/[MITgcm]/MITgcm/doc/tag-index
ViewVC logotype

Diff of /MITgcm/doc/tag-index

Parent Directory Parent Directory | Revision Log Revision Log | View Revision Graph Revision Graph | View Patch Patch

revision 1.614 by jmc, Fri Feb 24 00:57:55 2006 UTC revision 1.819 by jmc, Fri May 18 03:02:47 2007 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
8      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
9    
10    checkpoint59b
11    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
12      - export/import (between ocean & coupler) fields needed for ocean DIC.
13    o pkg/seaice:
14      - get rid of three more exchanges seaice_calc_viscosities (required
15        different loop boundaries in seaice_lsr and seaice_ocean_stress)
16      - bug fix in seaice_ocean_stress (update of lab_sea required)
17      - reduce loop boundaries to necessary minimum also in seaice_evp
18      - go back to the old way of computing deltaC/Z as the adjoint likes that
19        better
20    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
21      passive tracer to an Age Tracer) + update output.txt
22    o pkg/exf:
23      - implement A-grid / C-grid selection for wind-stress input files.
24      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
25      for now, in exf_bulk_largeyeager04.F only :
26      - change implementation for case where windspeed + 2. components wind-stress
27        are read-in. AND use rhoConstFresh to convert evap.
28    o pkg/seaice:
29      - use correct EXCH_UV for wind-forcing (on A-grid).
30      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
31        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
32    o pkg/exf:
33      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
34      EXF_INTERPOLATION:
35      - merge global_with_exf/code version of exf_interp_read.F
36        to the main code ;
37      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
38        reading the file ; Important: This options needs to be defined to recover
39        previous code.
40        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
41      - no longer loose real*8 precision along the way when using exf_iprec=64.
42    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
43      - change discretisation of evp-solver in order to avoid another exchange
44        (changes lab_sea) and clean up a little
45      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
46        help the adjoint (this also changes the results slightly)
47      - add a few "_d 0" where they had been missing in seaice_evp.F
48      - cleaning up: remove unused seaice_calc_rhs.F
49    o pkg/exf: some cleaning-up:
50      - change various "constants" into runtime parameters
51      - cleaned-up Large&Yeager04 routine which should eventually
52        replace exf_bulkformulae.F (changed names of S/R and CPP)
53        and merged various ALLOW_ATM_WIND options
54     only used with thsice pkg (in thsice_get_exf.F):
55      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
56        which are used when useStabilityFct_overIce=TRUE (= the default)
57      - change default values of ice & snow emissivity and scale downward LW
58        by ice & snow emissivity.
59    o pkg/thsice:
60     fix few little problems, in thsice_calc_thickn.F:
61      - growth vertically (and not laterally) if iceFrac == iceMaskMax
62      - melt laterally only if hIce < hThinIce (as the comments say)
63      and in thsice_extend.F:
64      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
65      - start to form ice as soon as the minimum ice-volume is reachable.
66     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
67      and cpl_aim+ocn
68    o pkg/kpp
69     - move computation of surface related input fields to KPP into a new
70       subroutine kpp_forcing_surf.F
71     - remove wrong (within bi,bj loops) EXCH calls.
72     - little cleaning (add argument myThid in last position, cvs header ...)
73     - for now, fix conservation problem by exchanging KPPviscAz (may not
74       be the best fix)
75    o pkg/seaice
76     - check for inconsistent evp parameter/cpp-flag combination
77     - remove leftover errIO flat for obsolete name list error handling
78    o OpenAD
79     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
80    
81    checkpoint59a
82    o pkg/seaice: some parameter clarifications and a little bit of clean up
83    o pkg/thsice: rename run-time parameters:
84       himin       -> hIceMin
85       himin0      -> hThinIce
86       hihig       -> hThickIce
87       i0          -> i0swFrac
88       transCoef   -> bMeltCoef
89       frac_energy -> fracMelting
90      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
91       with default values (for now) that do not change the results.
92      remove old version of thsice vars advection in pkg/seaice.
93    o in FFIELDS.h:
94      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
95      - make pLoad & sIceLoad always available (but still only used if
96         ATMOSPHERIC_LOADING is #define).
97    o pkg/kpp: replaced _KPP_RL with _RL
98    o bug fixes for vertical diffusivity computations when both KPP and
99        3D diffusivity arrays are used.
100    o pkg/seaice: fix bug in evp solver, while doing that
101      - change (improve?) discretization of stress computations for both
102        cgrid-lsr and evp solver
103      - add a new routine to compute strain rates
104      - the above changes lab_sea results
105      - add no slip conditions for evp solver (off by default), lsr-version
106        may follow
107      - fix exchange for shear at Z-points (does not change lab_sea)
108      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
109        (to force the user to pick a time step since there is not "safe" way
110        of choosing it)
111      - add principal stress diagnostics
112      - rearrange fields for evp a little to avoid having to call a: too many
113        exchanges and b: exchanges for stress trensor components which we do
114        not have.
115      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
116        of evp, complete rewrite for lsr case (latter is does not yet work
117        in all cases)
118    o pkg/kpp: add code to have mixing in shelf ice caverns
119      - add myThid to all kpp routines (long overdue)
120    
121    checkpoint59
122    o pkg/exf:
123      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
124        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
125      - move exf header files from lower_case.h to UPPER_CASE.h ;
126        add missing cvs Header & Name
127      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
128      - add namelist param. selectStressGridPosition, exf_monFreq
129      - retire many _CLIM routines, and remove data.exf_clim
130        + params moved to data.exf
131        + climsst, climsss now handled by exf_set_gen, i.e.
132          climss?period=0 refers to constant field,
133          climss?period=-12 to monthly forcing
134      - split up namelists in data.exf
135    o pkg/seaice:
136      - remove seaice_exch and seaice_exch_uv
137      - remove superfluous exchange of theta
138      - add myThid to seaice_budget_ocean/ice
139      - add new interface for atmospheric wind forcing (C-grid only)
140        + new routine
141        + two new field (taux, tauy for stress over ice)
142        + removed one global field (DAIRN) for C-grid case only
143    o pkg/thsise
144      - 2nd set of modifs for thsice adjoint in conjunction with exf
145    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
146    
147    checkpoint58y_post
148    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
149      vertical diffusivity, similar to that in MOM4; turned on using
150      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
151      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
152    o Added capability for 3D specification of background vertical diffusion
153      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
154      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
155      "data" file that contains the 3D vertical diffusivity coefficients.
156    o ice dynamics (pkg/seaice) with thsice thermodynamics:
157      - add code within pkg thsice to advect & diffuse sea-ice fields
158      similar to (and will replace) what has been added in  seaice_advdiff.F,
159      but: - conserving Mass, Heat & Salt.
160           - better when using non-linear advection scheme (not yet fully tested)
161           - can also be used in atmospheric set-up (for now, only the diffusion).
162    
163    checkpoint58x_post
164    o IO option for global-file compact format:
165      - add options when generating topology (utils/exch2/matlab-topology-generator)
166      - add I/O capability (pkg/mdsio).
167      - adapt utils/matlab/rdmds.m to read this format.
168      for now long-line format not yet supported by pkg/mdsio (& exch2).
169    o shelfice: add a few diagnostics
170    
171    checkpoint58w_post
172    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
173      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
174      (and replace horiVertRatio in NH code).
175      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
176                         and tutorial_plume_on_slope (sensitive to truncation)
177    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
178      directly to drive seaice model (C-grid only)
179    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
180     - reintroduce computation of wind from stress,
181     - compute tau (in exf_bulkformulae.F) from windstress averaged to
182       mass points to avoid tau = 0
183     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
184    o rdmnc.m: make it work with "global" files created with gluemnc
185    o rdmnc.m : some improvements in dealing with singleton dimension
186      (tested on all testreport mnc output files).
187    o genmake2: disable pkg/profiles if netcdf test fails.
188    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
189    o move call to cal_readparms up to make calendar parameters/variable available
190      to all packages
191    
192    checkpoint58v_post
193    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
194      useDynP_inEos_Zc tested.
195    o pkg/exf: changes to properly interpolate/mask/scale initial fields
196    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
197      and portions thereof.  See read_cs.txt for description and examples.
198    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
199      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
200      following the great-circle arc between those 2 points.
201    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
202      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
203    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
204     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
205     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
206     - still needs work (not working with some options ; efficiency to improve)
207       and serious testing.
208     - use this scheme for temperature & salinity in 2 advection test exp.:
209       advect_xy & advect_xz, respectively.
210    
211    checkpoint58u_post
212    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
213    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
214    o testreport: add option "-skipdir" to skip some test.
215    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
216      momentum calculation.
217    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
218    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
219      remove checkpoint.F and the_correction_step.F (no longer used);
220      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
221    o add option (linFSConserveTr) to correct for tracer source/sink due to
222      Linear Free surface
223    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
224    o pkg/thsice: fix reading mnc-pickups
225    
226    checkpoint58t_post
227    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
228    o pkg/mdsio:
229     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
230       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
231       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
232     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
233     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
234       either MDS_READ_FIELD or MDS_WRITE_FIELD )
235     - new S/R (to replace MDSWRITEMETA), which allows to write more
236       informations (variable names, time ...) to meta files.
237     - modify rdmds.m to give back the meta file content.
238    o pkg/diagnostics: change vertical interpolation to be safer, and more
239       flexible (define p-levels to interpolate to in data.diagnostics);
240      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
241       diagnostic pointer.
242    o pkg/seaice: more cleaning up of seaice_growth, added many comments
243    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
244    o fix multi-category seaice:
245     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
246       SEAICE_MULTICATEGORY
247     - fix short wave heat flux
248    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
249       and allow to use EVP solver. Change forward lab_sea: test both EVP
250       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
251    o Initial check-in of lab_sea adjoint
252      (very similar to natl_box_adjoint/code_seaice)
253      * used C-grid and EVP solver
254      * used KPP, GM/Redi
255      * uses inAdExact=.TRUE.
256      * gradient checks fail for both ADM and TLM
257        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
258        f.d. gradients actually seem more problematic than ADM, TLM gradients;
259        issue is related to forward mismatch between g77 an ifort
260    o pkg/seaice: overhaul of thermodynamics
261     - growth.F and groatb.F are replaced by new routine seaice_growth.F
262     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
263     - move a few global fields out of SEAICE.h into seaice_growth.F and
264       make them 2D (FICE/QNETO/ ...)
265     - remove FO (it is the same as QNETO)
266     - introduce a few local fields to avoid modifying external fields such
267       as atemp, etc.
268    
269    checkpoint58s_post
270    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
271      changed exf_set_gen.F so that
272        genperiod=0 means input file is one time-constant field and
273        genperiod=-12 means input file contains 12 monthly means
274    o CG2D: use pre-computed solver main-diagonal (stored in common block);
275      this affects truncation error ; generate new output file for exp. which
276      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
277        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
278        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
279        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
280        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
281        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
282    o start implementation of deep-atmosphere and anelastic formulation
283    o verification: remove 2nd copy of input files and use script "prepare_run"
284      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
285    o mom_common/vecinv/fluxform: fix a few initialisation isssues
286    o profiles: fix for multithreaded case
287    
288    o diagnostics: rename few diags:
289      s/'PRESSURE'/'RCENTER '/g
290      s/'TICE    '/'oceFreez'/g
291      s/'TAUX    '/'oceTAUX '/g
292      s/'TAUY    '/'oceTAUY '/g
293      s/'SWFLUX  '/'oceQsw  '/g
294      s/DIFx/DFxE/g
295      s/DIFy/DFyE/g
296      and add few ocean-forcing diagnostics:
297      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
298    o modifications to pkg/seaice/growth.F and budget.F, which change results of
299      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
300      as actual snow thickness.  It now refers everywhere to effective snow
301      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
302    
303    checkpoint58r_post
304    o modifications to pkg/seaice/growth.F, which change results of
305      lab_sea experiment: fixes pertain to melting snow over open water, to
306      masking EVAP under sea ice, and to using the correct AREA variable for
307      computations of EVAP, PRECIP, HSNOW, and GHEFF
308    o add ability to read bathy, salt, and theta using MNC (off by def)
309    o add flooding algorithm and advection of HSNOW for pkg/seaice;
310      both are turned off by default and do no change any results
311    o seaice advection with pkg/thsice: a step toward the use of non-linear
312      advection scheme, but #ifdef or commented out for now (requires more EXCH).
313    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
314      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
315      in natl_box (affects results @ truncation level: update output.txt)
316    o multi-threading and IO:
317      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
318      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
319        (needed to work with SingleCpuIO): tested in all verif. exp.
320    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
321      affects the results (but none of the verification test uses this scheme).
322    o Adding some pkg/diagnostics capability to pkg/seaice
323      (will certainly be subject to changes)
324    o ctrl: adding new control variables:
325      lwflux, lwdown, evap, snowprecip, apressure, runoff
326    
327    checkpoint58q_post
328    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
329      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
330      high_res_cube configuration by 4% on Columbia.
331    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
332      add (in global_with_exf/code) a version of EXF_INTERP_READ without
333      dynamical allocation (seems to work in multi-threaded).
334    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
335      single CPU io) so that TAF does not have to see EESUPPORT.h
336    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
337    
338    checkpoint58p_post
339    o obcs: stop if obcs is used with useCDscheme = .true.
340    o shelfice:
341     - fix a sign error so that no slip at shelfice interface works
342     - remove stop for combination non-hydrostatic code and shelfice. That does
343       not mean, that the results are correct, but at least they are numerically
344       stable
345    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
346    o added adjoint exch routined for all exch*3d* routines
347      and updated flow directives
348    
349    checkpoint58o_post
350    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
351      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
352    o change controling S/R for writing pickup file (new S/R do_write_pickup)
353      and clean-up reading/writing of pickup files.
354    o fix local version of read/write pickup (NH part) in rotating_tank/code
355    o simplify EXCH interface:
356     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
357     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
358    o added the regrid package
359    o shelfice:
360     - add a simple boundary layer scheme to reduce noise
361     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
362    
363    checkpoint58n_post
364    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
365       local variable (not in common block).
366    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
367      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
368      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
369        to work with SingleCpuIO.
370    o add "_d 0" to real constant of pkg/cfc subroutines ;
371       update exp. cfc_exemple & tutorial_cfc_offline output files.
372    o multi-threading and IO:
373      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
374        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
375      - barrier before and after reading.
376      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
377      - avoid using MDS_WRITELOCAL for LAND pkg output.
378      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
379        common-block variables ; Allows multi-threading with master-thread IO.
380    o change default MAX_NO_THREADS from 32 to 4 ;
381      and stop cleanly when MAX_NO_THREADS is too small.
382    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
383    
384    checkpoint58m_post
385    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
386       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
387    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
388       keep global_ocean.90x40x15 (for AD testing) with former secondary test
389       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
390    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
391        add MITgcm_tutorials (= code + all the tutorials)
392    o ecco, option to compute cost for total ssh (mean+anom)
393    o consistent with addition of ptracer and ssh in pkg/profiles
394    o profiles: adding ptracer and ssh
395    o testreport: change multi-test output-file name
396      (from output.txt.{name} to output.{name}.txt)
397    o profiles: now ok for mutli-tiles case
398    o seaice: add 4 parameters for different advection schemes for area,
399      (effective) seaice thickness, enthalphy, and snow height. Their default
400      is the standard parameter SEAICEadvScheme
401    o calc_gw:
402     - add cosFacU in zonal viscous flux (harmonic.visc.).
403     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
404       of tutorial_plume_on_slope.
405    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
406    o calc_gw: true flux-form, account for horizontal grid spacing.
407      update rotating_tank results, but not plume_on_slope (affected at
408      truncation level, 11 digits).
409    
410    checkpoint58l_post
411    o calc_gw:
412     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
413     - remove side-drag for now (need to fix it); update plume_on_slope results.
414     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
415    o commit code to make SST/SSS weights spatially variable
416      (based on either variable in-situ or variable initial T/S weights)
417    o pkg/ecco:
418      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
419        now based on horizontally varying weights wthetaLev, wsaltLev
420      * cost_averagesflags now returns year indices in addition to day, month
421      * sflux balance is performed on annual basis
422        (sflxumm, sfluxmm2, bal_sfluxmm)
423      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
424        including separate counting and multipliers
425    o pkg/rbcs
426      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
427    
428    checkpoint58k_post
429    o testreport:
430     - always build in dir. "build" (if not there, mkdir build instead of building
431       & running in input)
432     - run in dir run (if it exists), in build otherwise.
433     - call prepare_run (if input/prepare_run exists)
434     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
435    o pkg/exf modifications to interpolation and rotation routines for more
436       reasonable treatment of North Pole singularity: for tracers North Pole
437       value is set to northernmost zonal-mean value, for zonal velocity it is
438       set to zero, and for meridional velocity it is set to northernmost value.
439    o pkg/exf/exf_check_range.F
440     - add tile index to diagnostics and move stop statement to the very
441       end of the routine.
442    o pkg/diagnostics: (diagnostics_main_init.F)
443      define title of isomorphic variables according to the current config.
444    o pkg/thsice with pkg/seaice dynamics:
445    - fix domain of computation (interior only, required for exf) and do exchanges
446    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
447    o towards a standard way of dealing with multi-threading in MONITOR
448      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
449    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
450       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
451    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
452    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
453    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
454       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
455    o tracer advection:
456     - clean-up and simplify calc_common_factors.F
457     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
458       advection subroutine (but still not used within DST advection S/R)
459    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
460    
461    checkpoint58j_post
462    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
463      from file (collects calls previously in FORWARD_STEP)
464    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
465    o adjoint store dir. adjusted accordingly
466    o genmake2
467      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
468    
469    checkpoint58i_post
470    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
471      on wind stress (SEAICEstressFactor defaults to 1.)
472    o Total number of Timers is finite (<=40): comment out 2 non-essential one
473      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
474    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
475      on CS-grid: no longer loosing mass.
476    o exf & curvilinear-grid: no longer modify longitude xC & xG.
477    o pkg/ggl90: fix sloppy output and fix a bug
478    o pkg/seaice: added SEAICEuseEVPpickup parameter
479      - Set to false in order to start EVP solver with
480        non-EVP pickup files when using SEAICEuseEVP
481      - fix sign error in diffusion in seaice_calc_rhs
482    
483    checkpoint58h_post
484    * Modifications for bottom topography control
485      o replace hFacC by _hFacC at various places
486      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
487      o add non-self-adjoint cg2d_nsa
488      o update autodiff support routines
489      o re-initialise hfac after ctrl_depth_ini
490      o works for 5x5 box, doesnt work for global_ocean.90x40x15
491    * Adding verification for 5x5 box (4-layer) bottom topography control
492    
493    checkpoint58g_post
494    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
495       used for mean seasonal cycle, mean diurnal cycle); add an example
496       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
497    o pkg/ggl90:
498      - add parameter (minimum surface kinetic energy)
499      - fix bug (avoiding division by zero)
500    o couple pkg/thsice to pkg/seaice:
501      - modify advection in seaice to accomodate new scalar fields to be advected
502      - only muliDimAdection scheme work with seaice/thsice
503      - mapping of thsice-variables to seaice-variables, back and forth
504      - does not break the verification experiments, but does not give the
505        desired results either
506    o pkg/seaice
507      - make (default) second order advection a bit less confusing?
508    
509    checkpoint58f_post
510    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
511      to pkg/seaice):
512      - new routines thsice_map_exf and thsice_get_exf provide the interface
513      - add an additional formal parameter to thsice_solve4temp
514    o pkg/exf:
515      - add new fields wspeed, snowprecip (to be able to couple to thsice)
516      - correct Stefan-Boltzmann constant
517      - new parameter for longwave surface emittance
518      - separate some stuff from exf_bulkformulae into new routines  
519        exf_radiation, exf_wind
520      - add new parameters and constants: longwave emissivity for ocean, ice
521        and snow, evaporation parameters over ice
522      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
523        either wind from stress or stress from wind
524    o pkg/thSIce:
525    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
526    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
527       and THSICE_CALC_THICKN
528    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
529    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
530      to make debugging easier.
531    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
532    o pkg/bulk_force:
533      - clean-up comments and parameters ;
534      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
535    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
536      generate new output for test-experiment: aim.5l_cs.thSI
537    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
538      testreport accordingly
539    
540    checkpoint58e_post
541    o SEAICE_CGRID adjoint done
542    o R_STAR adjoint implemented.
543      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
544      * need to sort out init. of h0facc, etc.
545    o Make pkg/profile fully independent of ecco,cost, etc. stuff
546      to be able to use it in pure forward.
547    
548    checkpoint58d_post
549    o upgrade simple test-experiment to tutorial example:
550     step.1: duplicate the experiment and (step.2) will remove the old copy.
551      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
552      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
553      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
554      tutorial_global_oce_biogeo    <- copy of dic_example
555      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
556      tutorial_plume_on_slope       <- copy of plume_on_slope
557      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
558      tutorial_global_oce_optim     <- empty for now (David ?)
559      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
560     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
561    o correct a sign problem in cost_scat.F
562    o obcs and ptracers: fix boundary conditions for advections schemes
563      with larger stencil
564    o thsice adjoint: start
565    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
566      completeness
567    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
568      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
569    o ptracers adjoint:
570      * avoid extensive recomputatations
571      * fix missing re-init. of gptr (missed by TAF)
572    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
573      me to turn off the excessive output to STDOUT that this package produces
574    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
575      and add those terms in Vector-Invariant formulation.
576    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
577      if the control period (xx_hfluxperiod etc) is 0
578    o in profiles pkg, clean routines and fix details
579    o in ecco pkg, reading ssh data:
580      fix problem in case the model does not start at iter0=0
581    o fix mnc-pickup/restart for ptracers
582    o new package prifiles:
583      code to compute profile-based cost by Gael Forget
584      (modifs in ecco, ctrl, autodiff)
585    o Benign bug fix in initialization (spotted by M. Mazloff) of
586      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
587    
588    checkpoint58c_post
589    o adjoint: finish NLFS adjoint and provide reference output in
590      verification/global_ocean.90x40x15/results_ad_nlfs
591    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
592      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
593      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
594      with SEAICE_CGRID defined.
595    o move calendarDumps from "data" to "data.cal" and clean-up the code
596      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
597    o add useEXF & useCAL flags (for now, set in hard-coded way)
598    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
599      (were missing in NH mode, and wrong in quasihydrostatic mode).
600      waiting for Chris updated version of calc_gw to add those CALLs.
601    o fix bug in quasihydrostatic S/R ;
602      add a test for this option: global_ocean.90x40x15.qshyd
603    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
604      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
605    o add on/off flag useOffLine for package OFFLINE
606    o seaice:
607      - modify advection so that it works also on the C-grid
608      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
609        problem in multi-tile runs with C-grid
610      - add flags for clipping ice velocities and/or masking solver forcing
611      - fix drag (ocean on ice) formulation and a bug that caused noise in the
612        C-grid solver
613      - added a few comments to seaice_diffusion.F
614      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
615        are now exclusive)
616      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
617        required re-ordering the code a little:
618       + make DAIRN global variable (defined in SEAICE)
619       + move computation of the viscosities eta and zeta into a new separate
620         routine (because I need to recompute them in seaice_ocean_stress.F)
621    
622    checkpoint58b_post
623    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
624      update output.txt of exp. aim.5l_cs.thSI
625    o various mnc cleanups and improvements:
626      + shrink lookup tables by factor of ~4
627      + better error reporting when running out of lookup space
628      + able to handle longer path/file names (up to 500 chars)
629    o adjoint:
630      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
631      - TBD: "hidden" mom_vecinv recomp. in dynamics
632    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
633     (allow to differentiate between forcing components using new integer flags:
634      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
635     and add new flag to put Dissipation tendency out of Adams-Bashforth.
636    o ecco
637      - enable trend removal from SSH anomaly obs.
638    o adjoint
639      - a fix for PmEpR when #undef EXACT_CONSERV
640      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
641      - try to fix "hidden" recomp. in forward_step for NLFS
642        (NLFS seems broken sometimes after I checked it in)
643    o seaice:
644     - add c-grid version of the dynamic solver:
645       + three new routines that are the c-grid substitute lsr, dynsolver
646         and ostres
647       + put a few fields that were local to dynsolver into global common
648         blocks, so that I can move the computation of stresses etc into
649         seaice_lsr (saves coding but may break the adjoint).
650     - replace more hardwired parameters by runtime parameters
651     - add ice masks that mask the rhs of the implicit solvers where there
652       is no ice (commented out in seaice_dynsolver, because i am not sure
653       if this works properly), eventually this should replace the clipping
654       of ice velocities in seaice_dynsolver to +/-40cm/s.
655    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
656      include it only where its needed
657    o move balancing of fluxes before the call of external_forcing_surf
658    o seaice:
659      - correct units of turning angles (now they are really in degrees)
660      - move computation of GWATX/Y out of main routine into dynsolver
661      - initialize GWATX/Y in seaice_init
662    o Apply mask on Fresh-Water flux (needed for SSH forcing).
663      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
664    o seaice: add runtime flags for turning angles (default to zero)
665    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
666      and trend from exf forcing and ctrl control adjustments
667    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
668      (since checkpoint57x_post)
669    o change the default rotation period to 86164.s = the Earth rotation
670  o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)  o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
671    and based on a reference stratification. Tested within hs94.cs-32x32x5.    and based on a reference stratification. Tested within hs94.cs-32x32x5.
672  o seaice advection: add code for choosing between the default (2nd order  o seaice advection: add code for choosing between the default (2nd order

Legend:
Removed from v.1.614  
changed lines
  Added in v.1.819

  ViewVC Help
Powered by ViewVC 1.1.22