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revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.743 by edhill, Sun Nov 5 18:36:05 2006 UTC
# Line 3  $Name$ Line 3  $Name$
3    
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    o add ability to read bathy, salt, and theta using MNC (off by def)
7    o add flooding algorithm and advection of HSNOW for pkg/seaice;
8      both are turned off by default and do no change any results
9    o seaice advection with pkg/thsice: a step toward the use of non-linear
10      advection scheme, but #ifdef or commented out for now (requires more EXCH).
11    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
12      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
13      in natl_box (affects results @ truncation level: update output.txt)
14    o multi-threading and IO:
15      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
16      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
17        (needed to work with SingleCpuIO): tested in all verif. exp.
18    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
19      affects the results (but none of the verification test uses this scheme).
20    o Adding some pkg/diagnostics capability to pkg/seaice
21      (will certainly be subject to changes)
22    o ctrl: adding new control variables:
23      lwflux, lwdown, evap, snowprecip, apressure, runoff
24    
25  o adding precip control xx_precip  checkpoint58q_post
26  o moved ptracer ctrl index 17 -> 32  o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
27      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
28      high_res_cube configuration by 4% on Columbia.
29    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
30      add (in global_with_exf/code) a version of EXF_INTERP_READ without
31      dynamical allocation (seems to work in multi-threaded).
32    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
33      single CPU io) so that TAF does not have to see EESUPPORT.h
34    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
35    
36    checkpoint58p_post
37    o obcs: stop if obcs is used with useCDscheme = .true.
38    o shelfice:
39     - fix a sign error so that no slip at shelfice interface works
40     - remove stop for combination non-hydrostatic code and shelfice. That does
41       not mean, that the results are correct, but at least they are numerically
42       stable
43    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
44    o added adjoint exch routined for all exch*3d* routines
45      and updated flow directives
46    
47    checkpoint58o_post
48    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
49      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
50    o change controling S/R for writing pickup file (new S/R do_write_pickup)
51      and clean-up reading/writing of pickup files.
52    o fix local version of read/write pickup (NH part) in rotating_tank/code
53    o simplify EXCH interface:
54     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
55     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
56    o added the regrid package
57    o shelfice:
58     - add a simple boundary layer scheme to reduce noise
59     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
60    
61    checkpoint58n_post
62    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
63       local variable (not in common block).
64    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
65      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
66      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
67        to work with SingleCpuIO.
68    o add "_d 0" to real constant of pkg/cfc subroutines ;
69       update exp. cfc_exemple & tutorial_cfc_offline output files.
70    o multi-threading and IO:
71      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
72        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
73      - barrier before and after reading.
74      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
75      - avoid using MDS_WRITELOCAL for LAND pkg output.
76      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
77        common-block variables ; Allows multi-threading with master-thread IO.
78    o change default MAX_NO_THREADS from 32 to 4 ;
79      and stop cleanly when MAX_NO_THREADS is too small.
80    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
81    
82    checkpoint58m_post
83    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
84       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
85    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
86       keep global_ocean.90x40x15 (for AD testing) with former secondary test
87       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
88    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
89        add MITgcm_tutorials (= code + all the tutorials)
90    o ecco, option to compute cost for total ssh (mean+anom)
91    o consistent with addition of ptracer and ssh in pkg/profiles
92    o profiles: adding ptracer and ssh
93    o testreport: change multi-test output-file name
94      (from output.txt.{name} to output.{name}.txt)
95    o profiles: now ok for mutli-tiles case
96    o seaice: add 4 parameters for different advection schemes for area,
97      (effective) seaice thickness, enthalphy, and snow height. Their default
98      is the standard parameter SEAICEadvScheme
99    o calc_gw:
100     - add cosFacU in zonal viscous flux (harmonic.visc.).
101     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
102       of tutorial_plume_on_slope.
103    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
104    o calc_gw: true flux-form, account for horizontal grid spacing.
105      update rotating_tank results, but not plume_on_slope (affected at
106      truncation level, 11 digits).
107    
108    checkpoint58l_post
109    o calc_gw:
110     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
111     - remove side-drag for now (need to fix it); update plume_on_slope results.
112     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
113    o commit code to make SST/SSS weights spatially variable
114      (based on either variable in-situ or variable initial T/S weights)
115    o pkg/ecco:
116      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
117        now based on horizontally varying weights wthetaLev, wsaltLev
118      * cost_averagesflags now returns year indices in addition to day, month
119      * sflux balance is performed on annual basis
120        (sflxumm, sfluxmm2, bal_sfluxmm)
121      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
122        including separate counting and multipliers
123    o pkg/rbcs
124      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
125    
126    checkpoint58k_post
127    o testreport:
128     - always build in dir. "build" (if not there, mkdir build instead of building
129       & running in input)
130     - run in dir run (if it exists), in build otherwise.
131     - call prepare_run (if input/prepare_run exists)
132     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
133    o pkg/exf modifications to interpolation and rotation routines for more
134       reasonable treatment of North Pole singularity: for tracers North Pole
135       value is set to northernmost zonal-mean value, for zonal velocity it is
136       set to zero, and for meridional velocity it is set to northernmost value.
137    o pkg/exf/exf_check_range.F
138     - add tile index to diagnostics and move stop statement to the very
139       end of the routine.
140    o pkg/diagnostics: (diagnostics_main_init.F)
141      define title of isomorphic variables according to the current config.
142    o pkg/thsice with pkg/seaice dynamics:
143    - fix domain of computation (interior only, required for exf) and do exchanges
144    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
145    o towards a standard way of dealing with multi-threading in MONITOR
146      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
147    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
148       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
149    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
150    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
151    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
152       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
153    o tracer advection:
154     - clean-up and simplify calc_common_factors.F
155     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
156       advection subroutine (but still not used within DST advection S/R)
157    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
158    
159    checkpoint58j_post
160    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
161      from file (collects calls previously in FORWARD_STEP)
162    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
163    o adjoint store dir. adjusted accordingly
164    o genmake2
165      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
166    
167    checkpoint58i_post
168    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
169      on wind stress (SEAICEstressFactor defaults to 1.)
170    o Total number of Timers is finite (<=40): comment out 2 non-essential one
171      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
172    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
173      on CS-grid: no longer loosing mass.
174    o exf & curvilinear-grid: no longer modify longitude xC & xG.
175    o pkg/ggl90: fix sloppy output and fix a bug
176    o pkg/seaice: added SEAICEuseEVPpickup parameter
177      - Set to false in order to start EVP solver with
178        non-EVP pickup files when using SEAICEuseEVP
179      - fix sign error in diffusion in seaice_calc_rhs
180    
181    checkpoint58h_post
182    * Modifications for bottom topography control
183      o replace hFacC by _hFacC at various places
184      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
185      o add non-self-adjoint cg2d_nsa
186      o update autodiff support routines
187      o re-initialise hfac after ctrl_depth_ini
188      o works for 5x5 box, doesnt work for global_ocean.90x40x15
189    * Adding verification for 5x5 box (4-layer) bottom topography control
190    
191    checkpoint58g_post
192    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
193       used for mean seasonal cycle, mean diurnal cycle); add an example
194       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
195    o pkg/ggl90:
196      - add parameter (minimum surface kinetic energy)
197      - fix bug (avoiding division by zero)
198    o couple pkg/thsice to pkg/seaice:
199      - modify advection in seaice to accomodate new scalar fields to be advected
200      - only muliDimAdection scheme work with seaice/thsice
201      - mapping of thsice-variables to seaice-variables, back and forth
202      - does not break the verification experiments, but does not give the
203        desired results either
204    o pkg/seaice
205      - make (default) second order advection a bit less confusing?
206    
207    checkpoint58f_post
208    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
209      to pkg/seaice):
210      - new routines thsice_map_exf and thsice_get_exf provide the interface
211      - add an additional formal parameter to thsice_solve4temp
212    o pkg/exf:
213      - add new fields wspeed, snowprecip (to be able to couple to thsice)
214      - correct Stefan-Boltzmann constant
215      - new parameter for longwave surface emittance
216      - separate some stuff from exf_bulkformulae into new routines  
217        exf_radiation, exf_wind
218      - add new parameters and constants: longwave emissivity for ocean, ice
219        and snow, evaporation parameters over ice
220      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
221        either wind from stress or stress from wind
222    o pkg/thSIce:
223    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
224    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
225       and THSICE_CALC_THICKN
226    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
227    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
228      to make debugging easier.
229    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
230    o pkg/bulk_force:
231      - clean-up comments and parameters ;
232      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
233    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
234      generate new output for test-experiment: aim.5l_cs.thSI
235    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
236      testreport accordingly
237    
238    checkpoint58e_post
239    o SEAICE_CGRID adjoint done
240    o R_STAR adjoint implemented.
241      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
242      * need to sort out init. of h0facc, etc.
243    o Make pkg/profile fully independent of ecco,cost, etc. stuff
244      to be able to use it in pure forward.
245    
246    checkpoint58d_post
247    o upgrade simple test-experiment to tutorial example:
248     step.1: duplicate the experiment and (step.2) will remove the old copy.
249      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
250      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
251      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
252      tutorial_global_oce_biogeo    <- copy of dic_example
253      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
254      tutorial_plume_on_slope       <- copy of plume_on_slope
255      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
256      tutorial_global_oce_optim     <- empty for now (David ?)
257      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
258     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
259    o correct a sign problem in cost_scat.F
260    o obcs and ptracers: fix boundary conditions for advections schemes
261      with larger stencil
262    o thsice adjoint: start
263    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
264      completeness
265    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
266      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
267    o ptracers adjoint:
268      * avoid extensive recomputatations
269      * fix missing re-init. of gptr (missed by TAF)
270    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
271      me to turn off the excessive output to STDOUT that this package produces
272    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
273      and add those terms in Vector-Invariant formulation.
274    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
275      if the control period (xx_hfluxperiod etc) is 0
276    o in profiles pkg, clean routines and fix details
277    o in ecco pkg, reading ssh data:
278      fix problem in case the model does not start at iter0=0
279    o fix mnc-pickup/restart for ptracers
280    o new package prifiles:
281      code to compute profile-based cost by Gael Forget
282      (modifs in ecco, ctrl, autodiff)
283    o Benign bug fix in initialization (spotted by M. Mazloff) of
284      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
285    
286    checkpoint58c_post
287    o adjoint: finish NLFS adjoint and provide reference output in
288      verification/global_ocean.90x40x15/results_ad_nlfs
289    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
290      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
291      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
292      with SEAICE_CGRID defined.
293    o move calendarDumps from "data" to "data.cal" and clean-up the code
294      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
295    o add useEXF & useCAL flags (for now, set in hard-coded way)
296    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
297      (were missing in NH mode, and wrong in quasihydrostatic mode).
298      waiting for Chris updated version of calc_gw to add those CALLs.
299    o fix bug in quasihydrostatic S/R ;
300      add a test for this option: global_ocean.90x40x15.qshyd
301    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
302      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
303    o add on/off flag useOffLine for package OFFLINE
304    o seaice:
305      - modify advection so that it works also on the C-grid
306      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
307        problem in multi-tile runs with C-grid
308      - add flags for clipping ice velocities and/or masking solver forcing
309      - fix drag (ocean on ice) formulation and a bug that caused noise in the
310        C-grid solver
311      - added a few comments to seaice_diffusion.F
312      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
313        are now exclusive)
314      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
315        required re-ordering the code a little:
316       + make DAIRN global variable (defined in SEAICE)
317       + move computation of the viscosities eta and zeta into a new separate
318         routine (because I need to recompute them in seaice_ocean_stress.F)
319    
320    checkpoint58b_post
321    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
322      update output.txt of exp. aim.5l_cs.thSI
323    o various mnc cleanups and improvements:
324      + shrink lookup tables by factor of ~4
325      + better error reporting when running out of lookup space
326      + able to handle longer path/file names (up to 500 chars)
327    o adjoint:
328      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
329      - TBD: "hidden" mom_vecinv recomp. in dynamics
330    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
331     (allow to differentiate between forcing components using new integer flags:
332      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
333     and add new flag to put Dissipation tendency out of Adams-Bashforth.
334    o ecco
335      - enable trend removal from SSH anomaly obs.
336    o adjoint
337      - a fix for PmEpR when #undef EXACT_CONSERV
338      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
339      - try to fix "hidden" recomp. in forward_step for NLFS
340        (NLFS seems broken sometimes after I checked it in)
341    o seaice:
342     - add c-grid version of the dynamic solver:
343       + three new routines that are the c-grid substitute lsr, dynsolver
344         and ostres
345       + put a few fields that were local to dynsolver into global common
346         blocks, so that I can move the computation of stresses etc into
347         seaice_lsr (saves coding but may break the adjoint).
348     - replace more hardwired parameters by runtime parameters
349     - add ice masks that mask the rhs of the implicit solvers where there
350       is no ice (commented out in seaice_dynsolver, because i am not sure
351       if this works properly), eventually this should replace the clipping
352       of ice velocities in seaice_dynsolver to +/-40cm/s.
353    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
354      include it only where its needed
355    o move balancing of fluxes before the call of external_forcing_surf
356    o seaice:
357      - correct units of turning angles (now they are really in degrees)
358      - move computation of GWATX/Y out of main routine into dynsolver
359      - initialize GWATX/Y in seaice_init
360    o Apply mask on Fresh-Water flux (needed for SSH forcing).
361      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
362    o seaice: add runtime flags for turning angles (default to zero)
363    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
364      and trend from exf forcing and ctrl control adjustments
365    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
366      (since checkpoint57x_post)
367    o change the default rotation period to 86164.s = the Earth rotation
368    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
369      and based on a reference stratification. Tested within hs94.cs-32x32x5.
370    o seaice advection: add code for choosing between the default (2nd order
371      central differences) and multiDim advection schemes provided by
372      pkg/generic_advdiff
373    o seaice:
374      - removed all references to SEAICE_GRID.h fields from
375        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
376        (cubed-sphere configuration will change a little)
377      - grid computations in seaice_init are obsolete now.
378      - cleaned up code a little so that is easier to read (hopefully).
379      - added new (better?) discretizations of default advection and diffusion
380        (turn on with SEAICEuseFluxForm)
381      - replace 1 in 3d global fields by kSurface in growth.F
382      
383    checkpoint58a_post
384    o seaice:
385      - bug fix in advect.F
386    o shelfice:
387      - separate shelfice load anomaly from pload (breaks with time
388        dependent forcing), => introduce constant field shelficeLoadAnomaly.
389        Its default is 0., but it may be computed more cleverly from (unknown)
390        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
391        done offline. A good approximation of the pressure load anomaly is
392        necessary to avoid large initial adjustment processes underneath
393        deep-reaching shelfice.
394      - small fix in ISOMIP shelfice_thermodynamics
395      - add more sophisticated thermodynamics of Hellmer (1989), this is
396        now the default
397      - give a few constants more intuitive names
398    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
399      if bulk formulae are used in long integration (especially EmPmR). Turn
400      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
401      if balancePrintMean, the imbalance that is substracted is printed to
402      STDOUT.
403    o fix bug (typo) in obcs_apply_eta.F
404    o add a new package shelfice which enables us to model the circulation
405      underneath shelf-ice with draughts of hundreds of meters.
406     - works
407     - to do: + include improved thermodynamics
408              + check whether kSurfC (from model/inc/SURFACE.h) can be used
409                instead of new field kTopC
410              + can we use topoFile, Ro_surf and existing code in ini_depth.F
411                instead of new field R_shelfIce and new code in ini_depth.F
412                and ini_mask_etc.F?
413              + adjust vertical mixing schemes?
414    o seaice pkg:
415     - add a cpp-flag to include a simple formula for a salinity dependent
416       freezing point of sea water at the surface
417     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
418       meridional stresses are now different (and hopefully correct)
419    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
420       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
421       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
422    o pkg/diagnostics: add options and parameters for regional-statistics
423       diagnostics ; define regions by reading a region-mask from a file
424       (might add other options later)
425    o pkg/bulk_force:
426     - add option and parameters to use AIM surface-flux formulae.
427     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
428       others forcing fields (defined in PARM05, parameter file "data") are loaded
429       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
430     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
431     - use the right EXCH call for uwind,vwind (to work on CS-grid).
432     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
433       and parameters (note: calcWindStress replaces .NOT.readwindstress).
434     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
435    
436    checkpoint58
437    o add "--embed-source" option to genmake2 which, when the supporting
438      tools can be compiled (as determined by genmake2) will turn on the
439      embed_files package which then embeds the entire MITgcm source code
440      (*.[fFhc] + Makefile) used for the build within the executable
441      - requested by CNH but off by default
442      - adds a paltry <9MB to the mitgcmuv executable in most cases
443      - only writes the output when useEMBEDSRC in eedata is true
444    o clean up 3-dim. relaxation codes:
445      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
446      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
447      * Thanks to Tom Haine for testing!
448    
449    checkpoint57z_post
450    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
451      affects output (@ truncation level) of exp. plume_on_slope ; updated.
452    o fix the pickup behavior for obcs in combination with ptracers
453    o fix a bug in ptracers_external_fields_load
454    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
455      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
456    o transfered surface NH pressure to eta field (if exactConserv).
457    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
458         and update lab_sea output.txt file.
459    o completing 3-dim. relaxation code: additional term
460         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
461      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
462      * At compile time, in "EXF_OPTIONS.h" set
463          #define  ALLOW_CLIMTEMP_RELAXATION
464          #define  ALLOW_CLIMSALT_RELAXATION
465      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
466          tauThetaClimRelax3Dim = 15552000.0,
467          tauSaltClimRelax3Dim  = 15552000.0,
468      * 3 cases:
469          1) Use a constant-in-time 3-dim. field
470          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
471          3) Real-time relax. to time-evolving prescribed field
472    o Adding Laplacian-type smoothness constraint on
473      initial and boundary (forcing) controls (ic, bc)
474      * enable at compile-time via
475        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
476      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
477      * Absolute scale somewhat unclear so far
478      * no area weighting was included since no other cost term does so far
479    
480    checkpoint57y_post
481    First step for a NLFS adjoint
482    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
483    o new init. routines for calc_r_star, calc_surf_dr
484    o still need to deal with ini_masks_etc
485    o testreport seemed happy
486    checkpoint57y_pre
487    
488    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
489    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
490    o add new offset feature to offline pkg (plus minor cleanup)
491    o cfc fixes for final year of integration
492    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
493      be in GCHEM_OPTIONS).
494    
495    checkpoint57x_post
496    o fix testreport Pb in multiple test experiment.
497    o cleanup our namelist syntax in verification:
498      - make it more F95 standards compliant (some work still needed)
499      - allows the vast majority of our tests to work with gfortran
500    o Non-Hydrostatic:
501     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
502     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
503    o Allow to apply AB on T,S rather than on AB(gT,gS):
504     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
505     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
506       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
507     - need a "clever" read_pickup to restart from the other AB formulation
508    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
509    o remove some unused variables (reduces number of compiler warnings)
510    o adjoint
511      * Disable useVariableViscosity for adjoint for time being
512        (there are a number of extensive recomputations)
513      * Initialize certain variables needed for adjoint
514    
515    checkpoint57w_post
516    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
517                 fix the singleCpuIO RS version of MDSWRITEFIELD
518       and add a WARNING if using globalFiles=T with multi-processors.
519    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
520      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
521    o tracer advection scheme:
522      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
523       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
524       was not very convenient).
525      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
526       (further tests needed for the implicit DST & Flux-Limiter schemes).
527    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
528      and sRef for convenience, handy, when you want to initialize
529      ptracers in a large domain with a constant non-zero value. Also,
530      untangle ptracers_init.F a little.
531    
532    checkpoint57v_post
533    o change dome exp. to use variable viscosity in side-drag terms.
534    o remove all the files from the cfc_offline test since they are now
535      incorporated into tutorial_cfc_offline which has been producing
536      identical results for a few days of testing
537    o add new parameter: sideDragFactor to enable half-slip-side BC
538      and change side-drag S/R to use viscosity from mom_calc_visc
539      (can switch back by setting sideDragFactor=0.); affects results at
540      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
541       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
542    o vorticity & strain are now computed without masking, to account for
543      no-slip-side BC in variable viscosity calculation ; mask is applied
544      anyway later on, before computing advection/coriolis terms.
545    o modify exp4 to test new obcs support for reading from external files
546      and for passive tracers
547    o fix behavior of ptracers_monitor when monitor output is written to a
548      netcdf-file; still not independent of monitor.F (writes in the same
549      file).
550    o change default value of tRef (put a uniform, meaningful value for ocean
551      & atmos) and initialize sRef (was missing, as Martin mentioned).
552    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
553      to be proportional to enstrophy dissipation length.  Thus,
554       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
555      This is now consistent with Smagorinsky and with the manual.
556    
557    checkpoint57u_post
558    o OBCS and PTRACERS: add open boundary support for passive tracers
559      - either use homogenous (pseudo) v.Neumann conditions or prescribe
560        OB-values from file; this is not different from the way theta and salinity
561        are treated
562      - however, Orlanski-radiation conditions are not supported, and the model
563        will stop if you use pTracers and Orlanski at the same time.
564      - beefed up the rountine obcs_external_fields_load: now only those open
565        boundary values are overwritten with values from files for which there
566        are really files, otherwise the OB-fields remain untouched. This makes
567        it possible to use different OBs at different ends of the domain (as
568        with EXF)
569    o reduce number of exch calls in shap_filt (s2).
570    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
571      truncation level) 4/5 MLAdjust test results (11&12 digits match).
572    
573    checkpoint57t_post
574    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
575    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
576      same truncation, independent of the face number: affects affects several
577      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
578    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
579      note that biharmonic viscosity + no-slip was not tested in any experiment.
580    o fix bug in non-linear free-surf side-drag ; generate new output for
581      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
582    o make mnc honor the writeBinaryPrec flag for most kinds of output
583    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
584    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
585      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
586    o add brackets in multi-terms sum to get same truncation, independent of
587      the face number (manage to get exactly same value of gU,gV at the cs-edge)
588      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
589    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
590      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
591      a maximum grid-scale Reynolds number.  Also, changes all length calculations
592      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
593      Suggested values of viscosity parameters found in mom_calc_visc.
594      Many new viscosity diagnostics available.
595    
596    checkpoint57s_post
597    o Add clearing-house for viscosity calculations, mom_calc_visc and
598      correct numerous bugs in LeithD and Smagorinsky discretizations.  
599      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
600      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
601      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
602      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
603      The Strain-Tension form is now called with useStrainTensonVisc=.true.
604      ViscAhStrain and viscAhTension are now retired.
605    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
606    o In response to JMC's bug report, genmake2 now ignores any soft-links
607      that it finds in the *current* directory when searching for files.
608      Soft-links found in any other source directories will still work as
609      they did before.
610    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
611      a C routine to unlimit the stack size
612    o mnc-ify pkg/aim snapshot vars
613    o mnc-ify pkg/land as requested by Daniel
614    o various changes to mnc including:
615      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
616      - output can now be grouped so that all files within a group
617          change the ITER portion of their names in lock-step together
618      - can now read ("global") PER-FACE (in addition to PER-TILE) files
619          and works with both EXCH1 and EXCH2 (but needs more testing)
620      - writing works for all verification test cases w/ g77 on Linux
621    
622    checkpoint57r_post
623    o make MNC variable initialization happen earlier
624    o add diagnostics for (almost) each term of the momentum Eq.
625    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
626    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
627    o remove MINIMAL_TAVE_OUTPUT option ;
628      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
629    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
630      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
631    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
632    o add time-dependent SST, SSS control
633    o cost terms in ecco/ modularized (new cost_generic.F)
634    o cost_averages routines are modularized (new cost_averagesgeneric.F)
635    o new infrastructure for seaice model vs. obs misfits in seaice/
636      * driver from the_main_loop.F is seaice_cost_driver.F
637      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
638      * gradient check in Exp. 6a of natl_box_adjoint/
639    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
640      (see README file)
641    
642    checkpoint57q_post
643    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
644    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
645      - bug was reported by Jean-Michel and Ian Fenty
646    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
647      update exp. cpl_aim+ocn output.
648    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
649      Needed for high-res. runs with large global files
650      to be able to limit tapelev size
651    o Changed some tests for adjoint:
652      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
653      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
654      * global_ocean.90x40x15/ back to default 3-level checkpointing
655    o Modifications to enable scripted COMMON to MODULE conversion
656      * verification/OpenAD/code/ has necessary scripts and description;
657      * converts, compiles and runs successfully;
658    
659    checkpoint57p_post
660    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
661    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
662      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
663    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
664    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
665      (was already the case for dissipation with mom_vecinv,
666       and also the case for grad.PhiHyd when staggered-timeStep)
667      This will allow to put dissipation out-off the AB time-stepping.
668     Unfortunately, affects truncation error. Update output of exp. that "fails"
669      (cg2d matching number) and leave the others for later: front_relax(10),
670      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
671      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
672    
673    checkpoint57o_post
674    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
675      (2) its ready to be documented during the 20050801 DocFest
676    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
677      for ideal_2D_oce and lab_sea on linux_ia32_g77
678    o set to #undef CTRL_SET_OLD_MAXCVARS_30
679      in global1x1_tot/code_seaice_adj to access indices 32, 33
680      (worth another tag)
681    
682    checkpoint57n_post
683    o adding precip control xx_precip 32
684    o adding swflux control xx_swflux 33
685    o Replacing 10 forcing penalty cost routines by 1 generic.
686    o Implementing partitioning in time-mean and variable adjustment
687      for atmos. state.
688    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
689  o in natl_box_adjoint:  o in natl_box_adjoint:
690    * updated: results_bulk/    * updated exp 1 to 10
691    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
692    o updated global1x1/*_seaice_adj/
693      to incorporate latest changes
694    o enable useSingleCpuIO for mdsio vector routines
695      (applies in particular to tapelev I/O)
696    o removed inefficient K-loop in all active_file*control*.F
697    
698  checkpoint57m_post  checkpoint57m_post
699  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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