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revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.739 by jmc, Thu Oct 26 19:11:09 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  o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
8  o moved ptracer ctrl index 17 -> 32    (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
9      in natl_box (affects results @ truncation level: update output.txt)
10    o multi-threading and IO:
11      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
12      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
13        (needed to work with SingleCpuIO): tested in all verif. exp.
14    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
15      affects the results (but none of the verification test uses this scheme).
16    o Adding some pkg/diagnostics capability to pkg/seaice
17      (will certainly be subject to changes)
18    
19    checkpoint58q_post
20    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
21      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
22      high_res_cube configuration by 4% on Columbia.
23    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
24      add (in global_with_exf/code) a version of EXF_INTERP_READ without
25      dynamical allocation (seems to work in multi-threaded).
26    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
27      single CPU io) so that TAF does not have to see EESUPPORT.h
28    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
29    
30    checkpoint58p_post
31    o obcs: stop if obcs is used with useCDscheme = .true.
32    o shelfice:
33     - fix a sign error so that no slip at shelfice interface works
34     - remove stop for combination non-hydrostatic code and shelfice. That does
35       not mean, that the results are correct, but at least they are numerically
36       stable
37    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
38    o added adjoint exch routined for all exch*3d* routines
39      and updated flow directives
40    
41    checkpoint58o_post
42    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
43      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
44    o change controling S/R for writing pickup file (new S/R do_write_pickup)
45      and clean-up reading/writing of pickup files.
46    o fix local version of read/write pickup (NH part) in rotating_tank/code
47    o simplify EXCH interface:
48     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
49     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
50    o added the regrid package
51    o shelfice:
52     - add a simple boundary layer scheme to reduce noise
53     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
54    
55    checkpoint58n_post
56    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
57       local variable (not in common block).
58    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
59      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
60      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
61        to work with SingleCpuIO.
62    o add "_d 0" to real constant of pkg/cfc subroutines ;
63       update exp. cfc_exemple & tutorial_cfc_offline output files.
64    o multi-threading and IO:
65      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
66        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
67      - barrier before and after reading.
68      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
69      - avoid using MDS_WRITELOCAL for LAND pkg output.
70      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
71        common-block variables ; Allows multi-threading with master-thread IO.
72    o change default MAX_NO_THREADS from 32 to 4 ;
73      and stop cleanly when MAX_NO_THREADS is too small.
74    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
75    
76    checkpoint58m_post
77    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
78       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
79    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
80       keep global_ocean.90x40x15 (for AD testing) with former secondary test
81       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
82    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
83        add MITgcm_tutorials (= code + all the tutorials)
84    o ecco, option to compute cost for total ssh (mean+anom)
85    o consistent with addition of ptracer and ssh in pkg/profiles
86    o profiles: adding ptracer and ssh
87    o testreport: change multi-test output-file name
88      (from output.txt.{name} to output.{name}.txt)
89    o profiles: now ok for mutli-tiles case
90    o seaice: add 4 parameters for different advection schemes for area,
91      (effective) seaice thickness, enthalphy, and snow height. Their default
92      is the standard parameter SEAICEadvScheme
93    o calc_gw:
94     - add cosFacU in zonal viscous flux (harmonic.visc.).
95     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
96       of tutorial_plume_on_slope.
97    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
98    o calc_gw: true flux-form, account for horizontal grid spacing.
99      update rotating_tank results, but not plume_on_slope (affected at
100      truncation level, 11 digits).
101    
102    checkpoint58l_post
103    o calc_gw:
104     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
105     - remove side-drag for now (need to fix it); update plume_on_slope results.
106     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
107    o commit code to make SST/SSS weights spatially variable
108      (based on either variable in-situ or variable initial T/S weights)
109    o pkg/ecco:
110      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
111        now based on horizontally varying weights wthetaLev, wsaltLev
112      * cost_averagesflags now returns year indices in addition to day, month
113      * sflux balance is performed on annual basis
114        (sflxumm, sfluxmm2, bal_sfluxmm)
115      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
116        including separate counting and multipliers
117    o pkg/rbcs
118      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
119    
120    checkpoint58k_post
121    o testreport:
122     - always build in dir. "build" (if not there, mkdir build instead of building
123       & running in input)
124     - run in dir run (if it exists), in build otherwise.
125     - call prepare_run (if input/prepare_run exists)
126     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
127    o pkg/exf modifications to interpolation and rotation routines for more
128       reasonable treatment of North Pole singularity: for tracers North Pole
129       value is set to northernmost zonal-mean value, for zonal velocity it is
130       set to zero, and for meridional velocity it is set to northernmost value.
131    o pkg/exf/exf_check_range.F
132     - add tile index to diagnostics and move stop statement to the very
133       end of the routine.
134    o pkg/diagnostics: (diagnostics_main_init.F)
135      define title of isomorphic variables according to the current config.
136    o pkg/thsice with pkg/seaice dynamics:
137    - fix domain of computation (interior only, required for exf) and do exchanges
138    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
139    o towards a standard way of dealing with multi-threading in MONITOR
140      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
141    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
142       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
143    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
144    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
145    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
146       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
147    o tracer advection:
148     - clean-up and simplify calc_common_factors.F
149     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
150       advection subroutine (but still not used within DST advection S/R)
151    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
152    
153    checkpoint58j_post
154    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
155      from file (collects calls previously in FORWARD_STEP)
156    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
157    o adjoint store dir. adjusted accordingly
158    o genmake2
159      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
160    
161    checkpoint58i_post
162    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
163      on wind stress (SEAICEstressFactor defaults to 1.)
164    o Total number of Timers is finite (<=40): comment out 2 non-essential one
165      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
166    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
167      on CS-grid: no longer loosing mass.
168    o exf & curvilinear-grid: no longer modify longitude xC & xG.
169    o pkg/ggl90: fix sloppy output and fix a bug
170    o pkg/seaice: added SEAICEuseEVPpickup parameter
171      - Set to false in order to start EVP solver with
172        non-EVP pickup files when using SEAICEuseEVP
173      - fix sign error in diffusion in seaice_calc_rhs
174    
175    checkpoint58h_post
176    * Modifications for bottom topography control
177      o replace hFacC by _hFacC at various places
178      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
179      o add non-self-adjoint cg2d_nsa
180      o update autodiff support routines
181      o re-initialise hfac after ctrl_depth_ini
182      o works for 5x5 box, doesnt work for global_ocean.90x40x15
183    * Adding verification for 5x5 box (4-layer) bottom topography control
184    
185    checkpoint58g_post
186    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
187       used for mean seasonal cycle, mean diurnal cycle); add an example
188       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
189    o pkg/ggl90:
190      - add parameter (minimum surface kinetic energy)
191      - fix bug (avoiding division by zero)
192    o couple pkg/thsice to pkg/seaice:
193      - modify advection in seaice to accomodate new scalar fields to be advected
194      - only muliDimAdection scheme work with seaice/thsice
195      - mapping of thsice-variables to seaice-variables, back and forth
196      - does not break the verification experiments, but does not give the
197        desired results either
198    o pkg/seaice
199      - make (default) second order advection a bit less confusing?
200    
201    checkpoint58f_post
202    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
203      to pkg/seaice):
204      - new routines thsice_map_exf and thsice_get_exf provide the interface
205      - add an additional formal parameter to thsice_solve4temp
206    o pkg/exf:
207      - add new fields wspeed, snowprecip (to be able to couple to thsice)
208      - correct Stefan-Boltzmann constant
209      - new parameter for longwave surface emittance
210      - separate some stuff from exf_bulkformulae into new routines  
211        exf_radiation, exf_wind
212      - add new parameters and constants: longwave emissivity for ocean, ice
213        and snow, evaporation parameters over ice
214      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
215        either wind from stress or stress from wind
216    o pkg/thSIce:
217    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
218    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
219       and THSICE_CALC_THICKN
220    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
221    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
222      to make debugging easier.
223    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
224    o pkg/bulk_force:
225      - clean-up comments and parameters ;
226      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
227    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
228      generate new output for test-experiment: aim.5l_cs.thSI
229    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
230      testreport accordingly
231    
232    checkpoint58e_post
233    o SEAICE_CGRID adjoint done
234    o R_STAR adjoint implemented.
235      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
236      * need to sort out init. of h0facc, etc.
237    o Make pkg/profile fully independent of ecco,cost, etc. stuff
238      to be able to use it in pure forward.
239    
240    checkpoint58d_post
241    o upgrade simple test-experiment to tutorial example:
242     step.1: duplicate the experiment and (step.2) will remove the old copy.
243      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
244      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
245      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
246      tutorial_global_oce_biogeo    <- copy of dic_example
247      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
248      tutorial_plume_on_slope       <- copy of plume_on_slope
249      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
250      tutorial_global_oce_optim     <- empty for now (David ?)
251      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
252     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
253    o correct a sign problem in cost_scat.F
254    o obcs and ptracers: fix boundary conditions for advections schemes
255      with larger stencil
256    o thsice adjoint: start
257    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
258      completeness
259    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
260      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
261    o ptracers adjoint:
262      * avoid extensive recomputatations
263      * fix missing re-init. of gptr (missed by TAF)
264    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
265      me to turn off the excessive output to STDOUT that this package produces
266    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
267      and add those terms in Vector-Invariant formulation.
268    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
269      if the control period (xx_hfluxperiod etc) is 0
270    o in profiles pkg, clean routines and fix details
271    o in ecco pkg, reading ssh data:
272      fix problem in case the model does not start at iter0=0
273    o fix mnc-pickup/restart for ptracers
274    o new package prifiles:
275      code to compute profile-based cost by Gael Forget
276      (modifs in ecco, ctrl, autodiff)
277    o Benign bug fix in initialization (spotted by M. Mazloff) of
278      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
279    
280    checkpoint58c_post
281    o adjoint: finish NLFS adjoint and provide reference output in
282      verification/global_ocean.90x40x15/results_ad_nlfs
283    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
284      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
285      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
286      with SEAICE_CGRID defined.
287    o move calendarDumps from "data" to "data.cal" and clean-up the code
288      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
289    o add useEXF & useCAL flags (for now, set in hard-coded way)
290    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
291      (were missing in NH mode, and wrong in quasihydrostatic mode).
292      waiting for Chris updated version of calc_gw to add those CALLs.
293    o fix bug in quasihydrostatic S/R ;
294      add a test for this option: global_ocean.90x40x15.qshyd
295    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
296      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
297    o add on/off flag useOffLine for package OFFLINE
298    o seaice:
299      - modify advection so that it works also on the C-grid
300      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
301        problem in multi-tile runs with C-grid
302      - add flags for clipping ice velocities and/or masking solver forcing
303      - fix drag (ocean on ice) formulation and a bug that caused noise in the
304        C-grid solver
305      - added a few comments to seaice_diffusion.F
306      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
307        are now exclusive)
308      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
309        required re-ordering the code a little:
310       + make DAIRN global variable (defined in SEAICE)
311       + move computation of the viscosities eta and zeta into a new separate
312         routine (because I need to recompute them in seaice_ocean_stress.F)
313    
314    checkpoint58b_post
315    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
316      update output.txt of exp. aim.5l_cs.thSI
317    o various mnc cleanups and improvements:
318      + shrink lookup tables by factor of ~4
319      + better error reporting when running out of lookup space
320      + able to handle longer path/file names (up to 500 chars)
321    o adjoint:
322      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
323      - TBD: "hidden" mom_vecinv recomp. in dynamics
324    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
325     (allow to differentiate between forcing components using new integer flags:
326      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
327     and add new flag to put Dissipation tendency out of Adams-Bashforth.
328    o ecco
329      - enable trend removal from SSH anomaly obs.
330    o adjoint
331      - a fix for PmEpR when #undef EXACT_CONSERV
332      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
333      - try to fix "hidden" recomp. in forward_step for NLFS
334        (NLFS seems broken sometimes after I checked it in)
335    o seaice:
336     - add c-grid version of the dynamic solver:
337       + three new routines that are the c-grid substitute lsr, dynsolver
338         and ostres
339       + put a few fields that were local to dynsolver into global common
340         blocks, so that I can move the computation of stresses etc into
341         seaice_lsr (saves coding but may break the adjoint).
342     - replace more hardwired parameters by runtime parameters
343     - add ice masks that mask the rhs of the implicit solvers where there
344       is no ice (commented out in seaice_dynsolver, because i am not sure
345       if this works properly), eventually this should replace the clipping
346       of ice velocities in seaice_dynsolver to +/-40cm/s.
347    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
348      include it only where its needed
349    o move balancing of fluxes before the call of external_forcing_surf
350    o seaice:
351      - correct units of turning angles (now they are really in degrees)
352      - move computation of GWATX/Y out of main routine into dynsolver
353      - initialize GWATX/Y in seaice_init
354    o Apply mask on Fresh-Water flux (needed for SSH forcing).
355      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
356    o seaice: add runtime flags for turning angles (default to zero)
357    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
358      and trend from exf forcing and ctrl control adjustments
359    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
360      (since checkpoint57x_post)
361    o change the default rotation period to 86164.s = the Earth rotation
362    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
363      and based on a reference stratification. Tested within hs94.cs-32x32x5.
364    o seaice advection: add code for choosing between the default (2nd order
365      central differences) and multiDim advection schemes provided by
366      pkg/generic_advdiff
367    o seaice:
368      - removed all references to SEAICE_GRID.h fields from
369        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
370        (cubed-sphere configuration will change a little)
371      - grid computations in seaice_init are obsolete now.
372      - cleaned up code a little so that is easier to read (hopefully).
373      - added new (better?) discretizations of default advection and diffusion
374        (turn on with SEAICEuseFluxForm)
375      - replace 1 in 3d global fields by kSurface in growth.F
376      
377    checkpoint58a_post
378    o seaice:
379      - bug fix in advect.F
380    o shelfice:
381      - separate shelfice load anomaly from pload (breaks with time
382        dependent forcing), => introduce constant field shelficeLoadAnomaly.
383        Its default is 0., but it may be computed more cleverly from (unknown)
384        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
385        done offline. A good approximation of the pressure load anomaly is
386        necessary to avoid large initial adjustment processes underneath
387        deep-reaching shelfice.
388      - small fix in ISOMIP shelfice_thermodynamics
389      - add more sophisticated thermodynamics of Hellmer (1989), this is
390        now the default
391      - give a few constants more intuitive names
392    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
393      if bulk formulae are used in long integration (especially EmPmR). Turn
394      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
395      if balancePrintMean, the imbalance that is substracted is printed to
396      STDOUT.
397    o fix bug (typo) in obcs_apply_eta.F
398    o add a new package shelfice which enables us to model the circulation
399      underneath shelf-ice with draughts of hundreds of meters.
400     - works
401     - to do: + include improved thermodynamics
402              + check whether kSurfC (from model/inc/SURFACE.h) can be used
403                instead of new field kTopC
404              + can we use topoFile, Ro_surf and existing code in ini_depth.F
405                instead of new field R_shelfIce and new code in ini_depth.F
406                and ini_mask_etc.F?
407              + adjust vertical mixing schemes?
408    o seaice pkg:
409     - add a cpp-flag to include a simple formula for a salinity dependent
410       freezing point of sea water at the surface
411     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
412       meridional stresses are now different (and hopefully correct)
413    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
414       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
415       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
416    o pkg/diagnostics: add options and parameters for regional-statistics
417       diagnostics ; define regions by reading a region-mask from a file
418       (might add other options later)
419    o pkg/bulk_force:
420     - add option and parameters to use AIM surface-flux formulae.
421     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
422       others forcing fields (defined in PARM05, parameter file "data") are loaded
423       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
424     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
425     - use the right EXCH call for uwind,vwind (to work on CS-grid).
426     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
427       and parameters (note: calcWindStress replaces .NOT.readwindstress).
428     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
429    
430    checkpoint58
431    o add "--embed-source" option to genmake2 which, when the supporting
432      tools can be compiled (as determined by genmake2) will turn on the
433      embed_files package which then embeds the entire MITgcm source code
434      (*.[fFhc] + Makefile) used for the build within the executable
435      - requested by CNH but off by default
436      - adds a paltry <9MB to the mitgcmuv executable in most cases
437      - only writes the output when useEMBEDSRC in eedata is true
438    o clean up 3-dim. relaxation codes:
439      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
440      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
441      * Thanks to Tom Haine for testing!
442    
443    checkpoint57z_post
444    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
445      affects output (@ truncation level) of exp. plume_on_slope ; updated.
446    o fix the pickup behavior for obcs in combination with ptracers
447    o fix a bug in ptracers_external_fields_load
448    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
449      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
450    o transfered surface NH pressure to eta field (if exactConserv).
451    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
452         and update lab_sea output.txt file.
453    o completing 3-dim. relaxation code: additional term
454         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
455      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
456      * At compile time, in "EXF_OPTIONS.h" set
457          #define  ALLOW_CLIMTEMP_RELAXATION
458          #define  ALLOW_CLIMSALT_RELAXATION
459      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
460          tauThetaClimRelax3Dim = 15552000.0,
461          tauSaltClimRelax3Dim  = 15552000.0,
462      * 3 cases:
463          1) Use a constant-in-time 3-dim. field
464          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
465          3) Real-time relax. to time-evolving prescribed field
466    o Adding Laplacian-type smoothness constraint on
467      initial and boundary (forcing) controls (ic, bc)
468      * enable at compile-time via
469        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
470      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
471      * Absolute scale somewhat unclear so far
472      * no area weighting was included since no other cost term does so far
473    
474    checkpoint57y_post
475    First step for a NLFS adjoint
476    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
477    o new init. routines for calc_r_star, calc_surf_dr
478    o still need to deal with ini_masks_etc
479    o testreport seemed happy
480    checkpoint57y_pre
481    
482    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
483    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
484    o add new offset feature to offline pkg (plus minor cleanup)
485    o cfc fixes for final year of integration
486    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
487      be in GCHEM_OPTIONS).
488    
489    checkpoint57x_post
490    o fix testreport Pb in multiple test experiment.
491    o cleanup our namelist syntax in verification:
492      - make it more F95 standards compliant (some work still needed)
493      - allows the vast majority of our tests to work with gfortran
494    o Non-Hydrostatic:
495     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
496     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
497    o Allow to apply AB on T,S rather than on AB(gT,gS):
498     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
499     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
500       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
501     - need a "clever" read_pickup to restart from the other AB formulation
502    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
503    o remove some unused variables (reduces number of compiler warnings)
504    o adjoint
505      * Disable useVariableViscosity for adjoint for time being
506        (there are a number of extensive recomputations)
507      * Initialize certain variables needed for adjoint
508    
509    checkpoint57w_post
510    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
511                 fix the singleCpuIO RS version of MDSWRITEFIELD
512       and add a WARNING if using globalFiles=T with multi-processors.
513    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
514      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
515    o tracer advection scheme:
516      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
517       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
518       was not very convenient).
519      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
520       (further tests needed for the implicit DST & Flux-Limiter schemes).
521    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
522      and sRef for convenience, handy, when you want to initialize
523      ptracers in a large domain with a constant non-zero value. Also,
524      untangle ptracers_init.F a little.
525    
526    checkpoint57v_post
527    o change dome exp. to use variable viscosity in side-drag terms.
528    o remove all the files from the cfc_offline test since they are now
529      incorporated into tutorial_cfc_offline which has been producing
530      identical results for a few days of testing
531    o add new parameter: sideDragFactor to enable half-slip-side BC
532      and change side-drag S/R to use viscosity from mom_calc_visc
533      (can switch back by setting sideDragFactor=0.); affects results at
534      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
535       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
536    o vorticity & strain are now computed without masking, to account for
537      no-slip-side BC in variable viscosity calculation ; mask is applied
538      anyway later on, before computing advection/coriolis terms.
539    o modify exp4 to test new obcs support for reading from external files
540      and for passive tracers
541    o fix behavior of ptracers_monitor when monitor output is written to a
542      netcdf-file; still not independent of monitor.F (writes in the same
543      file).
544    o change default value of tRef (put a uniform, meaningful value for ocean
545      & atmos) and initialize sRef (was missing, as Martin mentioned).
546    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
547      to be proportional to enstrophy dissipation length.  Thus,
548       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
549      This is now consistent with Smagorinsky and with the manual.
550    
551    checkpoint57u_post
552    o OBCS and PTRACERS: add open boundary support for passive tracers
553      - either use homogenous (pseudo) v.Neumann conditions or prescribe
554        OB-values from file; this is not different from the way theta and salinity
555        are treated
556      - however, Orlanski-radiation conditions are not supported, and the model
557        will stop if you use pTracers and Orlanski at the same time.
558      - beefed up the rountine obcs_external_fields_load: now only those open
559        boundary values are overwritten with values from files for which there
560        are really files, otherwise the OB-fields remain untouched. This makes
561        it possible to use different OBs at different ends of the domain (as
562        with EXF)
563    o reduce number of exch calls in shap_filt (s2).
564    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
565      truncation level) 4/5 MLAdjust test results (11&12 digits match).
566    
567    checkpoint57t_post
568    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
569    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
570      same truncation, independent of the face number: affects affects several
571      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
572    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
573      note that biharmonic viscosity + no-slip was not tested in any experiment.
574    o fix bug in non-linear free-surf side-drag ; generate new output for
575      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
576    o make mnc honor the writeBinaryPrec flag for most kinds of output
577    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
578    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
579      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
580    o add brackets in multi-terms sum to get same truncation, independent of
581      the face number (manage to get exactly same value of gU,gV at the cs-edge)
582      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
583    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
584      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
585      a maximum grid-scale Reynolds number.  Also, changes all length calculations
586      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
587      Suggested values of viscosity parameters found in mom_calc_visc.
588      Many new viscosity diagnostics available.
589    
590    checkpoint57s_post
591    o Add clearing-house for viscosity calculations, mom_calc_visc and
592      correct numerous bugs in LeithD and Smagorinsky discretizations.  
593      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
594      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
595      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
596      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
597      The Strain-Tension form is now called with useStrainTensonVisc=.true.
598      ViscAhStrain and viscAhTension are now retired.
599    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
600    o In response to JMC's bug report, genmake2 now ignores any soft-links
601      that it finds in the *current* directory when searching for files.
602      Soft-links found in any other source directories will still work as
603      they did before.
604    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
605      a C routine to unlimit the stack size
606    o mnc-ify pkg/aim snapshot vars
607    o mnc-ify pkg/land as requested by Daniel
608    o various changes to mnc including:
609      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
610      - output can now be grouped so that all files within a group
611          change the ITER portion of their names in lock-step together
612      - can now read ("global") PER-FACE (in addition to PER-TILE) files
613          and works with both EXCH1 and EXCH2 (but needs more testing)
614      - writing works for all verification test cases w/ g77 on Linux
615    
616    checkpoint57r_post
617    o make MNC variable initialization happen earlier
618    o add diagnostics for (almost) each term of the momentum Eq.
619    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
620    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
621    o remove MINIMAL_TAVE_OUTPUT option ;
622      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
623    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
624      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
625    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
626    o add time-dependent SST, SSS control
627    o cost terms in ecco/ modularized (new cost_generic.F)
628    o cost_averages routines are modularized (new cost_averagesgeneric.F)
629    o new infrastructure for seaice model vs. obs misfits in seaice/
630      * driver from the_main_loop.F is seaice_cost_driver.F
631      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
632      * gradient check in Exp. 6a of natl_box_adjoint/
633    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
634      (see README file)
635    
636    checkpoint57q_post
637    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
638    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
639      - bug was reported by Jean-Michel and Ian Fenty
640    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
641      update exp. cpl_aim+ocn output.
642    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
643      Needed for high-res. runs with large global files
644      to be able to limit tapelev size
645    o Changed some tests for adjoint:
646      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
647      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
648      * global_ocean.90x40x15/ back to default 3-level checkpointing
649    o Modifications to enable scripted COMMON to MODULE conversion
650      * verification/OpenAD/code/ has necessary scripts and description;
651      * converts, compiles and runs successfully;
652    
653    checkpoint57p_post
654    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
655    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
656      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
657    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
658    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
659      (was already the case for dissipation with mom_vecinv,
660       and also the case for grad.PhiHyd when staggered-timeStep)
661      This will allow to put dissipation out-off the AB time-stepping.
662     Unfortunately, affects truncation error. Update output of exp. that "fails"
663      (cg2d matching number) and leave the others for later: front_relax(10),
664      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
665      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
666    
667    checkpoint57o_post
668    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
669      (2) its ready to be documented during the 20050801 DocFest
670    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
671      for ideal_2D_oce and lab_sea on linux_ia32_g77
672    o set to #undef CTRL_SET_OLD_MAXCVARS_30
673      in global1x1_tot/code_seaice_adj to access indices 32, 33
674      (worth another tag)
675    
676    checkpoint57n_post
677    o adding precip control xx_precip 32
678    o adding swflux control xx_swflux 33
679    o Replacing 10 forcing penalty cost routines by 1 generic.
680    o Implementing partitioning in time-mean and variable adjustment
681      for atmos. state.
682    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
683  o in natl_box_adjoint:  o in natl_box_adjoint:
684    * updated: results_bulk/    * updated exp 1 to 10
685    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
686    o updated global1x1/*_seaice_adj/
687      to incorporate latest changes
688    o enable useSingleCpuIO for mdsio vector routines
689      (applies in particular to tapelev I/O)
690    o removed inefficient K-loop in all active_file*control*.F
691    
692  checkpoint57m_post  checkpoint57m_post
693  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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