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revision 1.711 by jmc, Sun Aug 6 01:46:46 2006 UTC revision 1.814 by jmc, Fri May 11 14:32:32 2007 UTC
# Line 3  $Name$ Line 3  $Name$
3    
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/exf:
8      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
9      EXF_INTERPOLATION:
10      - merge global_with_exf/code version of exf_interp_read.F
11        to the main code ;
12      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
13        reading the file ; Important: This options needs to be defined to recover
14        previous code.
15        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
16      - no longer loose real*8 precision along the way when using exf_iprec=64.
17    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
18      - change discretisation of evp-solver in order to avoid another exchange
19        (changes lab_sea) and clean up a little
20      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
21        help the adjoint (this also changes the results slightly)
22      - add a few "_d 0" where they had been missing in seaice_evp.F
23      - cleaning up: remove unused seaice_calc_rhs.F
24    o pkg/exf: some cleaning-up:
25      - change various "constants" into runtime parameters
26      - cleaned-up Large&Yeager04 routine which should eventually
27        replace exf_bulkformulae.F (changed names of S/R and CPP)
28        and merged various ALLOW_ATM_WIND options
29     only used with thsice pkg (in thsice_get_exf.F):
30      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
31        which are used when useStabilityFct_overIce=TRUE (= the default)
32      - change default values of ice & snow emissivity and scale downward LW
33        by ice & snow emissivity.
34    o pkg/thsice:
35     fix few little problems, in thsice_calc_thickn.F:
36      - growth vertically (and not laterally) if iceFrac == iceMaskMax
37      - melt laterally only if hIce < hThinIce (as the comments say)
38      and in thsice_extend.F:
39      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
40      - start to form ice as soon as the minimum ice-volume is reachable.
41     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
42      and cpl_aim+ocn
43    o pkg/kpp
44     - move computation of surface related input fields to KPP into a new
45       subroutine kpp_forcing_surf.F
46     - remove wrong (within bi,bj loops) EXCH calls.
47     - little cleaning (add argument myThid in last position, cvs header ...)
48     - for now, fix conservation problem by exchanging KPPviscAz (may not
49       be the best fix)
50    o pkg/seaice
51     - check for inconsistent evp parameter/cpp-flag combination
52     - remove leftover errIO flat for obsolete name list error handling
53    o OpenAD
54     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
55    
56    checkpoint59a
57    o pkg/seaice: some parameter clarifications and a little bit of clean up
58    o pkg/thsice: rename run-time parameters:
59       himin       -> hIceMin
60       himin0      -> hThinIce
61       hihig       -> hThickIce
62       i0          -> i0swFrac
63       transCoef   -> bMeltCoef
64       frac_energy -> fracMelting
65      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
66       with default values (for now) that do not change the results.
67      remove old version of thsice vars advection in pkg/seaice.
68    o in FFIELDS.h:
69      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
70      - make pLoad & sIceLoad always available (but still only used if
71         ATMOSPHERIC_LOADING is #define).
72    o pkg/kpp: replaced _KPP_RL with _RL
73    o bug fixes for vertical diffusivity computations when both KPP and
74        3D diffusivity arrays are used.
75    o pkg/seaice: fix bug in evp solver, while doing that
76      - change (improve?) discretization of stress computations for both
77        cgrid-lsr and evp solver
78      - add a new routine to compute strain rates
79      - the above changes lab_sea results
80      - add no slip conditions for evp solver (off by default), lsr-version
81        may follow
82      - fix exchange for shear at Z-points (does not change lab_sea)
83      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
84        (to force the user to pick a time step since there is not "safe" way
85        of choosing it)
86      - add principal stress diagnostics
87      - rearrange fields for evp a little to avoid having to call a: too many
88        exchanges and b: exchanges for stress trensor components which we do
89        not have.
90      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
91        of evp, complete rewrite for lsr case (latter is does not yet work
92        in all cases)
93    o pkg/kpp: add code to have mixing in shelf ice caverns
94      - add myThid to all kpp routines (long overdue)
95    
96    checkpoint59
97    o pkg/exf:
98      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
99        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
100      - move exf header files from lower_case.h to UPPER_CASE.h ;
101        add missing cvs Header & Name
102      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
103      - add namelist param. selectStressGridPosition, exf_monFreq
104      - retire many _CLIM routines, and remove data.exf_clim
105        + params moved to data.exf
106        + climsst, climsss now handled by exf_set_gen, i.e.
107          climss?period=0 refers to constant field,
108          climss?period=-12 to monthly forcing
109      - split up namelists in data.exf
110    o pkg/seaice:
111      - remove seaice_exch and seaice_exch_uv
112      - remove superfluous exchange of theta
113      - add myThid to seaice_budget_ocean/ice
114      - add new interface for atmospheric wind forcing (C-grid only)
115        + new routine
116        + two new field (taux, tauy for stress over ice)
117        + removed one global field (DAIRN) for C-grid case only
118    o pkg/thsise
119      - 2nd set of modifs for thsice adjoint in conjunction with exf
120    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
121    
122    checkpoint58y_post
123    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
124      vertical diffusivity, similar to that in MOM4; turned on using
125      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
126      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
127    o Added capability for 3D specification of background vertical diffusion
128      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
129      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
130      "data" file that contains the 3D vertical diffusivity coefficients.
131    o ice dynamics (pkg/seaice) with thsice thermodynamics:
132      - add code within pkg thsice to advect & diffuse sea-ice fields
133      similar to (and will replace) what has been added in  seaice_advdiff.F,
134      but: - conserving Mass, Heat & Salt.
135           - better when using non-linear advection scheme (not yet fully tested)
136           - can also be used in atmospheric set-up (for now, only the diffusion).
137    
138    checkpoint58x_post
139    o IO option for global-file compact format:
140      - add options when generating topology (utils/exch2/matlab-topology-generator)
141      - add I/O capability (pkg/mdsio).
142      - adapt utils/matlab/rdmds.m to read this format.
143      for now long-line format not yet supported by pkg/mdsio (& exch2).
144    o shelfice: add a few diagnostics
145    
146    checkpoint58w_post
147    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
148      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
149      (and replace horiVertRatio in NH code).
150      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
151                         and tutorial_plume_on_slope (sensitive to truncation)
152    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
153      directly to drive seaice model (C-grid only)
154    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
155     - reintroduce computation of wind from stress,
156     - compute tau (in exf_bulkformulae.F) from windstress averaged to
157       mass points to avoid tau = 0
158     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
159    o rdmnc.m: make it work with "global" files created with gluemnc
160    o rdmnc.m : some improvements in dealing with singleton dimension
161      (tested on all testreport mnc output files).
162    o genmake2: disable pkg/profiles if netcdf test fails.
163    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
164    o move call to cal_readparms up to make calendar parameters/variable available
165      to all packages
166    
167    checkpoint58v_post
168    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
169      useDynP_inEos_Zc tested.
170    o pkg/exf: changes to properly interpolate/mask/scale initial fields
171    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
172      and portions thereof.  See read_cs.txt for description and examples.
173    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
174      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
175      following the great-circle arc between those 2 points.
176    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
177      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
178    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
179     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
180     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
181     - still needs work (not working with some options ; efficiency to improve)
182       and serious testing.
183     - use this scheme for temperature & salinity in 2 advection test exp.:
184       advect_xy & advect_xz, respectively.
185    
186    checkpoint58u_post
187    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
188    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
189    o testreport: add option "-skipdir" to skip some test.
190    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
191      momentum calculation.
192    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
193    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
194      remove checkpoint.F and the_correction_step.F (no longer used);
195      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
196    o add option (linFSConserveTr) to correct for tracer source/sink due to
197      Linear Free surface
198    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
199    o pkg/thsice: fix reading mnc-pickups
200    
201    checkpoint58t_post
202    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
203    o pkg/mdsio:
204     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
205       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
206       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
207     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
208     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
209       either MDS_READ_FIELD or MDS_WRITE_FIELD )
210     - new S/R (to replace MDSWRITEMETA), which allows to write more
211       informations (variable names, time ...) to meta files.
212     - modify rdmds.m to give back the meta file content.
213    o pkg/diagnostics: change vertical interpolation to be safer, and more
214       flexible (define p-levels to interpolate to in data.diagnostics);
215      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
216       diagnostic pointer.
217    o pkg/seaice: more cleaning up of seaice_growth, added many comments
218    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
219    o fix multi-category seaice:
220     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
221       SEAICE_MULTICATEGORY
222     - fix short wave heat flux
223    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
224       and allow to use EVP solver. Change forward lab_sea: test both EVP
225       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
226    o Initial check-in of lab_sea adjoint
227      (very similar to natl_box_adjoint/code_seaice)
228      * used C-grid and EVP solver
229      * used KPP, GM/Redi
230      * uses inAdExact=.TRUE.
231      * gradient checks fail for both ADM and TLM
232        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
233        f.d. gradients actually seem more problematic than ADM, TLM gradients;
234        issue is related to forward mismatch between g77 an ifort
235    o pkg/seaice: overhaul of thermodynamics
236     - growth.F and groatb.F are replaced by new routine seaice_growth.F
237     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
238     - move a few global fields out of SEAICE.h into seaice_growth.F and
239       make them 2D (FICE/QNETO/ ...)
240     - remove FO (it is the same as QNETO)
241     - introduce a few local fields to avoid modifying external fields such
242       as atemp, etc.
243    
244    checkpoint58s_post
245    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
246      changed exf_set_gen.F so that
247        genperiod=0 means input file is one time-constant field and
248        genperiod=-12 means input file contains 12 monthly means
249    o CG2D: use pre-computed solver main-diagonal (stored in common block);
250      this affects truncation error ; generate new output file for exp. which
251      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
252        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
253        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
254        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
255        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
256        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
257    o start implementation of deep-atmosphere and anelastic formulation
258    o verification: remove 2nd copy of input files and use script "prepare_run"
259      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
260    o mom_common/vecinv/fluxform: fix a few initialisation isssues
261    o profiles: fix for multithreaded case
262    
263    o diagnostics: rename few diags:
264      s/'PRESSURE'/'RCENTER '/g
265      s/'TICE    '/'oceFreez'/g
266      s/'TAUX    '/'oceTAUX '/g
267      s/'TAUY    '/'oceTAUY '/g
268      s/'SWFLUX  '/'oceQsw  '/g
269      s/DIFx/DFxE/g
270      s/DIFy/DFyE/g
271      and add few ocean-forcing diagnostics:
272      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
273    o modifications to pkg/seaice/growth.F and budget.F, which change results of
274      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
275      as actual snow thickness.  It now refers everywhere to effective snow
276      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
277    
278    checkpoint58r_post
279    o modifications to pkg/seaice/growth.F, which change results of
280      lab_sea experiment: fixes pertain to melting snow over open water, to
281      masking EVAP under sea ice, and to using the correct AREA variable for
282      computations of EVAP, PRECIP, HSNOW, and GHEFF
283    o add ability to read bathy, salt, and theta using MNC (off by def)
284    o add flooding algorithm and advection of HSNOW for pkg/seaice;
285      both are turned off by default and do no change any results
286    o seaice advection with pkg/thsice: a step toward the use of non-linear
287      advection scheme, but #ifdef or commented out for now (requires more EXCH).
288    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
289      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
290      in natl_box (affects results @ truncation level: update output.txt)
291    o multi-threading and IO:
292      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
293      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
294        (needed to work with SingleCpuIO): tested in all verif. exp.
295    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
296      affects the results (but none of the verification test uses this scheme).
297    o Adding some pkg/diagnostics capability to pkg/seaice
298      (will certainly be subject to changes)
299    o ctrl: adding new control variables:
300      lwflux, lwdown, evap, snowprecip, apressure, runoff
301    
302    checkpoint58q_post
303    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
304      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
305      high_res_cube configuration by 4% on Columbia.
306    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
307      add (in global_with_exf/code) a version of EXF_INTERP_READ without
308      dynamical allocation (seems to work in multi-threaded).
309    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
310      single CPU io) so that TAF does not have to see EESUPPORT.h
311    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
312    
313    checkpoint58p_post
314    o obcs: stop if obcs is used with useCDscheme = .true.
315    o shelfice:
316     - fix a sign error so that no slip at shelfice interface works
317     - remove stop for combination non-hydrostatic code and shelfice. That does
318       not mean, that the results are correct, but at least they are numerically
319       stable
320    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
321    o added adjoint exch routined for all exch*3d* routines
322      and updated flow directives
323    
324    checkpoint58o_post
325    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
326      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
327    o change controling S/R for writing pickup file (new S/R do_write_pickup)
328      and clean-up reading/writing of pickup files.
329    o fix local version of read/write pickup (NH part) in rotating_tank/code
330    o simplify EXCH interface:
331     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
332     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
333    o added the regrid package
334    o shelfice:
335     - add a simple boundary layer scheme to reduce noise
336     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
337    
338    checkpoint58n_post
339    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
340       local variable (not in common block).
341    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
342      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
343      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
344        to work with SingleCpuIO.
345  o add "_d 0" to real constant of pkg/cfc subroutines ;  o add "_d 0" to real constant of pkg/cfc subroutines ;
346     update exp. cfc_exemple & tutorial_cfc_offline output files.     update exp. cfc_exemple & tutorial_cfc_offline output files.
347  o multi-threading and IO:  o multi-threading and IO:
# Line 30  o consistent with addition of ptracer an Line 369  o consistent with addition of ptracer an
369  o profiles: adding ptracer and ssh  o profiles: adding ptracer and ssh
370  o testreport: change multi-test output-file name  o testreport: change multi-test output-file name
371    (from output.txt.{name} to output.{name}.txt)    (from output.txt.{name} to output.{name}.txt)
372  o profiles: now ok for mutli-threaded case  o profiles: now ok for mutli-tiles case
373  o seaice: add 4 parameters for different advection schemes for area,  o seaice: add 4 parameters for different advection schemes for area,
374    (effective) seaice thickness, enthalphy, and snow height. Their default    (effective) seaice thickness, enthalphy, and snow height. Their default
375    is the standard parameter SEAICEadvScheme    is the standard parameter SEAICEadvScheme

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