240      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
241      with SEAICE_CGRID defined.
242    o move calendarDumps from "data" to "data.cal" and clean-up the code
243      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
244    o add useEXF & useCAL flags (for now, set in hard-coded way)
245    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
246      (were missing in NH mode, and wrong in quasihydrostatic mode).
247      waiting for Chris updated version of calc_gw to add those CALLs.
248    o fix bug in quasihydrostatic S/R ;
249      add a test for this option: global_ocean.90x40x15.qshyd
250    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
251      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
252    o add on/off flag useOffLine for package OFFLINE
253    o seaice:
254      - modify advection so that it works also on the C-grid
255      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
256        problem in multi-tile runs with C-grid
257      - add flags for clipping ice velocities and/or masking solver forcing
258      - fix drag (ocean on ice) formulation and a bug that caused noise in the
259        C-grid solver
260      - added a few comments to seaice_diffusion.F
261      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
262        are now exclusive)
263      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
264        required re-ordering the code a little:
265       + make DAIRN global variable (defined in SEAICE)
266       + move computation of the viscosities eta and zeta into a new separate
267         routine (because I need to recompute them in seaice_ocean_stress.F)
268    
269    checkpoint58b_post
270    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
271      update output.txt of exp. aim.5l_cs.thSI
272    o various mnc cleanups and improvements:
273      + shrink lookup tables by factor of ~4
274      + better error reporting when running out of lookup space
275      + able to handle longer path/file names (up to 500 chars)
276    o adjoint:
277      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
278      - TBD: "hidden" mom_vecinv recomp. in dynamics
279    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
280     (allow to differentiate between forcing components using new integer flags:
281      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
282     and add new flag to put Dissipation tendency out of Adams-Bashforth.
283    o ecco
284      - enable trend removal from SSH anomaly obs.
285    o adjoint
286      - a fix for PmEpR when #undef EXACT_CONSERV
287      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
288      - try to fix "hidden" recomp. in forward_step for NLFS
289        (NLFS seems broken sometimes after I checked it in)
290    o seaice:
291     - add c-grid version of the dynamic solver:
292       + three new routines that are the c-grid substitute lsr, dynsolver
293         and ostres
294       + put a few fields that were local to dynsolver into global common
295         blocks, so that I can move the computation of stresses etc into
296         seaice_lsr (saves coding but may break the adjoint).
297     - replace more hardwired parameters by runtime parameters
298     - add ice masks that mask the rhs of the implicit solvers where there
299       is no ice (commented out in seaice_dynsolver, because i am not sure
300       if this works properly), eventually this should replace the clipping
301       of ice velocities in seaice_dynsolver to +/-40cm/s.
302    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
303      include it only where its needed
304    o move balancing of fluxes before the call of external_forcing_surf
305    o seaice:
306      - correct units of turning angles (now they are really in degrees)
307      - move computation of GWATX/Y out of main routine into dynsolver
308      - initialize GWATX/Y in seaice_init
309    o Apply mask on Fresh-Water flux (needed for SSH forcing).
310      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
311    o seaice: add runtime flags for turning angles (default to zero)
312    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
313      and trend from exf forcing and ctrl control adjustments
314    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
315      (since checkpoint57x_post)
316    o change the default rotation period to 86164.s = the Earth rotation
317    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
318      and based on a reference stratification. Tested within hs94.cs-32x32x5.
319    o seaice advection: add code for choosing between the default (2nd order
320      central differences) and multiDim advection schemes provided by
321      pkg/generic_advdiff
322    o seaice:
323      - removed all references to SEAICE_GRID.h fields from
324        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
325        (cubed-sphere configuration will change a little)
326      - grid computations in seaice_init are obsolete now.
327      - cleaned up code a little so that is easier to read (hopefully).
328      - added new (better?) discretizations of default advection and diffusion
329        (turn on with SEAICEuseFluxForm)
330      - replace 1 in 3d global fields by kSurface in growth.F
331      
332    checkpoint58a_post
333    o seaice:
334      - bug fix in advect.F
335    o shelfice:
336      - separate shelfice load anomaly from pload (breaks with time
337        dependent forcing), => introduce constant field shelficeLoadAnomaly.
338        Its default is 0., but it may be computed more cleverly from (unknown)
339        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
340        done offline. A good approximation of the pressure load anomaly is
341        necessary to avoid large initial adjustment processes underneath
342        deep-reaching shelfice.
343      - small fix in ISOMIP shelfice_thermodynamics
344      - add more sophisticated thermodynamics of Hellmer (1989), this is
345        now the default
346      - give a few constants more intuitive names
347    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
348      if bulk formulae are used in long integration (especially EmPmR). Turn
349      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
350      if balancePrintMean, the imbalance that is substracted is printed to
351      STDOUT.
352    o fix bug (typo) in obcs_apply_eta.F
353    o add a new package shelfice which enables us to model the circulation
354      underneath shelf-ice with draughts of hundreds of meters.
355     - works
356     - to do: + include improved thermodynamics
357              + check whether kSurfC (from model/inc/SURFACE.h) can be used
358                instead of new field kTopC
359              + can we use topoFile, Ro_surf and existing code in ini_depth.F
360                instead of new field R_shelfIce and new code in ini_depth.F
361                and ini_mask_etc.F?
362              + adjust vertical mixing schemes?
363    o seaice pkg:
364     - add a cpp-flag to include a simple formula for a salinity dependent
365       freezing point of sea water at the surface
366     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
367       meridional stresses are now different (and hopefully correct)
368    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
369       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
370       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
371    o pkg/diagnostics: add options and parameters for regional-statistics
372       diagnostics ; define regions by reading a region-mask from a file
373       (might add other options later)
374    o pkg/bulk_force:
375     - add option and parameters to use AIM surface-flux formulae.
376     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
377       others forcing fields (defined in PARM05, parameter file "data") are loaded
378       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
379     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
380     - use the right EXCH call for uwind,vwind (to work on CS-grid).
381     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
382       and parameters (note: calcWindStress replaces .NOT.readwindstress).
383     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
384    
385    checkpoint58
386    o add "--embed-source" option to genmake2 which, when the supporting
387      tools can be compiled (as determined by genmake2) will turn on the
388      embed_files package which then embeds the entire MITgcm source code
389      (*.[fFhc] + Makefile) used for the build within the executable
390      - requested by CNH but off by default
391      - adds a paltry <9MB to the mitgcmuv executable in most cases
392      - only writes the output when useEMBEDSRC in eedata is true
393    o clean up 3-dim. relaxation codes:
394      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
395      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
396      * Thanks to Tom Haine for testing!
397    
398    checkpoint57z_post
399    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
400      affects output (@ truncation level) of exp. plume_on_slope ; updated.
401    o fix the pickup behavior for obcs in combination with ptracers
402    o fix a bug in ptracers_external_fields_load
403    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
404      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
405    o transfered surface NH pressure to eta field (if exactConserv).
406    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
407         and update lab_sea output.txt file.
408    o completing 3-dim. relaxation code: additional term
409         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
410      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
411      * At compile time, in "EXF_OPTIONS.h" set
412          #define  ALLOW_CLIMTEMP_RELAXATION
413          #define  ALLOW_CLIMSALT_RELAXATION
414      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
415          tauThetaClimRelax3Dim = 15552000.0,
416          tauSaltClimRelax3Dim  = 15552000.0,
417      * 3 cases:
418          1) Use a constant-in-time 3-dim. field
419          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
420          3) Real-time relax. to time-evolving prescribed field
421    o Adding Laplacian-type smoothness constraint on
422      initial and boundary (forcing) controls (ic, bc)
423      * enable at compile-time via
424        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
425      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
426      * Absolute scale somewhat unclear so far
427      * no area weighting was included since no other cost term does so far
428    
429    checkpoint57y_post
430    First step for a NLFS adjoint
431    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
432    o new init. routines for calc_r_star, calc_surf_dr
433    o still need to deal with ini_masks_etc
434    o testreport seemed happy
435    checkpoint57y_pre
436    
437    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
438    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
439    o add new offset feature to offline pkg (plus minor cleanup)
440    o cfc fixes for final year of integration
441    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
442      be in GCHEM_OPTIONS).
443    
444    checkpoint57x_post
445    o fix testreport Pb in multiple test experiment.
446    o cleanup our namelist syntax in verification:
447      - make it more F95 standards compliant (some work still needed)
448      - allows the vast majority of our tests to work with gfortran
449    o Non-Hydrostatic:
450     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
451     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
452    o Allow to apply AB on T,S rather than on AB(gT,gS):
453     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
454     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
455       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
456     - need a "clever" read_pickup to restart from the other AB formulation
457    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
458    o remove some unused variables (reduces number of compiler warnings)
459    o adjoint
460      * Disable useVariableViscosity for adjoint for time being
461        (there are a number of extensive recomputations)
462      * Initialize certain variables needed for adjoint
463    
464    checkpoint57w_post
465    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
466                 fix the singleCpuIO RS version of MDSWRITEFIELD
467       and add a WARNING if using globalFiles=T with multi-processors.
468    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
469      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
470    o tracer advection scheme:
471      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
472       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
473       was not very convenient).
474      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
475       (further tests needed for the implicit DST & Flux-Limiter schemes).
476    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
477      and sRef for convenience, handy, when you want to initialize
478      ptracers in a large domain with a constant non-zero value. Also,
479      untangle ptracers_init.F a little.
480    
481    checkpoint57v_post
482    o change dome exp. to use variable viscosity in side-drag terms.
483    o remove all the files from the cfc_offline test since they are now
484      incorporated into tutorial_cfc_offline which has been producing
485      identical results for a few days of testing
486    o add new parameter: sideDragFactor to enable half-slip-side BC
487      and change side-drag S/R to use viscosity from mom_calc_visc
488      (can switch back by setting sideDragFactor=0.); affects results at
489      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
490       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
491    o vorticity & strain are now computed without masking, to account for
492      no-slip-side BC in variable viscosity calculation ; mask is applied
493      anyway later on, before computing advection/coriolis terms.
494    o modify exp4 to test new obcs support for reading from external files
495      and for passive tracers
496    o fix behavior of ptracers_monitor when monitor output is written to a
497      netcdf-file; still not independent of monitor.F (writes in the same
498      file).
499    o change default value of tRef (put a uniform, meaningful value for ocean
500      & atmos) and initialize sRef (was missing, as Martin mentioned).
501    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
502      to be proportional to enstrophy dissipation length.  Thus,
503       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
504      This is now consistent with Smagorinsky and with the manual.
505    
506    checkpoint57u_post
507    o OBCS and PTRACERS: add open boundary support for passive tracers
508      - either use homogenous (pseudo) v.Neumann conditions or prescribe
509        OB-values from file; this is not different from the way theta and salinity
510        are treated
511      - however, Orlanski-radiation conditions are not supported, and the model
512        will stop if you use pTracers and Orlanski at the same time.
513      - beefed up the rountine obcs_external_fields_load: now only those open
514        boundary values are overwritten with values from files for which there
515        are really files, otherwise the OB-fields remain untouched. This makes
516        it possible to use different OBs at different ends of the domain (as
517        with EXF)
518    o reduce number of exch calls in shap_filt (s2).
519    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
520      truncation level) 4/5 MLAdjust test results (11&12 digits match).
521    
522    checkpoint57t_post
523    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
524    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
525      same truncation, independent of the face number: affects affects several
526      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
527    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
528      note that biharmonic viscosity + no-slip was not tested in any experiment.
529    o fix bug in non-linear free-surf side-drag ; generate new output for
530      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
531    o make mnc honor the writeBinaryPrec flag for most kinds of output
532    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
533    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
534      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
535    o add brackets in multi-terms sum to get same truncation, independent of
536      the face number (manage to get exactly same value of gU,gV at the cs-edge)
537      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
538    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
539      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
540      a maximum grid-scale Reynolds number.  Also, changes all length calculations
541      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
542      Suggested values of viscosity parameters found in mom_calc_visc.
543      Many new viscosity diagnostics available.
544    
545    checkpoint57s_post
546    o Add clearing-house for viscosity calculations, mom_calc_visc and
547      correct numerous bugs in LeithD and Smagorinsky discretizations.  
548      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
549      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
550      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
551      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
552      The Strain-Tension form is now called with useStrainTensonVisc=.true.
553      ViscAhStrain and viscAhTension are now retired.
554    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
555    o In response to JMC's bug report, genmake2 now ignores any soft-links
556      that it finds in the *current* directory when searching for files.
557      Soft-links found in any other source directories will still work as
558      they did before.
559    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
560      a C routine to unlimit the stack size
561    o mnc-ify pkg/aim snapshot vars
562    o mnc-ify pkg/land as requested by Daniel
563    o various changes to mnc including:
564      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
565      - output can now be grouped so that all files within a group
566          change the ITER portion of their names in lock-step together
567      - can now read ("global") PER-FACE (in addition to PER-TILE) files
568          and works with both EXCH1 and EXCH2 (but needs more testing)
569      - writing works for all verification test cases w/ g77 on Linux
570    
571    checkpoint57r_post
572    o make MNC variable initialization happen earlier
573    o add diagnostics for (almost) each term of the momentum Eq.
574    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
575    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
576    o remove MINIMAL_TAVE_OUTPUT option ;
577      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
578    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
579      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
580    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
581    o add time-dependent SST, SSS control
582    o cost terms in ecco/ modularized (new cost_generic.F)
583    o cost_averages routines are modularized (new cost_averagesgeneric.F)
584    o new infrastructure for seaice model vs. obs misfits in seaice/
585      * driver from the_main_loop.F is seaice_cost_driver.F
586      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
587      * gradient check in Exp. 6a of natl_box_adjoint/
588    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
589      (see README file)
590    
591    checkpoint57q_post
592    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
593    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
594      - bug was reported by Jean-Michel and Ian Fenty
595    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
596      update exp. cpl_aim+ocn output.
597    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
598      Needed for high-res. runs with large global files
599      to be able to limit tapelev size
600    o Changed some tests for adjoint:
601      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
602      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
603      * global_ocean.90x40x15/ back to default 3-level checkpointing
604    o Modifications to enable scripted COMMON to MODULE conversion
605      * verification/OpenAD/code/ has necessary scripts and description;
606      * converts, compiles and runs successfully;
607    
608    checkpoint57p_post
609    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
610    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
611      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
612    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
613    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
614      (was already the case for dissipation with mom_vecinv,
615       and also the case for grad.PhiHyd when staggered-timeStep)
616      This will allow to put dissipation out-off the AB time-stepping.
617     Unfortunately, affects truncation error. Update output of exp. that "fails"
618      (cg2d matching number) and leave the others for later: front_relax(10),
619      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
620      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
621    
622    checkpoint57o_post
623    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
624      (2) its ready to be documented during the 20050801 DocFest
625    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
626      for ideal_2D_oce and lab_sea on linux_ia32_g77
627    o set to #undef CTRL_SET_OLD_MAXCVARS_30
628      in global1x1_tot/code_seaice_adj to access indices 32, 33
629      (worth another tag)
630    
631    checkpoint57n_post
632    o adding precip control xx_precip 32
633    o adding swflux control xx_swflux 33
634    o Replacing 10 forcing penalty cost routines by 1 generic.
635    o Implementing partitioning in time-mean and variable adjustment
636      for atmos. state.
637    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
638    o in natl_box_adjoint:
639      * updated exp 1 to 10
640        (but does not have time-mean vs. variable split results yet)
641    o updated global1x1/*_seaice_adj/
642      to incorporate latest changes
643    o enable useSingleCpuIO for mdsio vector routines
644      (applies in particular to tapelev I/O)
645    o removed inefficient K-loop in all active_file*control*.F
646    
647    checkpoint57m_post
648    o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
649      and advect_cs (use EXCH-2 and standard cs-32 grid files).
650    o pkg/exch2: filling of face-corner halo regions is optional
651      (ifdef W2_FILL_NULL_REGIONS) and is turned off by default.
652    
653    checkpoint57l_post
654     tag before updating tutorials (pre-release-2)
655    o add cos & sin of grid-direction orientation angle (curvilinear grid only,
656       for output and interpolation of input fields onto model grid)
657    o fix radius in mom_v_metric_cylinder.F (wrong by dy/2).
658       Affects results of exp. rotating_tank ; update output.txt.
659    o pkg/diagnostics: 2 new S/R to fill a diagnostics using a scaling factor
660          and taking the square quantity and/or using a fraction-weight field.
661    o fix aim_diagnostics_init.F mate numbers.
662    o add mnc output capability to diagnostics/diagstat and update
663      our cvsignore files for the ACSII output generated
664    
665    checkpoint57k_post
666    o lab_sea now uses diagnostics package and provides a suite of
667      new EXF diagnostics output.
668    
669    checkpoint57j_post
670    o exf
671      * bug fix in exf_bulkformulae for psimh (spotted by Eliyahu Biton):
672        Bracket missing in eqn. for psimh (eqn. 7 of Large & Pond, 1982);
673        terms -2*ATAN(x) + pi/2 were added to both stable and unstable case.
674      * extended diagnostics output
675        - now includes all EXF variables
676        - hs, hl moved to common block
677        - separate S/R for diagnostics, called after ctrl vector is added
678        - name changed for EXFsw -> EXFswnet, EXFlw -> EXFlwnet
679        - EXFqnet contains true Qnet (i.e. includes qsw)
680      * updated verif. lab_sea, global_with_exf
681      * Rearranging hflux (exf_mapfields -> exf_getforcing)
682        to ensure that diagnostics sees a true EXFqnet
683    o add matlab scripts for CS-grid vectors (in utils/cs_grid)
684    o diagnostics pkg: change pointers so that 1 diagnostic can be used
685      several times with different frequencies.
686    o mnc-ify the thsice package as requested by Daniel Enderton
687      - the monitor--MNC output needs work
688      - many attributes need to be added (most are currently blank)
689    o mnc-ify theaim_v23 package as requested by Daniel Enderton
690      - many attributes need to be added (most are currently blank)
691    o remove "groundAtK1" & "rkFac" (replaced by usingPCoords & -rkSign)
692    o add Sadourny like discretization to the 4th.O vorticity advection scheme
693    o fix bug in rStar code (calc_r_star.F) when used with topo/bathy.
694      update output.txt from: aim.5l_cs (& .thSI), cpl_aim+ocn,
695         fizhi-gridalt-hs and global_ocean.cs32x15 (& .thsice).
696    o fix few little things to avoid floating error with -ftrapuv (ifort v9)
697     (ini_spherical_polar_grid.F, calc_r_star.F, monitor/mon_surfcor.F)
698    
699    checkpoint57i_post
700    o Diagnostics package was changed: diagnostic allocation is now deactivated
701      by setting an empty file name in the namelist (used to be by setting 0 frequency)
702    o momentum advection (VI form) options: activate 4th.O vorticity Coriolis ;
703      add 1rst Order upwind vertical Shear.
704    o add a quick fix for A/B checkpointing in OFFLINE mode
705    o add IGNORE_TIME define and -ignore_time option to genmake2 as an
706      end-run around the C/Fortran linking horror in eesup/src/timers.F
707    o added pkg/runclock: allows user to terminate run based on wall clock
708    o added non-hydrostatic scaling parameter: nh_am2
709    o pkg/my82: futile attempt to make results compiler-independent by adding
710      some "_d 0", etc. no effect.
711    o for mnc output, fill the 'T' coordinate var with myTime and create a
712      separate 'iter' variable for iteration count
713    o pkg/diagnostics:
714      add new capability: output of Global/Regional & per-level statistics ;
715      tested against monitor output (including land & thSIce) on various exp.
716    o make seaice-pkg I/O type flags (MNC/MDS) more standard.
717    
718    checkpoint57h_done
719      tag after changing user customized files (DIAGNOSTICS_SIZE.h,
720      data.diagnostics, data.gchem, data.ptracers) is done.
721    
722    o pkg/diagnostics: prepare for Global/Regional statistics.
723      add 2nd namelist in data.diagnostics and update DIAGNOSTICS_SIZE.h
724    o remove "baseTime" (no used) from arg. list of DIFF_BASE_MULTIPLE
725      and rename it: DIFFERENT_MULTIPLE
726    
727    checkpoint57h_post
728    o move tIter0 from data.gchem to PTRACERS_Iter0 in data.ptracers
729    o pkg/diagnostics: change output frequency, now in seconds (instead
730      of Nb of iterations). This requires to change data.diagnostics.
731    checkpoint57h_pre
732    
733    o in mnc, let the user create the output dir if both mnc_outdir_date
734      and mnc_outdir_num are false
735    o add fflags() to pkg/diagnostics which allows one to specify, on a
736      per-file basis, the file precision [default behavior is unchanged]
737    o added diagnostics to pkg/kpp, including computation of mixed layer
738      depth based on a temperature/density criterion
739    o updated verification/natl_box to test the new pkg/kpp diagnostics
740    o bugs fixed (with useAbsVorticity=T & with useJamartMomAdv=T)
741    o test AB-3 code with 4th.Order advection scheme (advect_xy/input.ab3_c4)
742    o fix mnc flags in pkg/seaice so that they are "owned" by seaice,
743      not mnc -- this mistake was found by JMC and is now corrected
744    
745    checkpoint57g_post
746    o add Adams-Bashforth 3rd Order time stepping:
747      - default remains AB-2 (#undef ALLOW_ADAMSBASHFORTH_3)
748      - not yet implemented with NH, CD_Scheme, pTracers, MNC_pickup ...
749    checkpoint57g_pre
750    
751    o make lambda[Theta,Salt]ClimRelax spatially varying
752      (default remains spatially uniform constant based on tau)
753    o added new control variables
754      * init. uVel, vVel, etanN
755      * lambda[Theta,Salt]ClimRelax
756    o separate masks used for ctrl_pack/unpack 'from write_grid' output
757      (suggested by G. Forget)
758    
759    checkpoint57f_post
760    o add parameter "baseTime" = model base time = time at iteration zero
761      new function DIFF_BASE_MULTIPLE (replace DIFFERENT_MULTIPLE) to
762      account for baseTime shift
763    o move Coriolis arrays from PARAMS.h to GRID.h
764    checkpoint57f_pre
765    
766    o mnc-ifying the seaice package
767    o introduced an alternative length scale calculation for use in the limiting
768      maximum viscosity (off by default, see mom_vi_hdissip.F for details)
769    o S/R ptracers_calc_diff: argument list bug for CALL KPP_CALC_DIFF_S
770    o added modified Leith scheme with viscosity proportional to grad(Hdiv)
771      as well as grad(vort3).  Made it compatible with both approximate form
772      for the cubed sphere and full form of these gradients.  Added flag
773      useFullLeith to select between approximate and full form.  
774    o add "d0" in getcon.F to reduce differences between compilers/platforms
775      update output.txt of exp. fizhi-gridalt-hs
776    o change port_rand funtion to allow to set the seed.
777    o fix obscure MNC bug involving conversion between reals and integers
778      - it caused no problems with certain (eg. gcc, ifc) compilers but the
779        new version is now more standards-compliant
780    o adjoint-related modifications
781      * gad_dst3_adv_?: to be able to use advscheme=30 in adjoint
782      * gad_calc_rhs: fool adjoint, revert to advscheme=30 in reverse when using 33
783      * mom_vi_hdissip: to be able to use Leith scheme in adjoint
784    
785    checkpoint57e_post
786    o Adding eddy stress controls a la Ferreira et al.
787    checkpoint57e_pre (actually was tagged: eckpoint57e_pre)
788    
789    o fizhi pkg: fix AtoC and CtoA when called with same input & output array
790      update output.txt of exp. fizhi-gridalt-hs
791    o add more "Z" dimensions and associated coordinate vars to MNC
792    o pkg/exf: added twoDigitYear capability for option useExfYearlyFields
793    o parameter calendarDumps: when set, approximate months (30-31 days) and years
794      (360-372 days) for parameters chkPtFreq, pChkPtFreq, taveFreq, SEAICE_taveFreq,
795      KPP_taveFreq, and freq in pkg/diagnostics are converted to exact calendar
796      months and years.  Requires pkg/cal.
797    o diagnostics: add pickup functionality
798      - off by default for backwards compatibility
799      - current version only uses MDSIO -- MNC will be added
800    o allow to use pkg diagnostics for LAND pkg output & Shapiro Tendencies.
801    o pkg/shap_filt: fix for multi-tiles per face (CS-grid with EXCH2)
802    
803    checkpoint57d_post
804    o pkg/thsice used in the ocean: fix tile Pb related to sIceLoad forcing
805    o modify verification/ideal_2D_oce so that it tests the creation of mnc
806      output from the diagnostics package
807    o temporary fix in EXCH2_UV: add a 3rd call to fix the 24.tiles CS-grid set-up
808    o make genmake2 more portable by using ".$FS" instead of ".f" for more
809      of the test compilations (eg. IBM xlf on Mac OSX w/HFS filesys)
810    o add coordinate variables to the MNC output from the diagnostics package
811    o change MNC-flags default value: true when useMNC=TRUE
812    o add a "readgrid_mnc" flag to MNC and give model/src/ini_curvilinear_grid.F
813      the ability (off by default) to read the grid information using MNC
814    o lab_sea: use LSR_ERROR=1.E-12 for testing ; update output.txt
815    o diagnostics: fix a bug (sub-set of levels); keep full precision when averaging
816    o do snap-shot diagnostics at the middle of the time-interval (instead of
817      at the end).
818    o update exp. aim.5l_cs (use default LAND_OPTIONS.h file) and add
819      new test for AIM with thSIce + slab-ocean
820    o cpl_aim+ocn test: update output (optfile & default GMREDI_OPTIONS.h)
821    o move state variable diagnostics to the beginning of the time step ;
822      (note: still needs some work specially for snap-shot diagnostics)
823      duplicate & replace UVELVVEL diagnostics with UV_VEL_C & UV_VEL_Z
824    
825    checkpoint57c_post
826    o Change testing option (-ieee) to get closer agreement between g77 & ifort
827    o generate new output.txt files on faulks with g77 & the new -ieee option
828    checkpoint57c_pre
829    
830    o add "_d 0" in freeze ; change some "FLOAT" to "DFLOAT" and went back (TAF);
831      update output.txt of exp. global_ocean.90x40x15
832    o fix in ini_eos.F (one "_d 0" was missing): now g77 & ifc give much closer
833      results; update global_ocean_pressure & global_ocean.cs32x15 output.txt
834    o add saltFlux(+File) forcing capability with periodicExternalForcing
835    o allow to use pkg diagnostics for GM-Redi & ThSIce output
836    o diagnostics_fill: fill in up to sNx+1 or sNy+1 (if U,V or Z pt) for mnc.
837    o improvements for the MNC output from DIAGNOSTICS:
838      - correct handling of the unlimitied dimension
839      - all dims now have associated coordinate variables
840      - variables located at U, V, and Corner ("Z") points are now written
841        with the correct horzontal dimensions (eg. 'Xp1', 'Yp1') so that
842        *all* data points are output
843    o added seaice_summary.F and removed obsolete ALLOW_SEAICE's from pkg/seaice
844    o added pkg/seaice/seaice_monitor.F
845    o mdsio_readfield.F can now read files visible only to master MPI process.
846    o pkg/seaice: some test code for ice-modified ocean stress
847    o exf_getffields interpolation defaults to bilinear for all scalar forcing
848      fields (remains bicubic for wind velocity and stress).  This avoids, e.g.,
849      spurious negative numbers for precipitation and humidity.  Will cause
850      some small numerical differences for integrations using pkg/exf/exf_interp.F.
851    o pkg/ctrl/
852      * Add ctrlvec diagnostics in pack/unpack for nondimensional I/O
853        May be enabled via doPackDiag
854      *  introduce z-scaling of
855         + gradient (doZscalePack) and
856         + control (doZscaleUnpack)
857    o pkg/mdsio/
858      * enable useSingleCpuIO for state estimation (ctrl_pack/unpack) mdsio_gl.F
859      * N.B.: leave tiled I/O for tapelev (i.e. mds...vector)
860    
861    checkpoint57b_post
862    o simplify options in diagnostics_fill arguments (remove weird combinations)
863    o fix MNC coordinate variables so that they now contain per-face index
864      values (instead of xC,xG,yC,yG values) when run with EXCH2 since, in
865      general, EXCH2 grids are only aligned to a "local" coordinate system
866    o test diagnostics pkg in dic_example (no output) and ideal_2D_oce (with ouput)
867    o Implement instantaneous output within pkg diagnostics:
868      setting a negative frequency in data.diagnostics produces
869     "snap-shot" output (as opposed to time-average if freq > 0)
870    o move out off EQUIVALENCE all diagnostics that fizhi does not use ;
871      NOTE: change ptracer diagnostics name: use 2 characters to work with
872            more than 9 tracers. Add also diagnostics of advect & diffus flux.
873    o more CF compliance: convert all MNC 'iter' variables to 'T' so that it
874      becomes the coordinate variable for the 'T' dimension
875    o add CF-style coordinate variables to MNC
876      - just a first cut:  numbers are meaningless on the cubesphere and
877        missing along the T axis but otherwise it works!
878    o add surface flux diagnostics: TAUX, TAUY, TFLUX, TRELAX, TICE, SFLUX, SRELAX
879    o pkg/thSIce: read initial state from 6 files ; allow monitor to use MNC.
880    o add diagnostics of advective & diffusive flux for T & S (pTracers coming soon)
881      this is based directly on what the model compute, so that the content of
882      each diagnostics might be affected by switching options (e.g., implicitDiffusion)
883    o small changes for diagnostics (gad_biharm_?.F, arguments of S/R impldiff.F)
884    o clean up build options files for SunOS, in particular
885      - remove -traditional from xmakedepend
886      - change -xarch=v9 to -xarch=native for f77
887      - restore use of make (not gmake)
888      - add CC=gcc if using g77
889    o changes per discussion of AM, JMC, & EH3 today:
890      - move redundant "grid" variables out of "state" -- in preparation of
891        creating proper CF-style coordinate variables and in recognition
892        that any/all grid variables can be easily copied (eg. w/NCO) from
893        the grid files into any of the other NetCDF files
894      - *always* output grid variables with MDSIO (this will eventually be
895        changed)
896      - output MNC grid file if useMNC is true
897    o every instance of _END_MASTER() has been found and replaced with
898      _END_MASTER( myThid ) in order to satisfy certain picky Sun
899      preprocessors
900    o re-arrange diagnostics pkg initialisation:
901     - allow each package to extend the available diagnostics list
902     - add some checking and fix small problems (multi-threaded, ...)
903     - new S/R diagnostics_fill (replace fill_diagnostics):
904       look through the short list of active diag. (instead of the long list)
905       create function DIAGNOSTICS_IS_ON to tell if a diagnostics is active
906    
907    checkpoint57a_post
908    o this set of changes restores TAMC compatibility
909      tested for global_ocean.90x40x15 adjoint on trough
910      (what a pain)
911    
912    checkpoint57a_pre
913    o some modifs in tools/build_options for sunos
914    o call ctrl_pack for ctrl at end for optimcycle=0
915    
916    checkpoint57
917    o add horizontal bi-harmonic viscosity for vertical velocity
918      - new parameter viscA4W (defaults to viscA4)
919      - affects only non-hydrostatic code
920      - to be done: no-slip lateral boundary conditions
921    o switch back to "sflux = sflux - runoff" in exf_getforcing.F
922    o implement Implicit Vertical advection for pTracers
923    o depth convergence accelerator: replace deltaTtracer by dTtracerLev(k)
924      (implemented also for implicit vertical diffusion & advection)
925    o OBCS: extend application of tracer open boundary conditions
926      to a strip beyond the boundary of width Olx/Oly
927    o add call monitor to TAF set of required calls (flow directives)
928      and include in natl_box_adjoint
929    o untangle a few ifdefs related to cost, ctrl, autodiff
930      untangel a few ALLOW_ECCO_OPTIMIZATION
931    o Apply Cooper & Haines representative estimates also at sub-surface (k=Nr)
932      (theta2, salt2 in ecco_cost_weights)
933    
934    checkpoint56c_post
935    o OBCS as control variables
936      - update ctrl_ad_diff.list, obcs_ad_diff.list
937      - remove balance of obcs controls from default
938      - fix index bug nobcs in ctrl_init
939      - fix dummy fields filen in ctrl_pack
940      - add dummy weights for obcs
941    o lsopt: comment out fort.94 output
942    o optim:
943      - remove unnecessary header files
944      - adjusted namelists
945      - add xerbla.F to Makefile
946    o exf:
947      - multiple modifications of exf_check_range
948      - unit change in exf_init_runoff from [m/year] to [m/s]
949    o mdsio:
950      - i/o-vector change debugLevel from debLevA to debLevB
951    
952    checkpoint56b_post
953    o collect all ptracers output in an new routine (PTRACERS_OUTPUT) that
954      is called from DO_THE_MODEL_IO
955      - rename PTRACERS_STATV_WRITE to PTRACERS_WRITE_TIMEAVE
956      - introduce new parameter PTRACERS_dumpFreq (defaults to dumpFreq)
957      - clean up PTRACERS_WRITE_TIMEAVE a little
958    o add another verification experiment that tests both the cfc-pkg and
959      the gchem-pkg with GCHEM_SEPARATE_FORCING undefined, that is with
960      reactive tendencies treated inline with regular timestepping
961    o testreport previously did a lousy job of comparing small numbers, so
962      we (Ed and Martin) changed the  way the cut-off of 1.e-12 is
963      implemented in the little c-progam tmp_cmpnum.c which is embedded in
964      testreport.
965    o ptracers_monitor: bug fix for MPI
966    
967    checkpoint56a_post
968    o GCHEM: finish reorganizating the package
969      - forward_step calls GCHEM_CALC_TENDENDY, which computes gchemTendency
970        (introduces another 3D-array for each passive tracer, but only if
971        GCHEM_SEPARATE_FORCING is undefined. For GCHEM_SEPARATE_FORCING
972        gchemTendency is not needed because the timestep is done separately)
973      - gchemTendency is added to gPtr in GCHEM_ADD_TENDENCY
974      - GCHEM is now---more or less cleanly---separate from PTRACERS
975      - to bo done: handling of surfaceForcingPtr that is needed for KPP not
976        so clear to me how that should be done in a general way.
977    o CFC: improve formatting of output in CFC_ATMOS
978    o PTRACERS:
979      - rename GCHEM_MONITOR to PTRACERS_MONITOR and call it from MONITOR, so
980        that ALL experiments with ptracers enable can be checked. This makes
981        GCHEM_MONITOR obsolete.
982      - include a runtime parameter PTRACERS_monitorFreq that defaults to
983        monitorFreq
984      - set default PTRACERS_write_mdsio to false if PTRACERS_write_mnc is true
985    o add PTRACERS (PTR0[1-5]) to testreport output
986    o exf_check_range:
987      * default changed to .TRUE.
988      * will check values for niter0 if debLevA, every timestep if debLevB
989      * STOP in exf_check_range if 'out of range'
990      * range chosen generous to allow for potential extema
991      TBD: a version with stricter range
992           permitted range would be runtime parameters
993    o GMredi:
994      - fix ldd97 slope limit ; extend valid domain of Psi-Bolus ;
995      - change S/R GRAD_SIGMA to be valid in the overlap on CS-grid.
996      - change the default GMREDI_OPTIONS.h: compile everything except Visbeck
997    o GCHEM:
998      - move call to GCHEM_FORCING_SEP, so that it is now called before
999        the blocking exchanges to avoid computing halos in GCHEM_FORCING_SEP
1000      - introduced a useGCHEM runtime flag and applied it everywhere.
1001      - renamed PTRACERS_SEPARATE_FORCING to GCHEM_SEPARATE_FORCING;
1002        this flag is now only visible within GCHEM-pkg routines.
1003      - moved gchem_forcing_int temporarily into ptracers_forcing, this will
1004        be replaced by a 3D array that is computed before thermodynamics; for
1005        this, the tracer ID iTracer had to be included into the parameter list
1006        of ptracers_forcing
1007      - set up forward_step to call gchem_forcing, that will replace
1008        gchem_forcing_int in ptracers_forcing
1009      - cleaning up
1010    o small cleaning of exch2: remove files that are also in eesupp/src
1011    
1012    checkpoint56
1013    o AIM: read land-Fraction earlier (from ini-fixed) and monitor land at nIter0
1014    o mnc: cleanup "full" files--fixes out-of-memory problem
1015    o ECCO-GODAE
1016      * model/, pkg/, code/, input/ now complete w.r.t. ECCO-GODAE production setup
1017      * fully merged and updated from SIO code
1018        windstress sign change affects
1019        - exf_inscal_[u/v]stress
1020        - sign of xx_tau[u/v] adjustments
1021        - signs in cost_scat
1022      * ctrl_get_gen: avoid update of tau[u/v] for first few days
1023      * natl_box_adjoint updated and compressed
1024      * 2-level checkpoint switch added
1025        (tested in EXP. 1 of natl_box_adjoint)
1026      * new switch doInitXX to avoid init. of xx_... in optimcycle=0
1027    o SVD
1028      * first complete, non-hacked version for SVD calculations
1029      * all interfaces clean w.r.t to handling of xx_..., adxx_..., g_xx_...
1030        performed via direct access files admtlm_vector.it????
1031        (via ctrl_[un]pack)
1032      * optimcycle is used for ARPACK iteration counter
1033        (note: adxx_... is iterated, rather than xx_...; latter is constant!)
1034      * EV problem ok w.r.t. L2-norm in tangent space; need to check other norms
1035        and add linear transforms where necessary
1036      * controls are initial/final SST, SSS (can be extended; need to check
1037        ctrl_set_[un]pack_xyz.F according to ctrl_set_[un]pack_xy.F
1038    o mdsio: filename info to both stderr, stdout
1039    o exf: exf_inscal_runoff: separated default conversion [m/year] -> [m/sec]
1040      from sign change
1041    
1042    checkpoint55j_post
1043    o isolate dissipation tendency (allow to keep it out off AB) in V.I form.
1044      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
1045    o add consistent build directories and .cvsignore files to verification
1046    o added viscA4GridMin and viscA4GridMax for more control on biharmonic viscosity
1047    o make all subroutines 30 or less characters in length for certain older
1048      compilers to work (a thorough search only turns up two routines in
1049      pkg/ptracers)
1050    o allow (vecinv only) a different horiz. viscosity for Divergence and Vorticity;
1051      affects (truncation level) output.txt of global_ocean.cs32x15(&.thsice)
1052    
1053    checkpoint55i_post
1054    o change arrays for total vertical diffusivity (2.D if explicit,
1055      3.D if implicit) ; each ptracer uses its own background value.
1056    o added mnc/NetCDF output capability to ocn_compon_interf
1057      - added bits to verification/cpl_aim+ocn so that it can run on
1058        ITRDA and other clusters without the mpirun "-wd" option
1059    o fixed wayward endif in mom_fluxform.F that messed up cyclindrical
1060      configuration
1061    o give MNC the ability to create additional files rather than
1062      exceeding a specified file size limit "MNC_MAX_FILESIZE"
1063      - the default is just less than 2GB which is a practical limit
1064        on many systems
1065    o Compute the non-local term using either KPP vertical diffusivity (=default)
1066       or the total vertical diffusivity (when KPP_ghatUseTotalDiffus=T)
1067    
1068    checkpoint55h_post
1069    o add verification test "vermix"
1070    o remove all the *_ioinc flags and replace with the single global
1071      outputTypesInclusive flag
1072    o allow to set a vertical profile of vertical diffusivity for T & S
1073    o call PACKAGE_BOOT & PACKAGES_READPARMS just after INI_PARMS
1074    o useMNC moved from data.mnc to data.pkg
1075    
1076    checkpoint55g_post
1077    o Renaming carbon AD experiments to comply with testreport conventions
1078    o Updating adjoint of Held-Suarez hs94.1x64x5
1079    o Fixing directives for non-ECCO forward_step, after ECCO directives
1080      have been fixed to avoid recomp. of do_oceanic_phys
1081      Works well for global_ocean.90x40x15,
1082      but recomp. issue remains for carbon
1083    o Updating adjoint output for natl_box_adjoint after
1084      pkg/ecco has been modified (see taga c55d_post)
1085    
1086    checkpoint55f_post
1087    o rename to timeave_init_fixed
1088    
1089    checkpoint55e_post
1090    o some delicate re-shuffle of store directives to avoid one
1091      extra call of do_oceanic_physics
1092      affects ecco_the_main_loop.F, do_oceanic_physics.F
1093      checkpoint_lev1_directives.h
1094    o NB: this may break global_ocean adjoint temporarily,
1095      but it is clear how to fix it. Will do later, need this now.
1096    
1097    checkpoint55d_post
1098    o ECCO specific cost function terms (up-to-date with 1x1 runs)
1099    o ecco_cost_weights is modified to 1x1 runs
1100    o modifs to allow observations to be read in as
1101      single file or yearly files
1102    o enable to read exf forcing fields as either
1103      single file or yearly files (flag useExfYearlyFields)
1104    checkpoint55d_pre
1105    
1106    o switch between 2-level and 3-level checkpointing
1107    o add ability of MNC to write local and "partial" (eg. 2D slices where
1108      the full 3D field is never actually stored) arrays to NetCDF files
1109      with the correct (that is, the complete multi-dimensional) set of
1110      array indicies
1111      - used in mom_vecinv() to write the diagFreq output
1112      - tested (demonstrated) in verification/aim.5l_cs
1113    o further mnc-ification
1114      - add verification/lab_sea to the list with mnc setups
1115      - fix undefined mnc v-names in cd_code
1116      - add kpp to mnc output (both snapshot and timeave)
1117    o non-hydrostatic code
1118      - added horizontal viscosity parameter viscAhW for w, that replaces viscAh
1119        in calc_gw.F
1120      - defaults to viscAh
1121      - this is useful, when I want to use viscAh=0 (e.g., only biharmonic
1122        friction or Leith) in non-hydrostatic mode, as long as there is
1123        no biharmonic friction and/or Leigth or equivalent for vertical velocity.
1124    o pkg/cost
1125      extend simple cost functions to treat time mean quantities
1126      (T,U,V) via cost_accumulate_state from cost_tile
1127    o multidimAdvection on CS-grid: implement the full 3 pass ; overlap needs to
1128        be 2 times larger than the minimum size the advection scheme requires.
1129        now get a perfect conservation of salt in advect_cs test-exp (updated)
1130    o GGL90 (Gaspar's TKE mixed layer)
1131      - add horizontal diffusion of TKE, requires exchanges in
1132        do_fields_blocking_exchanges, horizontal diffusivity is zero by
1133        default. In OPA there is no horizontal diffusion of TKE but the
1134        mixing coefficients are computed from a horizontal average of TKE of
1135        6 points or so. I think that diffusion has a little more physical
1136        justification.
1137      - clean up ggl90_calc in the hope of reducing memory usage (this hope
1138        was in vain)
1139      - mask tke-variable in ggl90_init
1140    o fix mask Pb in multidimAdvection on CS-grid (still a small Pb with ipass)
1141    o fix biharmonic diffusion on CS-grid.
1142    o more obcs stuff
1143      - added obcs_external_fields_load as an alternative to the EXF-pkg option
1144        for reading boundary values. This routine is called from
1145        obcs_prescribe_read
1146      - updated obcs_check
1147      - changed sponge layer relaxation parameter units for days to seconds
1148      - turned off sponge layer by default
1149      - changed argument list of OBCS_CALC to myTime+deltaTclock
1150      - fixed about 35 bugs in obcs_external_fields_load
1151    
1152    checkpoint55c_post
1153    o obcs stuff
1154      - new runtime flags useOBCSprescribe, useOBCSbalance
1155      - re-arranged obcs_calc
1156      - moved exf_getobcs to obcs_prescibe_read
1157        obcs_prescibe_read is called after ORLANSKI stuff
1158        and independent of it (executable can contain all).
1159      - updated obcs_check
1160      - added exchanges for U,V,gU,gV for useOBCSprescribe=.TRUE.
1161        These may be necessary only if tangential velocities are
1162        prescribed at OB, not sure, needs testing.
1163    o make the MNC_CW_ADD_VATTR_* subroutines all take scalar arguments
1164      which simplifies the calls and passes the ifc check-bounds test
1165    
1166    checkpoint55b_post
1167    o add a 2D scalar, Z location, exchange_2 routine.
1168    o EXCH_UV for CS-grid: add one u,v in the corner-halo region, allows
1169      to compute vorticity on a wider stencil [e.g., vort3(0,1)&(1,0)]
1170      affects advect_cs results (for the wrong reason): update output.txt
1171    o use a more standard discretization for biharmonic viscosity ;
1172     (original version still available with #define MOM_VI_ORIGINAL_VISCA4 )
1173      affects results of dome set-up: update output.txt
1174    o fix gad_advection.F (CubedSphere part), back to version 1.23
1175    o fix bug in mom_vi_del2uv.F (CubedSphere part).
1176    
1177    checkpoint55a_post
1178    o merged code to
1179      * prescribe/read time-dependent open boundaries
1180        (works in conjunction with exf, cal)
1181      * sponge layer code for open boundaries
1182      * each boundary N/S/E/W now has its own CPP option
1183        (healthy for the adjoint)
1184    
1185    checkpoint55
1186    o up-to-date adjoint of previous breaks
1187      - natl_box_adjoint: problem for exp 12, 13: cost = 0. needs fix
1188      - global_ocean_ebm: adjoint still needs fix (TLM ok)
1189      - global_ocean.90x40x15: extended GMREDI_OPTIONS.h
1190      - carbon: * remove tr1-related adjoint verification
1191                * add ptracer as control variable
1192    o remove all tr1-related code (ALLOW_PASSIVE_TRACER)
1193      (adjoint stuff still has some tr1 'names', but all use ptracer arrays)
1194    
1195    checkpoint54f_post
1196    o in verification/carbin/ remove experiment related to
1197      ALLOW_PASSIVE_TRACER (array tr1 etc)
1198      code_ad/ input_ad/ results_ad
1199    
1200    o add two new packages
1201      - ggl90, TKE-model of Gaspar et al. (1990), Blanke+Delecluse (1993)
1202        + subject to optimization (memory)
1203      - opps, OPPS (ocean penetrative plume scheme) of Paluszkiewicz+Romea (1997)
1204        + subject to reordering (many GOTOs in the original code)
1205        + so far opps is called for every (i,j) point, and then operates in
1206          the vertical; one may want to reorder the scheme in order operate in
1207          horizontal slabs at the cost of (a lot of) memory, at least ten new 3D
1208          fields)
1209    o overhaul of IO so that we now have flags for MDSIO and/or MNC
1210      - all verification tests compile and run with linux_ia32_g77
1211      - defaults are compatible with current input files--nothing
1212        should change if you were not previously using MNC
1213      - MNC output has been added in numerous places (eg. timeave)
1214        but there are still a few writes not yet do-able with MNC
1215        (this is in progress)
1216      - flags now allow for either/or/both use of MDSIO and MNC and
1217        documentation will soon follow
1218      - numerous small formatting cleanups for ProTeX
1219    o add version info (via BUILD_INFO.h) to MNC and stdout
1220    
1221    checkpoint54e_post
1222    o add two new packages
1223      - pp81 (Packanowski and Philander, 1981), Richardson number and
1224        stratification dependent mixing
1225      - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
1226      - these scheme operate in a similar manner as KPP (without ghat, of
1227        course), however there is only one diffusivity that is used for both
1228        temperature and salinity (and passive tracers)ç
1229    o add offline package
1230    o add "verification/dic_example" which contains a dic-gchem-ptracer setup
1231      provided by Stephanie Dutkiewicz
1232    o genmake2: add ability to search for C compilers and cleanup test output
1233      - fixes recent SX-6 problems and should help with others (eg. HP-UX)
1234    
1235    checkpoint54d_post
1236    o data.diagnostics: if levels() is unspecified then ALL levels are diagnosed
1237    o bug fix in pkg/cal/cal_addtime.F for TheCalendar='model' day count is wrong,
1238      leading to additional shift by 5 days each year of integration
1239       (i.e. leading to considerable offset over the years)
1240    o update global_ocean.cs32x15/thsice: use z* + RealFW + staggerTimeStep
1241    o start with no AB and no initial filtering (staggerTimeStep):
1242      change the results of test-exp: hs94.128x64x5, hs94.1x64x5 & hs94.cs-32x32x5
1243    o move ocean specific S/R calls from forward_step.F to do_oceanic_phys.F
1244      (external loading & cpl import/export stay in forward_step.F)
1245    o update coupling interface to work with new staggerTimeStep
1246    o change MDSIO ptracers_pickup.
1247    o fix a bug in Flux deriv. vs Ts (pkg/aim_v23/phy_suflux_sice.F);
1248    o genmake2 fixes so netcdf now works on halem ("osf1_alpha_*")
1249    o bugs fixed in kpp_calc.F (ustarY) and external_forcing.F (Qsw & Partial-cell)
1250    
1251    checkpoint54c_post
1252    o replace surfaceTendency U,V,S,T,Tice,Ptr by surfaceForcing U,V,S,T,Tice,Ptr
1253      this affects (truncation error) output.txt of test-exp:
1254       global_ocean_ebm,_pressure,.cs32x15(&.thsice), lab_sea & natl_box
1255    o pkg/kpp: replace pMask by maskC to reduce memory size (one 3.D array)
1256    o change Qnet to always be the net heat flux, (+upward).
1257      affects (truncation error) output of natl_box exp.: updated
1258    o define the max number of passive tracers in PTRACERS_SIZE.h
1259    o start to test mnc routinely in exp0
1260    o add sea-ice loading (sIceLoad) as a new forcing field.
1261    
1262    checkpoint54b_post
1263    o add testreport "-j JOBS" option for parallel builds (tested and pretty
1264       impressive on Altix and Opteron systems)
1265    o diagnostics can now write NetCDF files through the mnc package
1266    o staggerTimeStep & NLFS: update pkg aim_v23 & thsice; update aim.5l_cs output
1267    o staggerTimeStep & multi-Dim-Advec: Exch(U,V) added
1268  o staggerTimeStep & NLFS: rescale T & S surface tendencies.  o staggerTimeStep & NLFS: rescale T & S surface tendencies.
1269    affects (truncation error) output of lab_sea & natl_box exp.: updated    affects (truncation error) output of lab_sea & natl_box exp.: updated
1270  o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)  o change pickup _cd & _ptracers (old pickup restart: usePickupBeforeC54=.T.)
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