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revision 1.637 by mlosch, Tue Mar 21 13:00:33 2006 UTC revision 1.756 by heimbach, Fri Dec 15 18:58:13 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 Initial check-in of lab_sea adjoint
8      (very similar to natl_box_adjoint/code_seaice)
9      * used C-grid and EVP solver
10      * used KPP, GM/Redi
11      * uses inAdExact=.TRUE.
12      * gradient checks fail for both ADM and TLM
13        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
14        f.d. gradients actually seem more problematic than ADM, TLM gradients;
15        issue is related to forward mismatch between g77 an ifort
16    o pkg/seaice: overhaul of thermodynamics
17     - growth.F and groatb.F are replaced by new routine seaice_growth.F
18     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
19     - move a few global fields out of SEAICE.h into seaice_growth.F and
20       make them 2D (FICE/QNETO/ ...)
21     - remove FO (it is the same as QNETO)
22     - introduce a few local fields to avoid modifying external fields such
23       as atemp, etc.
24    
25    checkpoint58s_post
26    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
27      changed exf_set_gen.F so that
28        genperiod=0 means input file is one time-constant field and
29        genperiod=-12 means input file contains 12 monthly means
30    o CG2D: use pre-computed solver main-diagonal (stored in common block);
31      this affects truncation error ; generate new output file for exp. which
32      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
33        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
34        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
35        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
36        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
37        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
38    o start implementation of deep-atmosphere and anelastic formulation
39    o verification: remove 2nd copy of input files and use script "prepare_run"
40      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
41    o mom_common/vecinv/fluxform: fix a few initialisation isssues
42    o profiles: fix for multithreaded case
43    
44    o diagnostics: rename few diags:
45      s/'PRESSURE'/'RCENTER '/g
46      s/'TICE    '/'oceFreez'/g
47      s/'TAUX    '/'oceTAUX '/g
48      s/'TAUY    '/'oceTAUY '/g
49      s/'SWFLUX  '/'oceQsw  '/g
50      s/DIFx/DFxE/g
51      s/DIFy/DFyE/g
52      and add few ocean-forcing diagnostics:
53      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
54    o modifications to pkg/seaice/growth.F and budget.F, which change results of
55      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
56      as actual snow thickness.  It now refers everywhere to effective snow
57      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
58    
59    checkpoint58r_post
60    o modifications to pkg/seaice/growth.F, which change results of
61      lab_sea experiment: fixes pertain to melting snow over open water, to
62      masking EVAP under sea ice, and to using the correct AREA variable for
63      computations of EVAP, PRECIP, HSNOW, and GHEFF
64    o add ability to read bathy, salt, and theta using MNC (off by def)
65    o add flooding algorithm and advection of HSNOW for pkg/seaice;
66      both are turned off by default and do no change any results
67    o seaice advection with pkg/thsice: a step toward the use of non-linear
68      advection scheme, but #ifdef or commented out for now (requires more EXCH).
69    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
70      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
71      in natl_box (affects results @ truncation level: update output.txt)
72    o multi-threading and IO:
73      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
74      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
75        (needed to work with SingleCpuIO): tested in all verif. exp.
76    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
77      affects the results (but none of the verification test uses this scheme).
78    o Adding some pkg/diagnostics capability to pkg/seaice
79      (will certainly be subject to changes)
80    o ctrl: adding new control variables:
81      lwflux, lwdown, evap, snowprecip, apressure, runoff
82    
83    checkpoint58q_post
84    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
85      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
86      high_res_cube configuration by 4% on Columbia.
87    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
88      add (in global_with_exf/code) a version of EXF_INTERP_READ without
89      dynamical allocation (seems to work in multi-threaded).
90    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
91      single CPU io) so that TAF does not have to see EESUPPORT.h
92    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
93    
94    checkpoint58p_post
95    o obcs: stop if obcs is used with useCDscheme = .true.
96    o shelfice:
97     - fix a sign error so that no slip at shelfice interface works
98     - remove stop for combination non-hydrostatic code and shelfice. That does
99       not mean, that the results are correct, but at least they are numerically
100       stable
101    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
102    o added adjoint exch routined for all exch*3d* routines
103      and updated flow directives
104    
105    checkpoint58o_post
106    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
107      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
108    o change controling S/R for writing pickup file (new S/R do_write_pickup)
109      and clean-up reading/writing of pickup files.
110    o fix local version of read/write pickup (NH part) in rotating_tank/code
111    o simplify EXCH interface:
112     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
113     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
114    o added the regrid package
115    o shelfice:
116     - add a simple boundary layer scheme to reduce noise
117     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
118    
119    checkpoint58n_post
120    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
121       local variable (not in common block).
122    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
123      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
124      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
125        to work with SingleCpuIO.
126    o add "_d 0" to real constant of pkg/cfc subroutines ;
127       update exp. cfc_exemple & tutorial_cfc_offline output files.
128    o multi-threading and IO:
129      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
130        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
131      - barrier before and after reading.
132      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
133      - avoid using MDS_WRITELOCAL for LAND pkg output.
134      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
135        common-block variables ; Allows multi-threading with master-thread IO.
136    o change default MAX_NO_THREADS from 32 to 4 ;
137      and stop cleanly when MAX_NO_THREADS is too small.
138    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
139    
140    checkpoint58m_post
141    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
142       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
143    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
144       keep global_ocean.90x40x15 (for AD testing) with former secondary test
145       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
146    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
147        add MITgcm_tutorials (= code + all the tutorials)
148    o ecco, option to compute cost for total ssh (mean+anom)
149    o consistent with addition of ptracer and ssh in pkg/profiles
150    o profiles: adding ptracer and ssh
151    o testreport: change multi-test output-file name
152      (from output.txt.{name} to output.{name}.txt)
153    o profiles: now ok for mutli-tiles case
154    o seaice: add 4 parameters for different advection schemes for area,
155      (effective) seaice thickness, enthalphy, and snow height. Their default
156      is the standard parameter SEAICEadvScheme
157    o calc_gw:
158     - add cosFacU in zonal viscous flux (harmonic.visc.).
159     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
160       of tutorial_plume_on_slope.
161    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
162    o calc_gw: true flux-form, account for horizontal grid spacing.
163      update rotating_tank results, but not plume_on_slope (affected at
164      truncation level, 11 digits).
165    
166    checkpoint58l_post
167    o calc_gw:
168     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
169     - remove side-drag for now (need to fix it); update plume_on_slope results.
170     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
171    o commit code to make SST/SSS weights spatially variable
172      (based on either variable in-situ or variable initial T/S weights)
173    o pkg/ecco:
174      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
175        now based on horizontally varying weights wthetaLev, wsaltLev
176      * cost_averagesflags now returns year indices in addition to day, month
177      * sflux balance is performed on annual basis
178        (sflxumm, sfluxmm2, bal_sfluxmm)
179      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
180        including separate counting and multipliers
181    o pkg/rbcs
182      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
183    
184    checkpoint58k_post
185    o testreport:
186     - always build in dir. "build" (if not there, mkdir build instead of building
187       & running in input)
188     - run in dir run (if it exists), in build otherwise.
189     - call prepare_run (if input/prepare_run exists)
190     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
191    o pkg/exf modifications to interpolation and rotation routines for more
192       reasonable treatment of North Pole singularity: for tracers North Pole
193       value is set to northernmost zonal-mean value, for zonal velocity it is
194       set to zero, and for meridional velocity it is set to northernmost value.
195    o pkg/exf/exf_check_range.F
196     - add tile index to diagnostics and move stop statement to the very
197       end of the routine.
198    o pkg/diagnostics: (diagnostics_main_init.F)
199      define title of isomorphic variables according to the current config.
200    o pkg/thsice with pkg/seaice dynamics:
201    - fix domain of computation (interior only, required for exf) and do exchanges
202    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
203    o towards a standard way of dealing with multi-threading in MONITOR
204      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
205    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
206       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
207    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
208    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
209    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
210       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
211    o tracer advection:
212     - clean-up and simplify calc_common_factors.F
213     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
214       advection subroutine (but still not used within DST advection S/R)
215    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
216    
217    checkpoint58j_post
218    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
219      from file (collects calls previously in FORWARD_STEP)
220    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
221    o adjoint store dir. adjusted accordingly
222    o genmake2
223      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
224    
225    checkpoint58i_post
226    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
227      on wind stress (SEAICEstressFactor defaults to 1.)
228    o Total number of Timers is finite (<=40): comment out 2 non-essential one
229      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
230    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
231      on CS-grid: no longer loosing mass.
232    o exf & curvilinear-grid: no longer modify longitude xC & xG.
233    o pkg/ggl90: fix sloppy output and fix a bug
234    o pkg/seaice: added SEAICEuseEVPpickup parameter
235      - Set to false in order to start EVP solver with
236        non-EVP pickup files when using SEAICEuseEVP
237      - fix sign error in diffusion in seaice_calc_rhs
238    
239    checkpoint58h_post
240    * Modifications for bottom topography control
241      o replace hFacC by _hFacC at various places
242      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
243      o add non-self-adjoint cg2d_nsa
244      o update autodiff support routines
245      o re-initialise hfac after ctrl_depth_ini
246      o works for 5x5 box, doesnt work for global_ocean.90x40x15
247    * Adding verification for 5x5 box (4-layer) bottom topography control
248    
249    checkpoint58g_post
250    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
251       used for mean seasonal cycle, mean diurnal cycle); add an example
252       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
253    o pkg/ggl90:
254      - add parameter (minimum surface kinetic energy)
255      - fix bug (avoiding division by zero)
256    o couple pkg/thsice to pkg/seaice:
257      - modify advection in seaice to accomodate new scalar fields to be advected
258      - only muliDimAdection scheme work with seaice/thsice
259      - mapping of thsice-variables to seaice-variables, back and forth
260      - does not break the verification experiments, but does not give the
261        desired results either
262    o pkg/seaice
263      - make (default) second order advection a bit less confusing?
264    
265    checkpoint58f_post
266    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
267      to pkg/seaice):
268      - new routines thsice_map_exf and thsice_get_exf provide the interface
269      - add an additional formal parameter to thsice_solve4temp
270    o pkg/exf:
271      - add new fields wspeed, snowprecip (to be able to couple to thsice)
272      - correct Stefan-Boltzmann constant
273      - new parameter for longwave surface emittance
274      - separate some stuff from exf_bulkformulae into new routines  
275        exf_radiation, exf_wind
276      - add new parameters and constants: longwave emissivity for ocean, ice
277        and snow, evaporation parameters over ice
278      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
279        either wind from stress or stress from wind
280    o pkg/thSIce:
281    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
282    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
283       and THSICE_CALC_THICKN
284    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
285    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
286      to make debugging easier.
287    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
288    o pkg/bulk_force:
289      - clean-up comments and parameters ;
290      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
291    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
292      generate new output for test-experiment: aim.5l_cs.thSI
293    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
294      testreport accordingly
295    
296    checkpoint58e_post
297    o SEAICE_CGRID adjoint done
298    o R_STAR adjoint implemented.
299      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
300      * need to sort out init. of h0facc, etc.
301    o Make pkg/profile fully independent of ecco,cost, etc. stuff
302      to be able to use it in pure forward.
303    
304    checkpoint58d_post
305    o upgrade simple test-experiment to tutorial example:
306     step.1: duplicate the experiment and (step.2) will remove the old copy.
307      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
308      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
309      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
310      tutorial_global_oce_biogeo    <- copy of dic_example
311      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
312      tutorial_plume_on_slope       <- copy of plume_on_slope
313      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
314      tutorial_global_oce_optim     <- empty for now (David ?)
315      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
316     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
317    o correct a sign problem in cost_scat.F
318    o obcs and ptracers: fix boundary conditions for advections schemes
319      with larger stencil
320    o thsice adjoint: start
321    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
322      completeness
323    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
324      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
325    o ptracers adjoint:
326      * avoid extensive recomputatations
327      * fix missing re-init. of gptr (missed by TAF)
328    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
329      me to turn off the excessive output to STDOUT that this package produces
330    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
331      and add those terms in Vector-Invariant formulation.
332    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
333      if the control period (xx_hfluxperiod etc) is 0
334    o in profiles pkg, clean routines and fix details
335    o in ecco pkg, reading ssh data:
336      fix problem in case the model does not start at iter0=0
337    o fix mnc-pickup/restart for ptracers
338    o new package prifiles:
339      code to compute profile-based cost by Gael Forget
340      (modifs in ecco, ctrl, autodiff)
341    o Benign bug fix in initialization (spotted by M. Mazloff) of
342      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
343    
344    checkpoint58c_post
345    o adjoint: finish NLFS adjoint and provide reference output in
346      verification/global_ocean.90x40x15/results_ad_nlfs
347  o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the  o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
348    documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in    documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
349    SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only    SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only

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