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revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.722 by jmc, Thu Aug 31 15:33:43 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  
8  o moved ptracer ctrl index 17 -> 32  o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
9    
10    checkpoint58o_post
11    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
12      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
13    o change controling S/R for writing pickup file (new S/R do_write_pickup)
14      and clean-up reading/writing of pickup files.
15    o fix local version of read/write pickup (NH part) in rotating_tank/code
16    o simplify EXCH interface:
17     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
18     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
19    o added the regrid package
20    o shelfice:
21     - add a simple boundary layer scheme to reduce noise
22     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
23    
24    checkpoint58n_post
25    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
26       local variable (not in common block).
27    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
28      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
29      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
30        to work with SingleCpuIO.
31    o add "_d 0" to real constant of pkg/cfc subroutines ;
32       update exp. cfc_exemple & tutorial_cfc_offline output files.
33    o multi-threading and IO:
34      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
35        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
36      - barrier before and after reading.
37      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
38      - avoid using MDS_WRITELOCAL for LAND pkg output.
39      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
40        common-block variables ; Allows multi-threading with master-thread IO.
41    o change default MAX_NO_THREADS from 32 to 4 ;
42      and stop cleanly when MAX_NO_THREADS is too small.
43    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
44    
45    checkpoint58m_post
46    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
47       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
48    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
49       keep global_ocean.90x40x15 (for AD testing) with former secondary test
50       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
51    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
52        add MITgcm_tutorials (= code + all the tutorials)
53    o ecco, option to compute cost for total ssh (mean+anom)
54    o consistent with addition of ptracer and ssh in pkg/profiles
55    o profiles: adding ptracer and ssh
56    o testreport: change multi-test output-file name
57      (from output.txt.{name} to output.{name}.txt)
58    o profiles: now ok for mutli-tiles case
59    o seaice: add 4 parameters for different advection schemes for area,
60      (effective) seaice thickness, enthalphy, and snow height. Their default
61      is the standard parameter SEAICEadvScheme
62    o calc_gw:
63     - add cosFacU in zonal viscous flux (harmonic.visc.).
64     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
65       of tutorial_plume_on_slope.
66    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
67    o calc_gw: true flux-form, account for horizontal grid spacing.
68      update rotating_tank results, but not plume_on_slope (affected at
69      truncation level, 11 digits).
70    
71    checkpoint58l_post
72    o calc_gw:
73     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
74     - remove side-drag for now (need to fix it); update plume_on_slope results.
75     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
76    o commit code to make SST/SSS weights spatially variable
77      (based on either variable in-situ or variable initial T/S weights)
78    o pkg/ecco:
79      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
80        now based on horizontally varying weights wthetaLev, wsaltLev
81      * cost_averagesflags now returns year indices in addition to day, month
82      * sflux balance is performed on annual basis
83        (sflxumm, sfluxmm2, bal_sfluxmm)
84      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
85        including separate counting and multipliers
86    o pkg/rbcs
87      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
88    
89    checkpoint58k_post
90    o testreport:
91     - always build in dir. "build" (if not there, mkdir build instead of building
92       & running in input)
93     - run in dir run (if it exists), in build otherwise.
94     - call prepare_run (if input/prepare_run exists)
95     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
96    o pkg/exf modifications to interpolation and rotation routines for more
97       reasonable treatment of North Pole singularity: for tracers North Pole
98       value is set to northernmost zonal-mean value, for zonal velocity it is
99       set to zero, and for meridional velocity it is set to northernmost value.
100    o pkg/exf/exf_check_range.F
101     - add tile index to diagnostics and move stop statement to the very
102       end of the routine.
103    o pkg/diagnostics: (diagnostics_main_init.F)
104      define title of isomorphic variables according to the current config.
105    o pkg/thsice with pkg/seaice dynamics:
106    - fix domain of computation (interior only, required for exf) and do exchanges
107    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
108    o towards a standard way of dealing with multi-threading in MONITOR
109      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
110    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
111       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
112    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
113    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
114    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
115       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
116    o tracer advection:
117     - clean-up and simplify calc_common_factors.F
118     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
119       advection subroutine (but still not used within DST advection S/R)
120    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
121    
122    checkpoint58j_post
123    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
124      from file (collects calls previously in FORWARD_STEP)
125    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
126    o adjoint store dir. adjusted accordingly
127    o genmake2
128      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
129    
130    checkpoint58i_post
131    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
132      on wind stress (SEAICEstressFactor defaults to 1.)
133    o Total number of Timers is finite (<=40): comment out 2 non-essential one
134      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
135    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
136      on CS-grid: no longer loosing mass.
137    o exf & curvilinear-grid: no longer modify longitude xC & xG.
138    o pkg/ggl90: fix sloppy output and fix a bug
139    o pkg/seaice: added SEAICEuseEVPpickup parameter
140      - Set to false in order to start EVP solver with
141        non-EVP pickup files when using SEAICEuseEVP
142      - fix sign error in diffusion in seaice_calc_rhs
143    
144    checkpoint58h_post
145    * Modifications for bottom topography control
146      o replace hFacC by _hFacC at various places
147      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
148      o add non-self-adjoint cg2d_nsa
149      o update autodiff support routines
150      o re-initialise hfac after ctrl_depth_ini
151      o works for 5x5 box, doesnt work for global_ocean.90x40x15
152    * Adding verification for 5x5 box (4-layer) bottom topography control
153    
154    checkpoint58g_post
155    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
156       used for mean seasonal cycle, mean diurnal cycle); add an example
157       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
158    o pkg/ggl90:
159      - add parameter (minimum surface kinetic energy)
160      - fix bug (avoiding division by zero)
161    o couple pkg/thsice to pkg/seaice:
162      - modify advection in seaice to accomodate new scalar fields to be advected
163      - only muliDimAdection scheme work with seaice/thsice
164      - mapping of thsice-variables to seaice-variables, back and forth
165      - does not break the verification experiments, but does not give the
166        desired results either
167    o pkg/seaice
168      - make (default) second order advection a bit less confusing?
169    
170    checkpoint58f_post
171    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
172      to pkg/seaice):
173      - new routines thsice_map_exf and thsice_get_exf provide the interface
174      - add an additional formal parameter to thsice_solve4temp
175    o pkg/exf:
176      - add new fields wspeed, snowprecip (to be able to couple to thsice)
177      - correct Stefan-Boltzmann constant
178      - new parameter for longwave surface emittance
179      - separate some stuff from exf_bulkformulae into new routines  
180        exf_radiation, exf_wind
181      - add new parameters and constants: longwave emissivity for ocean, ice
182        and snow, evaporation parameters over ice
183      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
184        either wind from stress or stress from wind
185    o pkg/thSIce:
186    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
187    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
188       and THSICE_CALC_THICKN
189    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
190    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
191      to make debugging easier.
192    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
193    o pkg/bulk_force:
194      - clean-up comments and parameters ;
195      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
196    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
197      generate new output for test-experiment: aim.5l_cs.thSI
198    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
199      testreport accordingly
200    
201    checkpoint58e_post
202    o SEAICE_CGRID adjoint done
203    o R_STAR adjoint implemented.
204      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
205      * need to sort out init. of h0facc, etc.
206    o Make pkg/profile fully independent of ecco,cost, etc. stuff
207      to be able to use it in pure forward.
208    
209    checkpoint58d_post
210    o upgrade simple test-experiment to tutorial example:
211     step.1: duplicate the experiment and (step.2) will remove the old copy.
212      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
213      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
214      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
215      tutorial_global_oce_biogeo    <- copy of dic_example
216      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
217      tutorial_plume_on_slope       <- copy of plume_on_slope
218      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
219      tutorial_global_oce_optim     <- empty for now (David ?)
220      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
221     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
222    o correct a sign problem in cost_scat.F
223    o obcs and ptracers: fix boundary conditions for advections schemes
224      with larger stencil
225    o thsice adjoint: start
226    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
227      completeness
228    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
229      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
230    o ptracers adjoint:
231      * avoid extensive recomputatations
232      * fix missing re-init. of gptr (missed by TAF)
233    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
234      me to turn off the excessive output to STDOUT that this package produces
235    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
236      and add those terms in Vector-Invariant formulation.
237    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
238      if the control period (xx_hfluxperiod etc) is 0
239    o in profiles pkg, clean routines and fix details
240    o in ecco pkg, reading ssh data:
241      fix problem in case the model does not start at iter0=0
242    o fix mnc-pickup/restart for ptracers
243    o new package prifiles:
244      code to compute profile-based cost by Gael Forget
245      (modifs in ecco, ctrl, autodiff)
246    o Benign bug fix in initialization (spotted by M. Mazloff) of
247      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
248    
249    checkpoint58c_post
250    o adjoint: finish NLFS adjoint and provide reference output in
251      verification/global_ocean.90x40x15/results_ad_nlfs
252    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
253      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
254      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
255      with SEAICE_CGRID defined.
256    o move calendarDumps from "data" to "data.cal" and clean-up the code
257      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
258    o add useEXF & useCAL flags (for now, set in hard-coded way)
259    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
260      (were missing in NH mode, and wrong in quasihydrostatic mode).
261      waiting for Chris updated version of calc_gw to add those CALLs.
262    o fix bug in quasihydrostatic S/R ;
263      add a test for this option: global_ocean.90x40x15.qshyd
264    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
265      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
266    o add on/off flag useOffLine for package OFFLINE
267    o seaice:
268      - modify advection so that it works also on the C-grid
269      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
270        problem in multi-tile runs with C-grid
271      - add flags for clipping ice velocities and/or masking solver forcing
272      - fix drag (ocean on ice) formulation and a bug that caused noise in the
273        C-grid solver
274      - added a few comments to seaice_diffusion.F
275      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
276        are now exclusive)
277      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
278        required re-ordering the code a little:
279       + make DAIRN global variable (defined in SEAICE)
280       + move computation of the viscosities eta and zeta into a new separate
281         routine (because I need to recompute them in seaice_ocean_stress.F)
282    
283    checkpoint58b_post
284    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
285      update output.txt of exp. aim.5l_cs.thSI
286    o various mnc cleanups and improvements:
287      + shrink lookup tables by factor of ~4
288      + better error reporting when running out of lookup space
289      + able to handle longer path/file names (up to 500 chars)
290    o adjoint:
291      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
292      - TBD: "hidden" mom_vecinv recomp. in dynamics
293    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
294     (allow to differentiate between forcing components using new integer flags:
295      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
296     and add new flag to put Dissipation tendency out of Adams-Bashforth.
297    o ecco
298      - enable trend removal from SSH anomaly obs.
299    o adjoint
300      - a fix for PmEpR when #undef EXACT_CONSERV
301      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
302      - try to fix "hidden" recomp. in forward_step for NLFS
303        (NLFS seems broken sometimes after I checked it in)
304    o seaice:
305     - add c-grid version of the dynamic solver:
306       + three new routines that are the c-grid substitute lsr, dynsolver
307         and ostres
308       + put a few fields that were local to dynsolver into global common
309         blocks, so that I can move the computation of stresses etc into
310         seaice_lsr (saves coding but may break the adjoint).
311     - replace more hardwired parameters by runtime parameters
312     - add ice masks that mask the rhs of the implicit solvers where there
313       is no ice (commented out in seaice_dynsolver, because i am not sure
314       if this works properly), eventually this should replace the clipping
315       of ice velocities in seaice_dynsolver to +/-40cm/s.
316    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
317      include it only where its needed
318    o move balancing of fluxes before the call of external_forcing_surf
319    o seaice:
320      - correct units of turning angles (now they are really in degrees)
321      - move computation of GWATX/Y out of main routine into dynsolver
322      - initialize GWATX/Y in seaice_init
323    o Apply mask on Fresh-Water flux (needed for SSH forcing).
324      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
325    o seaice: add runtime flags for turning angles (default to zero)
326    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
327      and trend from exf forcing and ctrl control adjustments
328    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
329      (since checkpoint57x_post)
330    o change the default rotation period to 86164.s = the Earth rotation
331    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
332      and based on a reference stratification. Tested within hs94.cs-32x32x5.
333    o seaice advection: add code for choosing between the default (2nd order
334      central differences) and multiDim advection schemes provided by
335      pkg/generic_advdiff
336    o seaice:
337      - removed all references to SEAICE_GRID.h fields from
338        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
339        (cubed-sphere configuration will change a little)
340      - grid computations in seaice_init are obsolete now.
341      - cleaned up code a little so that is easier to read (hopefully).
342      - added new (better?) discretizations of default advection and diffusion
343        (turn on with SEAICEuseFluxForm)
344      - replace 1 in 3d global fields by kSurface in growth.F
345      
346    checkpoint58a_post
347    o seaice:
348      - bug fix in advect.F
349    o shelfice:
350      - separate shelfice load anomaly from pload (breaks with time
351        dependent forcing), => introduce constant field shelficeLoadAnomaly.
352        Its default is 0., but it may be computed more cleverly from (unknown)
353        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
354        done offline. A good approximation of the pressure load anomaly is
355        necessary to avoid large initial adjustment processes underneath
356        deep-reaching shelfice.
357      - small fix in ISOMIP shelfice_thermodynamics
358      - add more sophisticated thermodynamics of Hellmer (1989), this is
359        now the default
360      - give a few constants more intuitive names
361    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
362      if bulk formulae are used in long integration (especially EmPmR). Turn
363      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
364      if balancePrintMean, the imbalance that is substracted is printed to
365      STDOUT.
366    o fix bug (typo) in obcs_apply_eta.F
367    o add a new package shelfice which enables us to model the circulation
368      underneath shelf-ice with draughts of hundreds of meters.
369     - works
370     - to do: + include improved thermodynamics
371              + check whether kSurfC (from model/inc/SURFACE.h) can be used
372                instead of new field kTopC
373              + can we use topoFile, Ro_surf and existing code in ini_depth.F
374                instead of new field R_shelfIce and new code in ini_depth.F
375                and ini_mask_etc.F?
376              + adjust vertical mixing schemes?
377    o seaice pkg:
378     - add a cpp-flag to include a simple formula for a salinity dependent
379       freezing point of sea water at the surface
380     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
381       meridional stresses are now different (and hopefully correct)
382    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
383       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
384       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
385    o pkg/diagnostics: add options and parameters for regional-statistics
386       diagnostics ; define regions by reading a region-mask from a file
387       (might add other options later)
388    o pkg/bulk_force:
389     - add option and parameters to use AIM surface-flux formulae.
390     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
391       others forcing fields (defined in PARM05, parameter file "data") are loaded
392       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
393     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
394     - use the right EXCH call for uwind,vwind (to work on CS-grid).
395     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
396       and parameters (note: calcWindStress replaces .NOT.readwindstress).
397     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
398    
399    checkpoint58
400    o add "--embed-source" option to genmake2 which, when the supporting
401      tools can be compiled (as determined by genmake2) will turn on the
402      embed_files package which then embeds the entire MITgcm source code
403      (*.[fFhc] + Makefile) used for the build within the executable
404      - requested by CNH but off by default
405      - adds a paltry <9MB to the mitgcmuv executable in most cases
406      - only writes the output when useEMBEDSRC in eedata is true
407    o clean up 3-dim. relaxation codes:
408      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
409      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
410      * Thanks to Tom Haine for testing!
411    
412    checkpoint57z_post
413    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
414      affects output (@ truncation level) of exp. plume_on_slope ; updated.
415    o fix the pickup behavior for obcs in combination with ptracers
416    o fix a bug in ptracers_external_fields_load
417    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
418      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
419    o transfered surface NH pressure to eta field (if exactConserv).
420    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
421         and update lab_sea output.txt file.
422    o completing 3-dim. relaxation code: additional term
423         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
424      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
425      * At compile time, in "EXF_OPTIONS.h" set
426          #define  ALLOW_CLIMTEMP_RELAXATION
427          #define  ALLOW_CLIMSALT_RELAXATION
428      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
429          tauThetaClimRelax3Dim = 15552000.0,
430          tauSaltClimRelax3Dim  = 15552000.0,
431      * 3 cases:
432          1) Use a constant-in-time 3-dim. field
433          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
434          3) Real-time relax. to time-evolving prescribed field
435    o Adding Laplacian-type smoothness constraint on
436      initial and boundary (forcing) controls (ic, bc)
437      * enable at compile-time via
438        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
439      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
440      * Absolute scale somewhat unclear so far
441      * no area weighting was included since no other cost term does so far
442    
443    checkpoint57y_post
444    First step for a NLFS adjoint
445    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
446    o new init. routines for calc_r_star, calc_surf_dr
447    o still need to deal with ini_masks_etc
448    o testreport seemed happy
449    checkpoint57y_pre
450    
451    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
452    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
453    o add new offset feature to offline pkg (plus minor cleanup)
454    o cfc fixes for final year of integration
455    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
456      be in GCHEM_OPTIONS).
457    
458    checkpoint57x_post
459    o fix testreport Pb in multiple test experiment.
460    o cleanup our namelist syntax in verification:
461      - make it more F95 standards compliant (some work still needed)
462      - allows the vast majority of our tests to work with gfortran
463    o Non-Hydrostatic:
464     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
465     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
466    o Allow to apply AB on T,S rather than on AB(gT,gS):
467     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
468     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
469       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
470     - need a "clever" read_pickup to restart from the other AB formulation
471    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
472    o remove some unused variables (reduces number of compiler warnings)
473    o adjoint
474      * Disable useVariableViscosity for adjoint for time being
475        (there are a number of extensive recomputations)
476      * Initialize certain variables needed for adjoint
477    
478    checkpoint57w_post
479    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
480                 fix the singleCpuIO RS version of MDSWRITEFIELD
481       and add a WARNING if using globalFiles=T with multi-processors.
482    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
483      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
484    o tracer advection scheme:
485      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
486       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
487       was not very convenient).
488      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
489       (further tests needed for the implicit DST & Flux-Limiter schemes).
490    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
491      and sRef for convenience, handy, when you want to initialize
492      ptracers in a large domain with a constant non-zero value. Also,
493      untangle ptracers_init.F a little.
494    
495    checkpoint57v_post
496    o change dome exp. to use variable viscosity in side-drag terms.
497    o remove all the files from the cfc_offline test since they are now
498      incorporated into tutorial_cfc_offline which has been producing
499      identical results for a few days of testing
500    o add new parameter: sideDragFactor to enable half-slip-side BC
501      and change side-drag S/R to use viscosity from mom_calc_visc
502      (can switch back by setting sideDragFactor=0.); affects results at
503      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
504       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
505    o vorticity & strain are now computed without masking, to account for
506      no-slip-side BC in variable viscosity calculation ; mask is applied
507      anyway later on, before computing advection/coriolis terms.
508    o modify exp4 to test new obcs support for reading from external files
509      and for passive tracers
510    o fix behavior of ptracers_monitor when monitor output is written to a
511      netcdf-file; still not independent of monitor.F (writes in the same
512      file).
513    o change default value of tRef (put a uniform, meaningful value for ocean
514      & atmos) and initialize sRef (was missing, as Martin mentioned).
515    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
516      to be proportional to enstrophy dissipation length.  Thus,
517       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
518      This is now consistent with Smagorinsky and with the manual.
519    
520    checkpoint57u_post
521    o OBCS and PTRACERS: add open boundary support for passive tracers
522      - either use homogenous (pseudo) v.Neumann conditions or prescribe
523        OB-values from file; this is not different from the way theta and salinity
524        are treated
525      - however, Orlanski-radiation conditions are not supported, and the model
526        will stop if you use pTracers and Orlanski at the same time.
527      - beefed up the rountine obcs_external_fields_load: now only those open
528        boundary values are overwritten with values from files for which there
529        are really files, otherwise the OB-fields remain untouched. This makes
530        it possible to use different OBs at different ends of the domain (as
531        with EXF)
532    o reduce number of exch calls in shap_filt (s2).
533    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
534      truncation level) 4/5 MLAdjust test results (11&12 digits match).
535    
536    checkpoint57t_post
537    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
538    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
539      same truncation, independent of the face number: affects affects several
540      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
541    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
542      note that biharmonic viscosity + no-slip was not tested in any experiment.
543    o fix bug in non-linear free-surf side-drag ; generate new output for
544      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
545    o make mnc honor the writeBinaryPrec flag for most kinds of output
546    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
547    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
548      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
549    o add brackets in multi-terms sum to get same truncation, independent of
550      the face number (manage to get exactly same value of gU,gV at the cs-edge)
551      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
552    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
553      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
554      a maximum grid-scale Reynolds number.  Also, changes all length calculations
555      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
556      Suggested values of viscosity parameters found in mom_calc_visc.
557      Many new viscosity diagnostics available.
558    
559    checkpoint57s_post
560    o Add clearing-house for viscosity calculations, mom_calc_visc and
561      correct numerous bugs in LeithD and Smagorinsky discretizations.  
562      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
563      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
564      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
565      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
566      The Strain-Tension form is now called with useStrainTensonVisc=.true.
567      ViscAhStrain and viscAhTension are now retired.
568    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
569    o In response to JMC's bug report, genmake2 now ignores any soft-links
570      that it finds in the *current* directory when searching for files.
571      Soft-links found in any other source directories will still work as
572      they did before.
573    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
574      a C routine to unlimit the stack size
575    o mnc-ify pkg/aim snapshot vars
576    o mnc-ify pkg/land as requested by Daniel
577    o various changes to mnc including:
578      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
579      - output can now be grouped so that all files within a group
580          change the ITER portion of their names in lock-step together
581      - can now read ("global") PER-FACE (in addition to PER-TILE) files
582          and works with both EXCH1 and EXCH2 (but needs more testing)
583      - writing works for all verification test cases w/ g77 on Linux
584    
585    checkpoint57r_post
586    o make MNC variable initialization happen earlier
587    o add diagnostics for (almost) each term of the momentum Eq.
588    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
589    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
590    o remove MINIMAL_TAVE_OUTPUT option ;
591      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
592    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
593      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
594    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
595    o add time-dependent SST, SSS control
596    o cost terms in ecco/ modularized (new cost_generic.F)
597    o cost_averages routines are modularized (new cost_averagesgeneric.F)
598    o new infrastructure for seaice model vs. obs misfits in seaice/
599      * driver from the_main_loop.F is seaice_cost_driver.F
600      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
601      * gradient check in Exp. 6a of natl_box_adjoint/
602    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
603      (see README file)
604    
605    checkpoint57q_post
606    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
607    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
608      - bug was reported by Jean-Michel and Ian Fenty
609    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
610      update exp. cpl_aim+ocn output.
611    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
612      Needed for high-res. runs with large global files
613      to be able to limit tapelev size
614    o Changed some tests for adjoint:
615      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
616      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
617      * global_ocean.90x40x15/ back to default 3-level checkpointing
618    o Modifications to enable scripted COMMON to MODULE conversion
619      * verification/OpenAD/code/ has necessary scripts and description;
620      * converts, compiles and runs successfully;
621    
622    checkpoint57p_post
623    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
624    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
625      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
626    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
627    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
628      (was already the case for dissipation with mom_vecinv,
629       and also the case for grad.PhiHyd when staggered-timeStep)
630      This will allow to put dissipation out-off the AB time-stepping.
631     Unfortunately, affects truncation error. Update output of exp. that "fails"
632      (cg2d matching number) and leave the others for later: front_relax(10),
633      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
634      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
635    
636    checkpoint57o_post
637    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
638      (2) its ready to be documented during the 20050801 DocFest
639    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
640      for ideal_2D_oce and lab_sea on linux_ia32_g77
641    o set to #undef CTRL_SET_OLD_MAXCVARS_30
642      in global1x1_tot/code_seaice_adj to access indices 32, 33
643      (worth another tag)
644    
645    checkpoint57n_post
646    o adding precip control xx_precip 32
647    o adding swflux control xx_swflux 33
648    o Replacing 10 forcing penalty cost routines by 1 generic.
649    o Implementing partitioning in time-mean and variable adjustment
650      for atmos. state.
651    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
652  o in natl_box_adjoint:  o in natl_box_adjoint:
653    * updated: results_bulk/    * updated exp 1 to 10
654    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
655    o updated global1x1/*_seaice_adj/
656      to incorporate latest changes
657    o enable useSingleCpuIO for mdsio vector routines
658      (applies in particular to tapelev I/O)
659    o removed inefficient K-loop in all active_file*control*.F
660    
661  checkpoint57m_post  checkpoint57m_post
662  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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