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revision 1.703 by gforget, Fri Jul 14 22:14:28 2006 UTC revision 1.809 by jmc, Fri May 4 21:51:31 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 pkg/thsice:
8     fix few little problems, in thsice_calc_thickn.F:
9      - growth vertically (and not laterally) if iceFrac == iceMaskMax
10      - melt laterally only if hIce < hThinIce (as the comments say)
11      and in thsice_extend.F:
12      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
13      - start to form ice as soon as the minimum ice-volume is reachable.
14     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
15      and cpl_aim+ocn
16    o pkg/kpp
17     - move computation of surface related input fields to KPP into a new
18       subroutine kpp_forcing_surf.F
19     - remove wrong (within bi,bj loops) EXCH calls.
20     - little cleaning (add argument myThid in last position, cvs header ...)
21     - for now, fix conservation problem by exchanging KPPviscAz (may not
22       be the best fix)
23    o pkg/seaice
24     - check for inconsistent evp parameter/cpp-flag combination
25     - remove leftover errIO flat for obsolete name list error handling
26    
27    checkpoint59a
28    o pkg/seaice: some parameter clarifications and a little bit of clean up
29    o pkg/thsice: rename run-time parameters:
30       himin       -> hIceMin
31       himin0      -> hThinIce
32       hihig       -> hThickIce
33       i0          -> i0swFrac
34       transCoef   -> bMeltCoef
35       frac_energy -> fracMelting
36      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
37       with default values (for now) that do not change the results.
38      remove old version of thsice vars advection in pkg/seaice.
39    o in FFIELDS.h:
40      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
41      - make pLoad & sIceLoad always available (but still only used if
42         ATMOSPHERIC_LOADING is #define).
43    o pkg/kpp: replaced _KPP_RL with _RL
44    o bug fixes for vertical diffusivity computations when both KPP and
45        3D diffusivity arrays are used.
46    o pkg/seaice: fix bug in evp solver, while doing that
47      - change (improve?) discretization of stress computations for both
48        cgrid-lsr and evp solver
49      - add a new routine to compute strain rates
50      - the above changes lab_sea results
51      - add no slip conditions for evp solver (off by default), lsr-version
52        may follow
53      - fix exchange for shear at Z-points (does not change lab_sea)
54      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
55        (to force the user to pick a time step since there is not "safe" way
56        of choosing it)
57      - add principal stress diagnostics
58      - rearrange fields for evp a little to avoid having to call a: too many
59        exchanges and b: exchanges for stress trensor components which we do
60        not have.
61      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
62        of evp, complete rewrite for lsr case (latter is does not yet work
63        in all cases)
64    o pkg/kpp: add code to have mixing in shelf ice caverns
65      - add myThid to all kpp routines (long overdue)
66    
67    checkpoint59
68    o pkg/exf:
69      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
70        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
71      - move exf header files from lower_case.h to UPPER_CASE.h ;
72        add missing cvs Header & Name
73      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
74      - add namelist param. selectStressGridPosition, exf_monFreq
75      - retire many _CLIM routines, and remove data.exf_clim
76        + params moved to data.exf
77        + climsst, climsss now handled by exf_set_gen, i.e.
78          climss?period=0 refers to constant field,
79          climss?period=-12 to monthly forcing
80      - split up namelists in data.exf
81    o pkg/seaice:
82      - remove seaice_exch and seaice_exch_uv
83      - remove superfluous exchange of theta
84      - add myThid to seaice_budget_ocean/ice
85      - add new interface for atmospheric wind forcing (C-grid only)
86        + new routine
87        + two new field (taux, tauy for stress over ice)
88        + removed one global field (DAIRN) for C-grid case only
89    o pkg/thsise
90      - 2nd set of modifs for thsice adjoint in conjunction with exf
91    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
92    
93    checkpoint58y_post
94    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
95      vertical diffusivity, similar to that in MOM4; turned on using
96      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
97      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
98    o Added capability for 3D specification of background vertical diffusion
99      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
100      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
101      "data" file that contains the 3D vertical diffusivity coefficients.
102    o ice dynamics (pkg/seaice) with thsice thermodynamics:
103      - add code within pkg thsice to advect & diffuse sea-ice fields
104      similar to (and will replace) what has been added in  seaice_advdiff.F,
105      but: - conserving Mass, Heat & Salt.
106           - better when using non-linear advection scheme (not yet fully tested)
107           - can also be used in atmospheric set-up (for now, only the diffusion).
108    
109    checkpoint58x_post
110    o IO option for global-file compact format:
111      - add options when generating topology (utils/exch2/matlab-topology-generator)
112      - add I/O capability (pkg/mdsio).
113      - adapt utils/matlab/rdmds.m to read this format.
114      for now long-line format not yet supported by pkg/mdsio (& exch2).
115    o shelfice: add a few diagnostics
116    
117    checkpoint58w_post
118    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
119      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
120      (and replace horiVertRatio in NH code).
121      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
122                         and tutorial_plume_on_slope (sensitive to truncation)
123    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
124      directly to drive seaice model (C-grid only)
125    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
126     - reintroduce computation of wind from stress,
127     - compute tau (in exf_bulkformulae.F) from windstress averaged to
128       mass points to avoid tau = 0
129     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
130    o rdmnc.m: make it work with "global" files created with gluemnc
131    o rdmnc.m : some improvements in dealing with singleton dimension
132      (tested on all testreport mnc output files).
133    o genmake2: disable pkg/profiles if netcdf test fails.
134    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
135    o move call to cal_readparms up to make calendar parameters/variable available
136      to all packages
137    
138    checkpoint58v_post
139    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
140      useDynP_inEos_Zc tested.
141    o pkg/exf: changes to properly interpolate/mask/scale initial fields
142    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
143      and portions thereof.  See read_cs.txt for description and examples.
144    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
145      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
146      following the great-circle arc between those 2 points.
147    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
148      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
149    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
150     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
151     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
152     - still needs work (not working with some options ; efficiency to improve)
153       and serious testing.
154     - use this scheme for temperature & salinity in 2 advection test exp.:
155       advect_xy & advect_xz, respectively.
156    
157    checkpoint58u_post
158    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
159    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
160    o testreport: add option "-skipdir" to skip some test.
161    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
162      momentum calculation.
163    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
164    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
165      remove checkpoint.F and the_correction_step.F (no longer used);
166      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
167    o add option (linFSConserveTr) to correct for tracer source/sink due to
168      Linear Free surface
169    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
170    o pkg/thsice: fix reading mnc-pickups
171    
172    checkpoint58t_post
173    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
174    o pkg/mdsio:
175     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
176       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
177       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
178     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
179     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
180       either MDS_READ_FIELD or MDS_WRITE_FIELD )
181     - new S/R (to replace MDSWRITEMETA), which allows to write more
182       informations (variable names, time ...) to meta files.
183     - modify rdmds.m to give back the meta file content.
184    o pkg/diagnostics: change vertical interpolation to be safer, and more
185       flexible (define p-levels to interpolate to in data.diagnostics);
186      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
187       diagnostic pointer.
188    o pkg/seaice: more cleaning up of seaice_growth, added many comments
189    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
190    o fix multi-category seaice:
191     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
192       SEAICE_MULTICATEGORY
193     - fix short wave heat flux
194    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
195       and allow to use EVP solver. Change forward lab_sea: test both EVP
196       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
197    o Initial check-in of lab_sea adjoint
198      (very similar to natl_box_adjoint/code_seaice)
199      * used C-grid and EVP solver
200      * used KPP, GM/Redi
201      * uses inAdExact=.TRUE.
202      * gradient checks fail for both ADM and TLM
203        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
204        f.d. gradients actually seem more problematic than ADM, TLM gradients;
205        issue is related to forward mismatch between g77 an ifort
206    o pkg/seaice: overhaul of thermodynamics
207     - growth.F and groatb.F are replaced by new routine seaice_growth.F
208     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
209     - move a few global fields out of SEAICE.h into seaice_growth.F and
210       make them 2D (FICE/QNETO/ ...)
211     - remove FO (it is the same as QNETO)
212     - introduce a few local fields to avoid modifying external fields such
213       as atemp, etc.
214    
215    checkpoint58s_post
216    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
217      changed exf_set_gen.F so that
218        genperiod=0 means input file is one time-constant field and
219        genperiod=-12 means input file contains 12 monthly means
220    o CG2D: use pre-computed solver main-diagonal (stored in common block);
221      this affects truncation error ; generate new output file for exp. which
222      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
223        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
224        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
225        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
226        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
227        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
228    o start implementation of deep-atmosphere and anelastic formulation
229    o verification: remove 2nd copy of input files and use script "prepare_run"
230      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
231    o mom_common/vecinv/fluxform: fix a few initialisation isssues
232    o profiles: fix for multithreaded case
233    
234    o diagnostics: rename few diags:
235      s/'PRESSURE'/'RCENTER '/g
236      s/'TICE    '/'oceFreez'/g
237      s/'TAUX    '/'oceTAUX '/g
238      s/'TAUY    '/'oceTAUY '/g
239      s/'SWFLUX  '/'oceQsw  '/g
240      s/DIFx/DFxE/g
241      s/DIFy/DFyE/g
242      and add few ocean-forcing diagnostics:
243      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
244    o modifications to pkg/seaice/growth.F and budget.F, which change results of
245      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
246      as actual snow thickness.  It now refers everywhere to effective snow
247      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
248    
249    checkpoint58r_post
250    o modifications to pkg/seaice/growth.F, which change results of
251      lab_sea experiment: fixes pertain to melting snow over open water, to
252      masking EVAP under sea ice, and to using the correct AREA variable for
253      computations of EVAP, PRECIP, HSNOW, and GHEFF
254    o add ability to read bathy, salt, and theta using MNC (off by def)
255    o add flooding algorithm and advection of HSNOW for pkg/seaice;
256      both are turned off by default and do no change any results
257    o seaice advection with pkg/thsice: a step toward the use of non-linear
258      advection scheme, but #ifdef or commented out for now (requires more EXCH).
259    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
260      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
261      in natl_box (affects results @ truncation level: update output.txt)
262    o multi-threading and IO:
263      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
264      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
265        (needed to work with SingleCpuIO): tested in all verif. exp.
266    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
267      affects the results (but none of the verification test uses this scheme).
268    o Adding some pkg/diagnostics capability to pkg/seaice
269      (will certainly be subject to changes)
270    o ctrl: adding new control variables:
271      lwflux, lwdown, evap, snowprecip, apressure, runoff
272    
273    checkpoint58q_post
274    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
275      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
276      high_res_cube configuration by 4% on Columbia.
277    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
278      add (in global_with_exf/code) a version of EXF_INTERP_READ without
279      dynamical allocation (seems to work in multi-threaded).
280    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
281      single CPU io) so that TAF does not have to see EESUPPORT.h
282    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
283    
284    checkpoint58p_post
285    o obcs: stop if obcs is used with useCDscheme = .true.
286    o shelfice:
287     - fix a sign error so that no slip at shelfice interface works
288     - remove stop for combination non-hydrostatic code and shelfice. That does
289       not mean, that the results are correct, but at least they are numerically
290       stable
291    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
292    o added adjoint exch routined for all exch*3d* routines
293      and updated flow directives
294    
295    checkpoint58o_post
296    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
297      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
298    o change controling S/R for writing pickup file (new S/R do_write_pickup)
299      and clean-up reading/writing of pickup files.
300    o fix local version of read/write pickup (NH part) in rotating_tank/code
301    o simplify EXCH interface:
302     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
303     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
304    o added the regrid package
305    o shelfice:
306     - add a simple boundary layer scheme to reduce noise
307     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
308    
309    checkpoint58n_post
310    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
311       local variable (not in common block).
312    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
313      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
314      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
315        to work with SingleCpuIO.
316    o add "_d 0" to real constant of pkg/cfc subroutines ;
317       update exp. cfc_exemple & tutorial_cfc_offline output files.
318    o multi-threading and IO:
319      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
320        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
321      - barrier before and after reading.
322      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
323      - avoid using MDS_WRITELOCAL for LAND pkg output.
324      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
325        common-block variables ; Allows multi-threading with master-thread IO.
326    o change default MAX_NO_THREADS from 32 to 4 ;
327      and stop cleanly when MAX_NO_THREADS is too small.
328    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
329    
330    checkpoint58m_post
331    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
332       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
333    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
334       keep global_ocean.90x40x15 (for AD testing) with former secondary test
335       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
336    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
337        add MITgcm_tutorials (= code + all the tutorials)
338    o ecco, option to compute cost for total ssh (mean+anom)
339    o consistent with addition of ptracer and ssh in pkg/profiles
340  o profiles: adding ptracer and ssh  o profiles: adding ptracer and ssh
341  o testreport: change multi-test output-file name  o testreport: change multi-test output-file name
342    (from output.txt.{name} to output.{name}.txt)    (from output.txt.{name} to output.{name}.txt)
343  o profiles: now ok for mutli-threaded case  o profiles: now ok for mutli-tiles case
344  o seaice: add 4 parameters for different advection schemes for area,  o seaice: add 4 parameters for different advection schemes for area,
345    (effective) seaice thickness, enthalphy, and snow height. Their default    (effective) seaice thickness, enthalphy, and snow height. Their default
346    is the standard parameter SEAICEadvScheme    is the standard parameter SEAICEadvScheme

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