/[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 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.883 by dimitri, Thu Sep 27 14:42:59 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 adding precip control xx_precip  o pkg/exf: improve vectorization by moving if-statement out of loops
8  o moved ptracer ctrl index 17 -> 32  o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
9    o testreport:
10      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
11        monitor & update offline_exf_seaice exp. output.
12      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
13    o pkg/seaice:
14      - bug fix in the evp solver: boundary conditions were affected be
15        masking of zMax/zMin (changes results)
16      - minor bug fix in boundary conditions in seaice_calc_strainrates
17        (changes results for no_slip)
18      - seaice_lsr.F: make interpolation of eta dependent on boundaries
19      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
20      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
21        stress formulation and no-slip boundary conditions
22    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
23      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
24    o pkg/seaice: a first HSALT time stepping equation has been checked in
25    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
26      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
27      without requiring DO-IF statements
28    o pkg/thsice:
29      use continuous power-law function for partition of energy between lateral
30      melting/freezing and thinning/thickening ; old code using step function
31      still available with #undef THSICE_FRACEN_POWERLAW
32      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
33    o testreport: change AD testing : check against results/output_adm.txt
34      using same scripts as for forward test.
35    
36    checkpoint59g
37    o adjoint testing: in preparation for changing testreport:
38      - output format: cost and grad written on separated lines
39      - ad output results in directory "results" (instead of "results_ad")
40    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
41    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
42    o pkg/ecco: allow user defined cost function contributions
43    o testreport:
44      Allow to choose (per experiment) the list of tested output variables
45       and the main variable (used to issue a pass/FAIL ) ;
46      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
47      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
48      Also modify printing of summary:
49       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
50       b) echo the list of tested variables in the individual summary.txt of
51          each experiment.
52    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
53      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
54      (but still depend on the tile decompostion of the domain).
55    o pkg/seaice: change a discretization detail to make the B-grid code
56      "more symmetric". This change is likely to remove all "ridges/leads" that
57      where quasi-aligned with the grid in B-grid solutions. It may also be
58      the solution to the stress coupling issues with the B-grid.
59    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
60      remove .cvsignore from input dir. (since testreport no longer run here).
61    o pkg/thsice:
62     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
63     - fix reshaping of sea-ice just after advection:
64       melt all the ice only if ice-volume is too small.
65     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
66       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
67     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
68    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
69      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
70    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
71      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
72      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
73      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
74      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
75      -> update output.txt
76    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
77     this affects truncation error: -> update output.txt of exp:
78      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
79      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
80    
81    checkpoint59f
82    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
83    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
84      a bounded range (in forward mode)
85    o pkg/ecco, ctrl, autodiff and mom_common:
86     internal parameter controls, completements of implementations
87    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
88    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
89      (not seem any difference in testing results).
90    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
91       at face corners.
92    o pkg/generic_advdiff:
93     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
94      loop range indices for computing vertical advection tendency
95      and do the calculation in the interior only (no overlap) ;
96      for now, only implemented for SOM advection (to save CPU time).
97     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
98    o exch2 adjoint
99      First set of changes:
100      - add exch2 hand-written adjoint templates
101      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
102        This will require cleanup in pkg/autodiff/*.F
103        (changed routines currently kept separate in verif. code/)
104      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
105        that used to hide exch2 or cubed-sphere specific code
106        (commented via 'cph-exch2')
107    o pkg/seaice
108      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
109    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
110       output of global_ocean.cs32x15.thsice .
111    
112    checkpoint59e
113    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
114      for B-grid vector (not yet tested) and C-grid vector (<- only used
115      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
116    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
117      (#ifdef ALLOW_SALT_PLUME)
118    o gather_2d/scatter_2d: removed halo regions
119    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
120      scheme and the corresponding test case (under front_relax dir). For now,
121      only available with Skew-flux form and not yet tested in realistic set-up.
122      adjoint: store directives updated, but gradient checks deteriorated,
123      so maybe GM/Redi adjoint is now broken.
124    o seaice adjoint
125      * add AREA, HEFF, HSNOW as control variable
126        (should not change lab_sea results)
127      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
128    o pkg/seaice:
129      * added computation of saltFlux in seaice_growth;
130        For time being, sea ice salinity is assumed constant
131        contribution of snow flooding to freshening of sea ice is neglected.
132        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
133        defaults to 0.0 in order to maintain backward compatibility.
134        Typical values for SEAICE_salinity are 4 to 10 g/kg.
135      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
136      * added SEAICE_availHeatFrac, which specifies fraction of surface level
137        heat content used to melt or grow ice
138      * commented out cap of HICE: it helps keep ice thinner
139      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
140      * applied OBCS T/S mask to HEFFM sea ice mask
141    
142    checkpoint59d
143    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
144     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
145     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
146    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
147     and change default value of parameter "GM_Small_Number";
148     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
149       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
150       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
151    o pkg/ecco: cost function when applying pkg/smooth to controls
152    o pkg/ctrl: add forcingPrecond run time parameter
153    o pkg/seaice:
154     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
155     - fix bug in metric terms of u-equation in LSR solver (implicit part),
156       changes verification/lab_sea
157     - rearrange implicit part of u-equation in LSR solver to make it easier to
158       read, understand, and debug. This causes changes at the truncation level.
159     - fix (serious) bug in the boundary conditions (sign error in the implicit
160       part) of the LSR solver. Changes all LSR results.
161     - fixed problem with HSNOW initialization to avoid thick snow when AREA
162       is initilized with small values - does not change lab_sea results.
163     - added HsnowFile initialization capability
164    o pkg/smooth: addition to model/src and pkg/ctrl so allow
165     initialization of pkg/smooth and application to control vector
166    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
167    o dependencies: pkg/profiles requires pkg/cal
168    o pkg/profiles:
169     - added option ALLOW_PROFILES_GENERICGRID
170         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
171         that interpolation information (grid points and coefficients) is provided
172         within the netcdf input files.
173         -> sample matlab scripts can be found in MITgcm_contrib/gael
174         that allow you to prepare netcdf input files.
175     - also modified: cleaner include statements, cleaner error print statements,
176       cleaner stops when error, and more tests of the netcdf input files consistency.
177    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
178    o pkg/seaice:
179     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
180       requires a new routine: seaice_diagnostics_fill.F
181     - make sure that seaice does not move if not forced (pressure replacement
182       method, Hibler and Ip, 1995), changes results
183     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
184     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
185       It is turned off by default (=-1.), because it changes the results.
186     - make it possible to read AREA from a file, too.
187    
188    checkpoint59c
189    o add S/R and diagnostics for oceanic mixed-layer depth
190    o move GMRedi call after all vertical mixing schemes (including KPP)
191    o pkg/thsice:
192     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
193      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
194    o pkg/obcs:
195     - bug fix for balance code
196    o pkg/seaice:
197      - allow values of SEAICE_elasticParm > 1
198      - add new parameter SEAICE_evpTauRelax as an alternative
199        to SEAICE_elasticParm
200      - make lsr boundary conditions free slip (by default), changes result
201      - add code for no slip boundary conditions for lsr
202      - set minimum of zeta to zero (and not 4e8) (changes results)
203      - add a cap on AREA after advecting AREA if seaice_growth is not called
204    o change calculation of Visbeck K:
205      - no longer depend on tapering scheme; instead, compute slope (limited
206        by GM_maxSlope). this is equivalent to what was comuted before with
207        clipping or linear tappering.
208      - fix vertical averaging (wrong by 1/2 level)
209      - leave the old version (but will not be maintained) within
210        #ifdef OLD_VISBECK_CALC / #endif
211      - update output of exp. ideal_2D_oce
212    o change error catch in calc_r_star to improve vectorization
213    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
214      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
215    o adjoint:
216      Re-organized adjoint checkpointing according to Matt Mazloff
217      (but with modifs/completions/cleanups)
218      Storing is now bundled into large arrays to optimized I/O
219      (and second step in cleanup of the_main_loop)
220    
221    checkpoint59b
222    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
223      - export/import (between ocean & coupler) fields needed for ocean DIC.
224    o pkg/seaice:
225      - get rid of three more exchanges seaice_calc_viscosities (required
226        different loop boundaries in seaice_lsr and seaice_ocean_stress)
227      - bug fix in seaice_ocean_stress (update of lab_sea required)
228      - reduce loop boundaries to necessary minimum also in seaice_evp
229      - go back to the old way of computing deltaC/Z as the adjoint likes that
230        better
231    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
232      passive tracer to an Age Tracer) + update output.txt
233    o pkg/exf:
234      - implement A-grid / C-grid selection for wind-stress input files.
235      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
236      for now, in exf_bulk_largeyeager04.F only :
237      - change implementation for case where windspeed + 2. components wind-stress
238        are read-in. AND use rhoConstFresh to convert evap.
239    o pkg/seaice:
240      - use correct EXCH_UV for wind-forcing (on A-grid).
241      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
242        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
243    o pkg/exf:
244      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
245      EXF_INTERPOLATION:
246      - merge global_with_exf/code version of exf_interp_read.F
247        to the main code ;
248      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
249        reading the file ; Important: This options needs to be defined to recover
250        previous code.
251        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
252      - no longer loose real*8 precision along the way when using exf_iprec=64.
253    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
254      - change discretisation of evp-solver in order to avoid another exchange
255        (changes lab_sea) and clean up a little
256      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
257        help the adjoint (this also changes the results slightly)
258      - add a few "_d 0" where they had been missing in seaice_evp.F
259      - cleaning up: remove unused seaice_calc_rhs.F
260    o pkg/exf: some cleaning-up:
261      - change various "constants" into runtime parameters
262      - cleaned-up Large&Yeager04 routine which should eventually
263        replace exf_bulkformulae.F (changed names of S/R and CPP)
264        and merged various ALLOW_ATM_WIND options
265     only used with thsice pkg (in thsice_get_exf.F):
266      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
267        which are used when useStabilityFct_overIce=TRUE (= the default)
268      - change default values of ice & snow emissivity and scale downward LW
269        by ice & snow emissivity.
270    o pkg/thsice:
271     fix few little problems, in thsice_calc_thickn.F:
272      - growth vertically (and not laterally) if iceFrac == iceMaskMax
273      - melt only laterally if hIce < hThinIce (as the comments say)
274      and in thsice_extend.F:
275      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
276      - start to form ice as soon as the minimum ice-volume is reachable.
277     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
278      and cpl_aim+ocn
279    o pkg/kpp
280     - move computation of surface related input fields to KPP into a new
281       subroutine kpp_forcing_surf.F
282     - remove wrong (within bi,bj loops) EXCH calls.
283     - little cleaning (add argument myThid in last position, cvs header ...)
284     - for now, fix conservation problem by exchanging KPPviscAz (may not
285       be the best fix)
286    o pkg/seaice
287     - check for inconsistent evp parameter/cpp-flag combination
288     - remove leftover errIO flat for obsolete name list error handling
289    o OpenAD
290     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
291    
292    checkpoint59a
293    o pkg/seaice: some parameter clarifications and a little bit of clean up
294    o pkg/thsice: rename run-time parameters:
295       himin       -> hIceMin
296       himin0      -> hThinIce
297       hihig       -> hThickIce
298       i0          -> i0swFrac
299       transCoef   -> bMeltCoef
300       frac_energy -> fracMelting
301      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
302       with default values (for now) that do not change the results.
303      remove old version of thsice vars advection in pkg/seaice.
304    o in FFIELDS.h:
305      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
306      - make pLoad & sIceLoad always available (but still only used if
307         ATMOSPHERIC_LOADING is #define).
308    o pkg/kpp: replaced _KPP_RL with _RL
309    o bug fixes for vertical diffusivity computations when both KPP and
310        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
311        are no longer updating the vertical diffusivity array
312        (passed as argument) but are (re-) setting those arrays.
313    o pkg/seaice: fix bug in evp solver, while doing that
314      - change (improve?) discretization of stress computations for both
315        cgrid-lsr and evp solver
316      - add a new routine to compute strain rates
317      - the above changes lab_sea results
318      - add no slip conditions for evp solver (off by default), lsr-version
319        may follow
320      - fix exchange for shear at Z-points (does not change lab_sea)
321      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
322        (to force the user to pick a time step since there is not "safe" way
323        of choosing it)
324      - add principal stress diagnostics
325      - rearrange fields for evp a little to avoid having to call a: too many
326        exchanges and b: exchanges for stress trensor components which we do
327        not have.
328      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
329        of evp, complete rewrite for lsr case (latter is does not yet work
330        in all cases)
331    o pkg/kpp: add code to have mixing in shelf ice caverns
332      - add myThid to all kpp routines (long overdue)
333    
334    checkpoint59
335    o pkg/exf:
336      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
337        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
338      - move exf header files from lower_case.h to UPPER_CASE.h ;
339        add missing cvs Header & Name
340      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
341      - add namelist param. selectStressGridPosition, exf_monFreq
342      - retire many _CLIM routines, and remove data.exf_clim
343        + params moved to data.exf
344        + climsst, climsss now handled by exf_set_gen, i.e.
345          climss?period=0 refers to constant field,
346          climss?period=-12 to monthly forcing
347      - split up namelists in data.exf
348    o pkg/seaice:
349      - remove seaice_exch and seaice_exch_uv
350      - remove superfluous exchange of theta
351      - add myThid to seaice_budget_ocean/ice
352      - add new interface for atmospheric wind forcing (C-grid only)
353        + new routine
354        + two new field (taux, tauy for stress over ice)
355        + removed one global field (DAIRN) for C-grid case only
356    o pkg/thsise
357      - 2nd set of modifs for thsice adjoint in conjunction with exf
358    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
359    
360    checkpoint58y_post
361    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
362      vertical diffusivity, similar to that in MOM4; turned on using
363      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
364      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
365    o Added capability for 3D specification of background vertical diffusion
366      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
367      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
368      "data" file that contains the 3D vertical diffusivity coefficients.
369    o ice dynamics (pkg/seaice) with thsice thermodynamics:
370      - add code within pkg thsice to advect & diffuse sea-ice fields
371      similar to (and will replace) what has been added in  seaice_advdiff.F,
372      but: - conserving Mass, Heat & Salt.
373           - better when using non-linear advection scheme (not yet fully tested)
374           - can also be used in atmospheric set-up (for now, only the diffusion).
375    
376    checkpoint58x_post
377    o IO option for global-file compact format:
378      - add options when generating topology (utils/exch2/matlab-topology-generator)
379      - add I/O capability (pkg/mdsio).
380      - adapt utils/matlab/rdmds.m to read this format.
381      for now long-line format not yet supported by pkg/mdsio (& exch2).
382    o shelfice: add a few diagnostics
383    
384    checkpoint58w_post
385    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
386      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
387      (and replace horiVertRatio in NH code).
388      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
389                         and tutorial_plume_on_slope (sensitive to truncation)
390    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
391      directly to drive seaice model (C-grid only)
392    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
393     - reintroduce computation of wind from stress,
394     - compute tau (in exf_bulkformulae.F) from windstress averaged to
395       mass points to avoid tau = 0
396     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
397    o rdmnc.m: make it work with "global" files created with gluemnc
398    o rdmnc.m : some improvements in dealing with singleton dimension
399      (tested on all testreport mnc output files).
400    o genmake2: disable pkg/profiles if netcdf test fails.
401    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
402    o move call to cal_readparms up to make calendar parameters/variable available
403      to all packages
404    
405    checkpoint58v_post
406    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
407      useDynP_inEos_Zc tested.
408    o pkg/exf: changes to properly interpolate/mask/scale initial fields
409    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
410      and portions thereof.  See read_cs.txt for description and examples.
411    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
412      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
413      following the great-circle arc between those 2 points.
414    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
415      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
416    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
417     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
418     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
419     - still needs work (not working with some options ; efficiency to improve)
420       and serious testing.
421     - use this scheme for temperature & salinity in 2 advection test exp.:
422       advect_xy & advect_xz, respectively.
423    
424    checkpoint58u_post
425    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
426    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
427    o testreport: add option "-skipdir" to skip some test.
428    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
429      momentum calculation.
430    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
431    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
432      remove checkpoint.F and the_correction_step.F (no longer used);
433      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
434    o add option (linFSConserveTr) to correct for tracer source/sink due to
435      Linear Free surface
436    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
437    o pkg/thsice: fix reading mnc-pickups
438    
439    checkpoint58t_post
440    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
441    o pkg/mdsio:
442     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
443       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
444       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
445     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
446     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
447       either MDS_READ_FIELD or MDS_WRITE_FIELD )
448     - new S/R (to replace MDSWRITEMETA), which allows to write more
449       informations (variable names, time ...) to meta files.
450     - modify rdmds.m to give back the meta file content.
451    o pkg/diagnostics: change vertical interpolation to be safer, and more
452       flexible (define p-levels to interpolate to in data.diagnostics);
453      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
454       diagnostic pointer.
455    o pkg/seaice: more cleaning up of seaice_growth, added many comments
456    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
457    o fix multi-category seaice:
458     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
459       SEAICE_MULTICATEGORY
460     - fix short wave heat flux
461    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
462       and allow to use EVP solver. Change forward lab_sea: test both EVP
463       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
464    o Initial check-in of lab_sea adjoint
465      (very similar to natl_box_adjoint/code_seaice)
466      * used C-grid and EVP solver
467      * used KPP, GM/Redi
468      * uses inAdExact=.TRUE.
469      * gradient checks fail for both ADM and TLM
470        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
471        f.d. gradients actually seem more problematic than ADM, TLM gradients;
472        issue is related to forward mismatch between g77 an ifort
473    o pkg/seaice: overhaul of thermodynamics
474     - growth.F and groatb.F are replaced by new routine seaice_growth.F
475     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
476     - move a few global fields out of SEAICE.h into seaice_growth.F and
477       make them 2D (FICE/QNETO/ ...)
478     - remove FO (it is the same as QNETO)
479     - introduce a few local fields to avoid modifying external fields such
480       as atemp, etc.
481    
482    checkpoint58s_post
483    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
484      changed exf_set_gen.F so that
485        genperiod=0 means input file is one time-constant field and
486        genperiod=-12 means input file contains 12 monthly means
487    o CG2D: use pre-computed solver main-diagonal (stored in common block);
488      this affects truncation error ; generate new output file for exp. which
489      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
490        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
491        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
492        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
493        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
494        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
495    o start implementation of deep-atmosphere and anelastic formulation
496    o verification: remove 2nd copy of input files and use script "prepare_run"
497      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
498    o mom_common/vecinv/fluxform: fix a few initialisation isssues
499    o profiles: fix for multithreaded case
500    
501    o diagnostics: rename few diags:
502      s/'PRESSURE'/'RCENTER '/g
503      s/'TICE    '/'oceFreez'/g
504      s/'TAUX    '/'oceTAUX '/g
505      s/'TAUY    '/'oceTAUY '/g
506      s/'SWFLUX  '/'oceQsw  '/g
507      s/DIFx/DFxE/g
508      s/DIFy/DFyE/g
509      and add few ocean-forcing diagnostics:
510      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
511    o modifications to pkg/seaice/growth.F and budget.F, which change results of
512      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
513      as actual snow thickness.  It now refers everywhere to effective snow
514      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
515    
516    checkpoint58r_post
517    o modifications to pkg/seaice/growth.F, which change results of
518      lab_sea experiment: fixes pertain to melting snow over open water, to
519      masking EVAP under sea ice, and to using the correct AREA variable for
520      computations of EVAP, PRECIP, HSNOW, and GHEFF
521    o add ability to read bathy, salt, and theta using MNC (off by def)
522    o add flooding algorithm and advection of HSNOW for pkg/seaice;
523      both are turned off by default and do no change any results
524    o seaice advection with pkg/thsice: a step toward the use of non-linear
525      advection scheme, but #ifdef or commented out for now (requires more EXCH).
526    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
527      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
528      in natl_box (affects results @ truncation level: update output.txt)
529    o multi-threading and IO:
530      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
531      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
532        (needed to work with SingleCpuIO): tested in all verif. exp.
533    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
534      affects the results (but none of the verification test uses this scheme).
535    o Adding some pkg/diagnostics capability to pkg/seaice
536      (will certainly be subject to changes)
537    o ctrl: adding new control variables:
538      lwflux, lwdown, evap, snowprecip, apressure, runoff
539    
540    checkpoint58q_post
541    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
542      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
543      high_res_cube configuration by 4% on Columbia.
544    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
545      add (in global_with_exf/code) a version of EXF_INTERP_READ without
546      dynamical allocation (seems to work in multi-threaded).
547    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
548      single CPU io) so that TAF does not have to see EESUPPORT.h
549    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
550    
551    checkpoint58p_post
552    o obcs: stop if obcs is used with useCDscheme = .true.
553    o shelfice:
554     - fix a sign error so that no slip at shelfice interface works
555     - remove stop for combination non-hydrostatic code and shelfice. That does
556       not mean, that the results are correct, but at least they are numerically
557       stable
558    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
559    o added adjoint exch routined for all exch*3d* routines
560      and updated flow directives
561    
562    checkpoint58o_post
563    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
564      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
565    o change controling S/R for writing pickup file (new S/R do_write_pickup)
566      and clean-up reading/writing of pickup files.
567    o fix local version of read/write pickup (NH part) in rotating_tank/code
568    o simplify EXCH interface:
569     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
570     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
571    o added the regrid package
572    o shelfice:
573     - add a simple boundary layer scheme to reduce noise
574     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
575    
576    checkpoint58n_post
577    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
578       local variable (not in common block).
579    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
580      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
581      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
582        to work with SingleCpuIO.
583    o add "_d 0" to real constant of pkg/cfc subroutines ;
584       update exp. cfc_exemple & tutorial_cfc_offline output files.
585    o multi-threading and IO:
586      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
587        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
588      - barrier before and after reading.
589      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
590      - avoid using MDS_WRITELOCAL for LAND pkg output.
591      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
592        common-block variables ; Allows multi-threading with master-thread IO.
593    o change default MAX_NO_THREADS from 32 to 4 ;
594      and stop cleanly when MAX_NO_THREADS is too small.
595    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
596    
597    checkpoint58m_post
598    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
599       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
600    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
601       keep global_ocean.90x40x15 (for AD testing) with former secondary test
602       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
603    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
604        add MITgcm_tutorials (= code + all the tutorials)
605    o ecco, option to compute cost for total ssh (mean+anom)
606    o consistent with addition of ptracer and ssh in pkg/profiles
607    o profiles: adding ptracer and ssh
608    o testreport: change multi-test output-file name
609      (from output.txt.{name} to output.{name}.txt)
610    o profiles: now ok for mutli-tiles case
611    o seaice: add 4 parameters for different advection schemes for area,
612      (effective) seaice thickness, enthalphy, and snow height. Their default
613      is the standard parameter SEAICEadvScheme
614    o calc_gw:
615     - add cosFacU in zonal viscous flux (harmonic.visc.).
616     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
617       of tutorial_plume_on_slope.
618    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
619    o calc_gw: true flux-form, account for horizontal grid spacing.
620      update rotating_tank results, but not plume_on_slope (affected at
621      truncation level, 11 digits).
622    
623    checkpoint58l_post
624    o calc_gw:
625     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
626     - remove side-drag for now (need to fix it); update plume_on_slope results.
627     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
628    o commit code to make SST/SSS weights spatially variable
629      (based on either variable in-situ or variable initial T/S weights)
630    o pkg/ecco:
631      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
632        now based on horizontally varying weights wthetaLev, wsaltLev
633      * cost_averagesflags now returns year indices in addition to day, month
634      * sflux balance is performed on annual basis
635        (sflxumm, sfluxmm2, bal_sfluxmm)
636      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
637        including separate counting and multipliers
638    o pkg/rbcs
639      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
640    
641    checkpoint58k_post
642    o testreport:
643     - always build in dir. "build" (if not there, mkdir build instead of building
644       & running in input)
645     - run in dir run (if it exists), in build otherwise.
646     - call prepare_run (if input/prepare_run exists)
647     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
648    o pkg/exf modifications to interpolation and rotation routines for more
649       reasonable treatment of North Pole singularity: for tracers North Pole
650       value is set to northernmost zonal-mean value, for zonal velocity it is
651       set to zero, and for meridional velocity it is set to northernmost value.
652    o pkg/exf/exf_check_range.F
653     - add tile index to diagnostics and move stop statement to the very
654       end of the routine.
655    o pkg/diagnostics: (diagnostics_main_init.F)
656      define title of isomorphic variables according to the current config.
657    o pkg/thsice with pkg/seaice dynamics:
658    - fix domain of computation (interior only, required for exf) and do exchanges
659    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
660    o towards a standard way of dealing with multi-threading in MONITOR
661      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
662    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
663       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
664    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
665    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
666    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
667       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
668    o tracer advection:
669     - clean-up and simplify calc_common_factors.F
670     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
671       advection subroutine (but still not used within DST advection S/R)
672    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
673    
674    checkpoint58j_post
675    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
676      from file (collects calls previously in FORWARD_STEP)
677    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
678    o adjoint store dir. adjusted accordingly
679    o genmake2
680      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
681    
682    checkpoint58i_post
683    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
684      on wind stress (SEAICEstressFactor defaults to 1.)
685    o Total number of Timers is finite (<=40): comment out 2 non-essential one
686      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
687    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
688      on CS-grid: no longer loosing mass.
689    o exf & curvilinear-grid: no longer modify longitude xC & xG.
690    o pkg/ggl90: fix sloppy output and fix a bug
691    o pkg/seaice: added SEAICEuseEVPpickup parameter
692      - Set to false in order to start EVP solver with
693        non-EVP pickup files when using SEAICEuseEVP
694      - fix sign error in diffusion in seaice_calc_rhs
695    
696    checkpoint58h_post
697    * Modifications for bottom topography control
698      o replace hFacC by _hFacC at various places
699      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
700      o add non-self-adjoint cg2d_nsa
701      o update autodiff support routines
702      o re-initialise hfac after ctrl_depth_ini
703      o works for 5x5 box, doesnt work for global_ocean.90x40x15
704    * Adding verification for 5x5 box (4-layer) bottom topography control
705    
706    checkpoint58g_post
707    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
708       used for mean seasonal cycle, mean diurnal cycle); add an example
709       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
710    o pkg/ggl90:
711      - add parameter (minimum surface kinetic energy)
712      - fix bug (avoiding division by zero)
713    o couple pkg/thsice to pkg/seaice:
714      - modify advection in seaice to accomodate new scalar fields to be advected
715      - only muliDimAdection scheme work with seaice/thsice
716      - mapping of thsice-variables to seaice-variables, back and forth
717      - does not break the verification experiments, but does not give the
718        desired results either
719    o pkg/seaice
720      - make (default) second order advection a bit less confusing?
721    
722    checkpoint58f_post
723    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
724      to pkg/seaice):
725      - new routines thsice_map_exf and thsice_get_exf provide the interface
726      - add an additional formal parameter to thsice_solve4temp
727    o pkg/exf:
728      - add new fields wspeed, snowprecip (to be able to couple to thsice)
729      - correct Stefan-Boltzmann constant
730      - new parameter for longwave surface emittance
731      - separate some stuff from exf_bulkformulae into new routines  
732        exf_radiation, exf_wind
733      - add new parameters and constants: longwave emissivity for ocean, ice
734        and snow, evaporation parameters over ice
735      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
736        either wind from stress or stress from wind
737    o pkg/thSIce:
738    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
739    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
740       and THSICE_CALC_THICKN
741    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
742    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
743      to make debugging easier.
744    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
745    o pkg/bulk_force:
746      - clean-up comments and parameters ;
747      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
748    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
749      generate new output for test-experiment: aim.5l_cs.thSI
750    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
751      testreport accordingly
752    
753    checkpoint58e_post
754    o SEAICE_CGRID adjoint done
755    o R_STAR adjoint implemented.
756      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
757      * need to sort out init. of h0facc, etc.
758    o Make pkg/profile fully independent of ecco,cost, etc. stuff
759      to be able to use it in pure forward.
760    
761    checkpoint58d_post
762    o upgrade simple test-experiment to tutorial example:
763     step.1: duplicate the experiment and (step.2) will remove the old copy.
764      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
765      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
766      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
767      tutorial_global_oce_biogeo    <- copy of dic_example
768      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
769      tutorial_plume_on_slope       <- copy of plume_on_slope
770      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
771      tutorial_global_oce_optim     <- empty for now (David ?)
772      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
773     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
774    o correct a sign problem in cost_scat.F
775    o obcs and ptracers: fix boundary conditions for advections schemes
776      with larger stencil
777    o thsice adjoint: start
778    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
779      completeness
780    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
781      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
782    o ptracers adjoint:
783      * avoid extensive recomputatations
784      * fix missing re-init. of gptr (missed by TAF)
785    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
786      me to turn off the excessive output to STDOUT that this package produces
787    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
788      and add those terms in Vector-Invariant formulation.
789    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
790      if the control period (xx_hfluxperiod etc) is 0
791    o in profiles pkg, clean routines and fix details
792    o in ecco pkg, reading ssh data:
793      fix problem in case the model does not start at iter0=0
794    o fix mnc-pickup/restart for ptracers
795    o new package prifiles:
796      code to compute profile-based cost by Gael Forget
797      (modifs in ecco, ctrl, autodiff)
798    o Benign bug fix in initialization (spotted by M. Mazloff) of
799      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
800    
801    checkpoint58c_post
802    o adjoint: finish NLFS adjoint and provide reference output in
803      verification/global_ocean.90x40x15/results_ad_nlfs
804    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
805      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
806      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
807      with SEAICE_CGRID defined.
808    o move calendarDumps from "data" to "data.cal" and clean-up the code
809      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
810    o add useEXF & useCAL flags (for now, set in hard-coded way)
811    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
812      (were missing in NH mode, and wrong in quasihydrostatic mode).
813      waiting for Chris updated version of calc_gw to add those CALLs.
814    o fix bug in quasihydrostatic S/R ;
815      add a test for this option: global_ocean.90x40x15.qshyd
816    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
817      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
818    o add on/off flag useOffLine for package OFFLINE
819    o seaice:
820      - modify advection so that it works also on the C-grid
821      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
822        problem in multi-tile runs with C-grid
823      - add flags for clipping ice velocities and/or masking solver forcing
824      - fix drag (ocean on ice) formulation and a bug that caused noise in the
825        C-grid solver
826      - added a few comments to seaice_diffusion.F
827      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
828        are now exclusive)
829      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
830        required re-ordering the code a little:
831       + make DAIRN global variable (defined in SEAICE)
832       + move computation of the viscosities eta and zeta into a new separate
833         routine (because I need to recompute them in seaice_ocean_stress.F)
834    
835    checkpoint58b_post
836    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
837      update output.txt of exp. aim.5l_cs.thSI
838    o various mnc cleanups and improvements:
839      + shrink lookup tables by factor of ~4
840      + better error reporting when running out of lookup space
841      + able to handle longer path/file names (up to 500 chars)
842    o adjoint:
843      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
844      - TBD: "hidden" mom_vecinv recomp. in dynamics
845    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
846     (allow to differentiate between forcing components using new integer flags:
847      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
848     and add new flag to put Dissipation tendency out of Adams-Bashforth.
849    o ecco
850      - enable trend removal from SSH anomaly obs.
851    o adjoint
852      - a fix for PmEpR when #undef EXACT_CONSERV
853      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
854      - try to fix "hidden" recomp. in forward_step for NLFS
855        (NLFS seems broken sometimes after I checked it in)
856    o seaice:
857     - add c-grid version of the dynamic solver:
858       + three new routines that are the c-grid substitute lsr, dynsolver
859         and ostres
860       + put a few fields that were local to dynsolver into global common
861         blocks, so that I can move the computation of stresses etc into
862         seaice_lsr (saves coding but may break the adjoint).
863     - replace more hardwired parameters by runtime parameters
864     - add ice masks that mask the rhs of the implicit solvers where there
865       is no ice (commented out in seaice_dynsolver, because i am not sure
866       if this works properly), eventually this should replace the clipping
867       of ice velocities in seaice_dynsolver to +/-40cm/s.
868    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
869      include it only where its needed
870    o move balancing of fluxes before the call of external_forcing_surf
871    o seaice:
872      - correct units of turning angles (now they are really in degrees)
873      - move computation of GWATX/Y out of main routine into dynsolver
874      - initialize GWATX/Y in seaice_init
875    o Apply mask on Fresh-Water flux (needed for SSH forcing).
876      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
877    o seaice: add runtime flags for turning angles (default to zero)
878    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
879      and trend from exf forcing and ctrl control adjustments
880    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
881      (since checkpoint57x_post)
882    o change the default rotation period to 86164.s = the Earth rotation
883    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
884      and based on a reference stratification. Tested within hs94.cs-32x32x5.
885    o seaice advection: add code for choosing between the default (2nd order
886      central differences) and multiDim advection schemes provided by
887      pkg/generic_advdiff
888    o seaice:
889      - removed all references to SEAICE_GRID.h fields from
890        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
891        (cubed-sphere configuration will change a little)
892      - grid computations in seaice_init are obsolete now.
893      - cleaned up code a little so that is easier to read (hopefully).
894      - added new (better?) discretizations of default advection and diffusion
895        (turn on with SEAICEuseFluxForm)
896      - replace 1 in 3d global fields by kSurface in growth.F
897      
898    checkpoint58a_post
899    o seaice:
900      - bug fix in advect.F
901    o shelfice:
902      - separate shelfice load anomaly from pload (breaks with time
903        dependent forcing), => introduce constant field shelficeLoadAnomaly.
904        Its default is 0., but it may be computed more cleverly from (unknown)
905        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
906        done offline. A good approximation of the pressure load anomaly is
907        necessary to avoid large initial adjustment processes underneath
908        deep-reaching shelfice.
909      - small fix in ISOMIP shelfice_thermodynamics
910      - add more sophisticated thermodynamics of Hellmer (1989), this is
911        now the default
912      - give a few constants more intuitive names
913    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
914      if bulk formulae are used in long integration (especially EmPmR). Turn
915      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
916      if balancePrintMean, the imbalance that is substracted is printed to
917      STDOUT.
918    o fix bug (typo) in obcs_apply_eta.F
919    o add a new package shelfice which enables us to model the circulation
920      underneath shelf-ice with draughts of hundreds of meters.
921     - works
922     - to do: + include improved thermodynamics
923              + check whether kSurfC (from model/inc/SURFACE.h) can be used
924                instead of new field kTopC
925              + can we use topoFile, Ro_surf and existing code in ini_depth.F
926                instead of new field R_shelfIce and new code in ini_depth.F
927                and ini_mask_etc.F?
928              + adjust vertical mixing schemes?
929    o seaice pkg:
930     - add a cpp-flag to include a simple formula for a salinity dependent
931       freezing point of sea water at the surface
932     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
933       meridional stresses are now different (and hopefully correct)
934    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
935       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
936       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
937    o pkg/diagnostics: add options and parameters for regional-statistics
938       diagnostics ; define regions by reading a region-mask from a file
939       (might add other options later)
940    o pkg/bulk_force:
941     - add option and parameters to use AIM surface-flux formulae.
942     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
943       others forcing fields (defined in PARM05, parameter file "data") are loaded
944       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
945     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
946     - use the right EXCH call for uwind,vwind (to work on CS-grid).
947     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
948       and parameters (note: calcWindStress replaces .NOT.readwindstress).
949     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
950    
951    checkpoint58
952    o add "--embed-source" option to genmake2 which, when the supporting
953      tools can be compiled (as determined by genmake2) will turn on the
954      embed_files package which then embeds the entire MITgcm source code
955      (*.[fFhc] + Makefile) used for the build within the executable
956      - requested by CNH but off by default
957      - adds a paltry <9MB to the mitgcmuv executable in most cases
958      - only writes the output when useEMBEDSRC in eedata is true
959    o clean up 3-dim. relaxation codes:
960      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
961      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
962      * Thanks to Tom Haine for testing!
963    
964    checkpoint57z_post
965    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
966      affects output (@ truncation level) of exp. plume_on_slope ; updated.
967    o fix the pickup behavior for obcs in combination with ptracers
968    o fix a bug in ptracers_external_fields_load
969    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
970      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
971    o transfered surface NH pressure to eta field (if exactConserv).
972    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
973         and update lab_sea output.txt file.
974    o completing 3-dim. relaxation code: additional term
975         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
976      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
977      * At compile time, in "EXF_OPTIONS.h" set
978          #define  ALLOW_CLIMTEMP_RELAXATION
979          #define  ALLOW_CLIMSALT_RELAXATION
980      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
981          tauThetaClimRelax3Dim = 15552000.0,
982          tauSaltClimRelax3Dim  = 15552000.0,
983      * 3 cases:
984          1) Use a constant-in-time 3-dim. field
985          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
986          3) Real-time relax. to time-evolving prescribed field
987    o Adding Laplacian-type smoothness constraint on
988      initial and boundary (forcing) controls (ic, bc)
989      * enable at compile-time via
990        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
991      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
992      * Absolute scale somewhat unclear so far
993      * no area weighting was included since no other cost term does so far
994    
995    checkpoint57y_post
996    First step for a NLFS adjoint
997    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
998    o new init. routines for calc_r_star, calc_surf_dr
999    o still need to deal with ini_masks_etc
1000    o testreport seemed happy
1001    checkpoint57y_pre
1002    
1003    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
1004    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
1005    o add new offset feature to offline pkg (plus minor cleanup)
1006    o cfc fixes for final year of integration
1007    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
1008      be in GCHEM_OPTIONS).
1009    
1010    checkpoint57x_post
1011    o fix testreport Pb in multiple test experiment.
1012    o cleanup our namelist syntax in verification:
1013      - make it more F95 standards compliant (some work still needed)
1014      - allows the vast majority of our tests to work with gfortran
1015    o Non-Hydrostatic:
1016     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
1017     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
1018    o Allow to apply AB on T,S rather than on AB(gT,gS):
1019     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
1020     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
1021       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
1022     - need a "clever" read_pickup to restart from the other AB formulation
1023    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
1024    o remove some unused variables (reduces number of compiler warnings)
1025    o adjoint
1026      * Disable useVariableViscosity for adjoint for time being
1027        (there are a number of extensive recomputations)
1028      * Initialize certain variables needed for adjoint
1029    
1030    checkpoint57w_post
1031    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
1032                 fix the singleCpuIO RS version of MDSWRITEFIELD
1033       and add a WARNING if using globalFiles=T with multi-processors.
1034    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
1035      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
1036    o tracer advection scheme:
1037      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
1038       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
1039       was not very convenient).
1040      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
1041       (further tests needed for the implicit DST & Flux-Limiter schemes).
1042    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
1043      and sRef for convenience, handy, when you want to initialize
1044      ptracers in a large domain with a constant non-zero value. Also,
1045      untangle ptracers_init.F a little.
1046    
1047    checkpoint57v_post
1048    o change dome exp. to use variable viscosity in side-drag terms.
1049    o remove all the files from the cfc_offline test since they are now
1050      incorporated into tutorial_cfc_offline which has been producing
1051      identical results for a few days of testing
1052    o add new parameter: sideDragFactor to enable half-slip-side BC
1053      and change side-drag S/R to use viscosity from mom_calc_visc
1054      (can switch back by setting sideDragFactor=0.); affects results at
1055      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
1056       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
1057    o vorticity & strain are now computed without masking, to account for
1058      no-slip-side BC in variable viscosity calculation ; mask is applied
1059      anyway later on, before computing advection/coriolis terms.
1060    o modify exp4 to test new obcs support for reading from external files
1061      and for passive tracers
1062    o fix behavior of ptracers_monitor when monitor output is written to a
1063      netcdf-file; still not independent of monitor.F (writes in the same
1064      file).
1065    o change default value of tRef (put a uniform, meaningful value for ocean
1066      & atmos) and initialize sRef (was missing, as Martin mentioned).
1067    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
1068      to be proportional to enstrophy dissipation length.  Thus,
1069       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
1070      This is now consistent with Smagorinsky and with the manual.
1071    
1072    checkpoint57u_post
1073    o OBCS and PTRACERS: add open boundary support for passive tracers
1074      - either use homogenous (pseudo) v.Neumann conditions or prescribe
1075        OB-values from file; this is not different from the way theta and salinity
1076        are treated
1077      - however, Orlanski-radiation conditions are not supported, and the model
1078        will stop if you use pTracers and Orlanski at the same time.
1079      - beefed up the rountine obcs_external_fields_load: now only those open
1080        boundary values are overwritten with values from files for which there
1081        are really files, otherwise the OB-fields remain untouched. This makes
1082        it possible to use different OBs at different ends of the domain (as
1083        with EXF)
1084    o reduce number of exch calls in shap_filt (s2).
1085    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
1086      truncation level) 4/5 MLAdjust test results (11&12 digits match).
1087    
1088    checkpoint57t_post
1089    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
1090    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
1091      same truncation, independent of the face number: affects affects several
1092      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
1093    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
1094      note that biharmonic viscosity + no-slip was not tested in any experiment.
1095    o fix bug in non-linear free-surf side-drag ; generate new output for
1096      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
1097    o make mnc honor the writeBinaryPrec flag for most kinds of output
1098    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
1099    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
1100      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
1101    o add brackets in multi-terms sum to get same truncation, independent of
1102      the face number (manage to get exactly same value of gU,gV at the cs-edge)
1103      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
1104    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
1105      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
1106      a maximum grid-scale Reynolds number.  Also, changes all length calculations
1107      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
1108      Suggested values of viscosity parameters found in mom_calc_visc.
1109      Many new viscosity diagnostics available.
1110    
1111    checkpoint57s_post
1112    o Add clearing-house for viscosity calculations, mom_calc_visc and
1113      correct numerous bugs in LeithD and Smagorinsky discretizations.  
1114      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
1115      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
1116      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
1117      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
1118      The Strain-Tension form is now called with useStrainTensonVisc=.true.
1119      ViscAhStrain and viscAhTension are now retired.
1120    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
1121    o In response to JMC's bug report, genmake2 now ignores any soft-links
1122      that it finds in the *current* directory when searching for files.
1123      Soft-links found in any other source directories will still work as
1124      they did before.
1125    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
1126      a C routine to unlimit the stack size
1127    o mnc-ify pkg/aim snapshot vars
1128    o mnc-ify pkg/land as requested by Daniel
1129    o various changes to mnc including:
1130      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
1131      - output can now be grouped so that all files within a group
1132          change the ITER portion of their names in lock-step together
1133      - can now read ("global") PER-FACE (in addition to PER-TILE) files
1134          and works with both EXCH1 and EXCH2 (but needs more testing)
1135      - writing works for all verification test cases w/ g77 on Linux
1136    
1137    checkpoint57r_post
1138    o make MNC variable initialization happen earlier
1139    o add diagnostics for (almost) each term of the momentum Eq.
1140    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
1141    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
1142    o remove MINIMAL_TAVE_OUTPUT option ;
1143      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
1144    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
1145      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
1146    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
1147    o add time-dependent SST, SSS control
1148    o cost terms in ecco/ modularized (new cost_generic.F)
1149    o cost_averages routines are modularized (new cost_averagesgeneric.F)
1150    o new infrastructure for seaice model vs. obs misfits in seaice/
1151      * driver from the_main_loop.F is seaice_cost_driver.F
1152      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
1153      * gradient check in Exp. 6a of natl_box_adjoint/
1154    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
1155      (see README file)
1156    
1157    checkpoint57q_post
1158    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
1159    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
1160      - bug was reported by Jean-Michel and Ian Fenty
1161    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
1162      update exp. cpl_aim+ocn output.
1163    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
1164      Needed for high-res. runs with large global files
1165      to be able to limit tapelev size
1166    o Changed some tests for adjoint:
1167      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
1168      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
1169      * global_ocean.90x40x15/ back to default 3-level checkpointing
1170    o Modifications to enable scripted COMMON to MODULE conversion
1171      * verification/OpenAD/code/ has necessary scripts and description;
1172      * converts, compiles and runs successfully;
1173    
1174    checkpoint57p_post
1175    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
1176    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
1177      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
1178    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
1179    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
1180      (was already the case for dissipation with mom_vecinv,
1181       and also the case for grad.PhiHyd when staggered-timeStep)
1182      This will allow to put dissipation out-off the AB time-stepping.
1183     Unfortunately, affects truncation error. Update output of exp. that "fails"
1184      (cg2d matching number) and leave the others for later: front_relax(10),
1185      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
1186      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
1187    
1188    checkpoint57o_post
1189    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
1190      (2) its ready to be documented during the 20050801 DocFest
1191    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
1192      for ideal_2D_oce and lab_sea on linux_ia32_g77
1193    o set to #undef CTRL_SET_OLD_MAXCVARS_30
1194      in global1x1_tot/code_seaice_adj to access indices 32, 33
1195      (worth another tag)
1196    
1197    checkpoint57n_post
1198    o adding precip control xx_precip 32
1199    o adding swflux control xx_swflux 33
1200    o Replacing 10 forcing penalty cost routines by 1 generic.
1201    o Implementing partitioning in time-mean and variable adjustment
1202      for atmos. state.
1203    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
1204  o in natl_box_adjoint:  o in natl_box_adjoint:
1205    * updated: results_bulk/    * updated exp 1 to 10
1206    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
1207    o updated global1x1/*_seaice_adj/
1208      to incorporate latest changes
1209    o enable useSingleCpuIO for mdsio vector routines
1210      (applies in particular to tapelev I/O)
1211    o removed inefficient K-loop in all active_file*control*.F
1212    
1213  checkpoint57m_post  checkpoint57m_post
1214  o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)  o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
Legend:
Removed from v.1.519  
changed lines
  Added in v.1.883
  ViewVC Help
Powered by ViewVC 1.1.22