/[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 1.880 by jmc, Fri Sep 21 21:37:11 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 testreport:
8  o moved ptracer ctrl index 17 -> 32    - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
9        monitor & update offline_exf_seaice exp. output.
10      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
11    o pkg/seaice:
12      - bug fix in the evp solver: boundary conditions were affected be
13        masking of zMax/zMin (changes results)
14      - minor bug fix in boundary conditions in seaice_calc_strainrates
15        (changes results for no_slip)
16      - seaice_lsr.F: make interpolation of eta dependent on boundaries
17      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
18      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
19        stress formulation and no-slip boundary conditions
20    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
21      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
22    o pkg/seaice: a first HSALT time stepping equation has been checked in
23    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
24      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
25      without requiring DO-IF statements
26    o pkg/thsice:
27      use continuous power-law function for partition of energy between lateral
28      melting/freezing and thinning/thickening ; old code using step function
29      still available with #undef THSICE_FRACEN_POWERLAW
30      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
31    o testreport: change AD testing : check against results/output_adm.txt
32      using same scripts as for forward test.
33    
34    checkpoint59g
35    o adjoint testing: in preparation for changing testreport:
36      - output format: cost and grad written on separated lines
37      - ad output results in directory "results" (instead of "results_ad")
38    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
39    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
40    o pkg/ecco: allow user defined cost function contributions
41    o testreport:
42      Allow to choose (per experiment) the list of tested output variables
43       and the main variable (used to issue a pass/FAIL ) ;
44      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
45      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
46      Also modify printing of summary:
47       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
48       b) echo the list of tested variables in the individual summary.txt of
49          each experiment.
50    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
51      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
52      (but still depend on the tile decompostion of the domain).
53    o pkg/seaice: change a discretization detail to make the B-grid code
54      "more symmetric". This change is likely to remove all "ridges/leads" that
55      where quasi-aligned with the grid in B-grid solutions. It may also be
56      the solution to the stress coupling issues with the B-grid.
57    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
58      remove .cvsignore from input dir. (since testreport no longer run here).
59    o pkg/thsice:
60     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
61     - fix reshaping of sea-ice just after advection:
62       melt all the ice only if ice-volume is too small.
63     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
64       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
65     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
66    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
67      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
68    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
69      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
70      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
71      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
72      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
73      -> update output.txt
74    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
75     this affects truncation error: -> update output.txt of exp:
76      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
77      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
78    
79    checkpoint59f
80    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
81    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
82      a bounded range (in forward mode)
83    o pkg/ecco, ctrl, autodiff and mom_common:
84     internal parameter controls, completements of implementations
85    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
86    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
87      (not seem any difference in testing results).
88    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
89       at face corners.
90    o pkg/generic_advdiff:
91     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
92      loop range indices for computing vertical advection tendency
93      and do the calculation in the interior only (no overlap) ;
94      for now, only implemented for SOM advection (to save CPU time).
95     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
96    o exch2 adjoint
97      First set of changes:
98      - add exch2 hand-written adjoint templates
99      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
100        This will require cleanup in pkg/autodiff/*.F
101        (changed routines currently kept separate in verif. code/)
102      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
103        that used to hide exch2 or cubed-sphere specific code
104        (commented via 'cph-exch2')
105    o pkg/seaice
106      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
107    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
108       output of global_ocean.cs32x15.thsice .
109    
110    checkpoint59e
111    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
112      for B-grid vector (not yet tested) and C-grid vector (<- only used
113      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
114    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
115      (#ifdef ALLOW_SALT_PLUME)
116    o gather_2d/scatter_2d: removed halo regions
117    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
118      scheme and the corresponding test case (under front_relax dir). For now,
119      only available with Skew-flux form and not yet tested in realistic set-up.
120      adjoint: store directives updated, but gradient checks deteriorated,
121      so maybe GM/Redi adjoint is now broken.
122    o seaice adjoint
123      * add AREA, HEFF, HSNOW as control variable
124        (should not change lab_sea results)
125      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
126    o pkg/seaice:
127      * added computation of saltFlux in seaice_growth;
128        For time being, sea ice salinity is assumed constant
129        contribution of snow flooding to freshening of sea ice is neglected.
130        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
131        defaults to 0.0 in order to maintain backward compatibility.
132        Typical values for SEAICE_salinity are 4 to 10 g/kg.
133      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
134      * added SEAICE_availHeatFrac, which specifies fraction of surface level
135        heat content used to melt or grow ice
136      * commented out cap of HICE: it helps keep ice thinner
137      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
138      * applied OBCS T/S mask to HEFFM sea ice mask
139    
140    checkpoint59d
141    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
142     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
143     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
144    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
145     and change default value of parameter "GM_Small_Number";
146     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
147       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
148       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
149    o pkg/ecco: cost function when applying pkg/smooth to controls
150    o pkg/ctrl: add forcingPrecond run time parameter
151    o pkg/seaice:
152     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
153     - fix bug in metric terms of u-equation in LSR solver (implicit part),
154       changes verification/lab_sea
155     - rearrange implicit part of u-equation in LSR solver to make it easier to
156       read, understand, and debug. This causes changes at the truncation level.
157     - fix (serious) bug in the boundary conditions (sign error in the implicit
158       part) of the LSR solver. Changes all LSR results.
159     - fixed problem with HSNOW initialization to avoid thick snow when AREA
160       is initilized with small values - does not change lab_sea results.
161     - added HsnowFile initialization capability
162    o pkg/smooth: addition to model/src and pkg/ctrl so allow
163     initialization of pkg/smooth and application to control vector
164    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
165    o dependencies: pkg/profiles requires pkg/cal
166    o pkg/profiles:
167     - added option ALLOW_PROFILES_GENERICGRID
168         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
169         that interpolation information (grid points and coefficients) is provided
170         within the netcdf input files.
171         -> sample matlab scripts can be found in MITgcm_contrib/gael
172         that allow you to prepare netcdf input files.
173     - also modified: cleaner include statements, cleaner error print statements,
174       cleaner stops when error, and more tests of the netcdf input files consistency.
175    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
176    o pkg/seaice:
177     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
178       requires a new routine: seaice_diagnostics_fill.F
179     - make sure that seaice does not move if not forced (pressure replacement
180       method, Hibler and Ip, 1995), changes results
181     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
182     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
183       It is turned off by default (=-1.), because it changes the results.
184     - make it possible to read AREA from a file, too.
185    
186    checkpoint59c
187    o add S/R and diagnostics for oceanic mixed-layer depth
188    o move GMRedi call after all vertical mixing schemes (including KPP)
189    o pkg/thsice:
190     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
191      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
192    o pkg/obcs:
193     - bug fix for balance code
194    o pkg/seaice:
195      - allow values of SEAICE_elasticParm > 1
196      - add new parameter SEAICE_evpTauRelax as an alternative
197        to SEAICE_elasticParm
198      - make lsr boundary conditions free slip (by default), changes result
199      - add code for no slip boundary conditions for lsr
200      - set minimum of zeta to zero (and not 4e8) (changes results)
201      - add a cap on AREA after advecting AREA if seaice_growth is not called
202    o change calculation of Visbeck K:
203      - no longer depend on tapering scheme; instead, compute slope (limited
204        by GM_maxSlope). this is equivalent to what was comuted before with
205        clipping or linear tappering.
206      - fix vertical averaging (wrong by 1/2 level)
207      - leave the old version (but will not be maintained) within
208        #ifdef OLD_VISBECK_CALC / #endif
209      - update output of exp. ideal_2D_oce
210    o change error catch in calc_r_star to improve vectorization
211    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
212      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
213    o adjoint:
214      Re-organized adjoint checkpointing according to Matt Mazloff
215      (but with modifs/completions/cleanups)
216      Storing is now bundled into large arrays to optimized I/O
217      (and second step in cleanup of the_main_loop)
218    
219    checkpoint59b
220    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
221      - export/import (between ocean & coupler) fields needed for ocean DIC.
222    o pkg/seaice:
223      - get rid of three more exchanges seaice_calc_viscosities (required
224        different loop boundaries in seaice_lsr and seaice_ocean_stress)
225      - bug fix in seaice_ocean_stress (update of lab_sea required)
226      - reduce loop boundaries to necessary minimum also in seaice_evp
227      - go back to the old way of computing deltaC/Z as the adjoint likes that
228        better
229    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
230      passive tracer to an Age Tracer) + update output.txt
231    o pkg/exf:
232      - implement A-grid / C-grid selection for wind-stress input files.
233      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
234      for now, in exf_bulk_largeyeager04.F only :
235      - change implementation for case where windspeed + 2. components wind-stress
236        are read-in. AND use rhoConstFresh to convert evap.
237    o pkg/seaice:
238      - use correct EXCH_UV for wind-forcing (on A-grid).
239      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
240        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
241    o pkg/exf:
242      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
243      EXF_INTERPOLATION:
244      - merge global_with_exf/code version of exf_interp_read.F
245        to the main code ;
246      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
247        reading the file ; Important: This options needs to be defined to recover
248        previous code.
249        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
250      - no longer loose real*8 precision along the way when using exf_iprec=64.
251    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
252      - change discretisation of evp-solver in order to avoid another exchange
253        (changes lab_sea) and clean up a little
254      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
255        help the adjoint (this also changes the results slightly)
256      - add a few "_d 0" where they had been missing in seaice_evp.F
257      - cleaning up: remove unused seaice_calc_rhs.F
258    o pkg/exf: some cleaning-up:
259      - change various "constants" into runtime parameters
260      - cleaned-up Large&Yeager04 routine which should eventually
261        replace exf_bulkformulae.F (changed names of S/R and CPP)
262        and merged various ALLOW_ATM_WIND options
263     only used with thsice pkg (in thsice_get_exf.F):
264      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
265        which are used when useStabilityFct_overIce=TRUE (= the default)
266      - change default values of ice & snow emissivity and scale downward LW
267        by ice & snow emissivity.
268    o pkg/thsice:
269     fix few little problems, in thsice_calc_thickn.F:
270      - growth vertically (and not laterally) if iceFrac == iceMaskMax
271      - melt only laterally if hIce < hThinIce (as the comments say)
272      and in thsice_extend.F:
273      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
274      - start to form ice as soon as the minimum ice-volume is reachable.
275     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
276      and cpl_aim+ocn
277    o pkg/kpp
278     - move computation of surface related input fields to KPP into a new
279       subroutine kpp_forcing_surf.F
280     - remove wrong (within bi,bj loops) EXCH calls.
281     - little cleaning (add argument myThid in last position, cvs header ...)
282     - for now, fix conservation problem by exchanging KPPviscAz (may not
283       be the best fix)
284    o pkg/seaice
285     - check for inconsistent evp parameter/cpp-flag combination
286     - remove leftover errIO flat for obsolete name list error handling
287    o OpenAD
288     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
289    
290    checkpoint59a
291    o pkg/seaice: some parameter clarifications and a little bit of clean up
292    o pkg/thsice: rename run-time parameters:
293       himin       -> hIceMin
294       himin0      -> hThinIce
295       hihig       -> hThickIce
296       i0          -> i0swFrac
297       transCoef   -> bMeltCoef
298       frac_energy -> fracMelting
299      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
300       with default values (for now) that do not change the results.
301      remove old version of thsice vars advection in pkg/seaice.
302    o in FFIELDS.h:
303      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
304      - make pLoad & sIceLoad always available (but still only used if
305         ATMOSPHERIC_LOADING is #define).
306    o pkg/kpp: replaced _KPP_RL with _RL
307    o bug fixes for vertical diffusivity computations when both KPP and
308        3D diffusivity arrays are used.
309    o pkg/seaice: fix bug in evp solver, while doing that
310      - change (improve?) discretization of stress computations for both
311        cgrid-lsr and evp solver
312      - add a new routine to compute strain rates
313      - the above changes lab_sea results
314      - add no slip conditions for evp solver (off by default), lsr-version
315        may follow
316      - fix exchange for shear at Z-points (does not change lab_sea)
317      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
318        (to force the user to pick a time step since there is not "safe" way
319        of choosing it)
320      - add principal stress diagnostics
321      - rearrange fields for evp a little to avoid having to call a: too many
322        exchanges and b: exchanges for stress trensor components which we do
323        not have.
324      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
325        of evp, complete rewrite for lsr case (latter is does not yet work
326        in all cases)
327    o pkg/kpp: add code to have mixing in shelf ice caverns
328      - add myThid to all kpp routines (long overdue)
329    
330    checkpoint59
331    o pkg/exf:
332      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
333        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
334      - move exf header files from lower_case.h to UPPER_CASE.h ;
335        add missing cvs Header & Name
336      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
337      - add namelist param. selectStressGridPosition, exf_monFreq
338      - retire many _CLIM routines, and remove data.exf_clim
339        + params moved to data.exf
340        + climsst, climsss now handled by exf_set_gen, i.e.
341          climss?period=0 refers to constant field,
342          climss?period=-12 to monthly forcing
343      - split up namelists in data.exf
344    o pkg/seaice:
345      - remove seaice_exch and seaice_exch_uv
346      - remove superfluous exchange of theta
347      - add myThid to seaice_budget_ocean/ice
348      - add new interface for atmospheric wind forcing (C-grid only)
349        + new routine
350        + two new field (taux, tauy for stress over ice)
351        + removed one global field (DAIRN) for C-grid case only
352    o pkg/thsise
353      - 2nd set of modifs for thsice adjoint in conjunction with exf
354    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
355    
356    checkpoint58y_post
357    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
358      vertical diffusivity, similar to that in MOM4; turned on using
359      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
360      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
361    o Added capability for 3D specification of background vertical diffusion
362      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
363      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
364      "data" file that contains the 3D vertical diffusivity coefficients.
365    o ice dynamics (pkg/seaice) with thsice thermodynamics:
366      - add code within pkg thsice to advect & diffuse sea-ice fields
367      similar to (and will replace) what has been added in  seaice_advdiff.F,
368      but: - conserving Mass, Heat & Salt.
369           - better when using non-linear advection scheme (not yet fully tested)
370           - can also be used in atmospheric set-up (for now, only the diffusion).
371    
372    checkpoint58x_post
373    o IO option for global-file compact format:
374      - add options when generating topology (utils/exch2/matlab-topology-generator)
375      - add I/O capability (pkg/mdsio).
376      - adapt utils/matlab/rdmds.m to read this format.
377      for now long-line format not yet supported by pkg/mdsio (& exch2).
378    o shelfice: add a few diagnostics
379    
380    checkpoint58w_post
381    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
382      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
383      (and replace horiVertRatio in NH code).
384      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
385                         and tutorial_plume_on_slope (sensitive to truncation)
386    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
387      directly to drive seaice model (C-grid only)
388    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
389     - reintroduce computation of wind from stress,
390     - compute tau (in exf_bulkformulae.F) from windstress averaged to
391       mass points to avoid tau = 0
392     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
393    o rdmnc.m: make it work with "global" files created with gluemnc
394    o rdmnc.m : some improvements in dealing with singleton dimension
395      (tested on all testreport mnc output files).
396    o genmake2: disable pkg/profiles if netcdf test fails.
397    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
398    o move call to cal_readparms up to make calendar parameters/variable available
399      to all packages
400    
401    checkpoint58v_post
402    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
403      useDynP_inEos_Zc tested.
404    o pkg/exf: changes to properly interpolate/mask/scale initial fields
405    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
406      and portions thereof.  See read_cs.txt for description and examples.
407    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
408      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
409      following the great-circle arc between those 2 points.
410    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
411      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
412    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
413     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
414     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
415     - still needs work (not working with some options ; efficiency to improve)
416       and serious testing.
417     - use this scheme for temperature & salinity in 2 advection test exp.:
418       advect_xy & advect_xz, respectively.
419    
420    checkpoint58u_post
421    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
422    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
423    o testreport: add option "-skipdir" to skip some test.
424    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
425      momentum calculation.
426    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
427    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
428      remove checkpoint.F and the_correction_step.F (no longer used);
429      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
430    o add option (linFSConserveTr) to correct for tracer source/sink due to
431      Linear Free surface
432    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
433    o pkg/thsice: fix reading mnc-pickups
434    
435    checkpoint58t_post
436    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
437    o pkg/mdsio:
438     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
439       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
440       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
441     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
442     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
443       either MDS_READ_FIELD or MDS_WRITE_FIELD )
444     - new S/R (to replace MDSWRITEMETA), which allows to write more
445       informations (variable names, time ...) to meta files.
446     - modify rdmds.m to give back the meta file content.
447    o pkg/diagnostics: change vertical interpolation to be safer, and more
448       flexible (define p-levels to interpolate to in data.diagnostics);
449      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
450       diagnostic pointer.
451    o pkg/seaice: more cleaning up of seaice_growth, added many comments
452    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
453    o fix multi-category seaice:
454     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
455       SEAICE_MULTICATEGORY
456     - fix short wave heat flux
457    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
458       and allow to use EVP solver. Change forward lab_sea: test both EVP
459       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
460    o Initial check-in of lab_sea adjoint
461      (very similar to natl_box_adjoint/code_seaice)
462      * used C-grid and EVP solver
463      * used KPP, GM/Redi
464      * uses inAdExact=.TRUE.
465      * gradient checks fail for both ADM and TLM
466        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
467        f.d. gradients actually seem more problematic than ADM, TLM gradients;
468        issue is related to forward mismatch between g77 an ifort
469    o pkg/seaice: overhaul of thermodynamics
470     - growth.F and groatb.F are replaced by new routine seaice_growth.F
471     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
472     - move a few global fields out of SEAICE.h into seaice_growth.F and
473       make them 2D (FICE/QNETO/ ...)
474     - remove FO (it is the same as QNETO)
475     - introduce a few local fields to avoid modifying external fields such
476       as atemp, etc.
477    
478    checkpoint58s_post
479    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
480      changed exf_set_gen.F so that
481        genperiod=0 means input file is one time-constant field and
482        genperiod=-12 means input file contains 12 monthly means
483    o CG2D: use pre-computed solver main-diagonal (stored in common block);
484      this affects truncation error ; generate new output file for exp. which
485      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
486        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
487        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
488        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
489        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
490        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
491    o start implementation of deep-atmosphere and anelastic formulation
492    o verification: remove 2nd copy of input files and use script "prepare_run"
493      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
494    o mom_common/vecinv/fluxform: fix a few initialisation isssues
495    o profiles: fix for multithreaded case
496    
497    o diagnostics: rename few diags:
498      s/'PRESSURE'/'RCENTER '/g
499      s/'TICE    '/'oceFreez'/g
500      s/'TAUX    '/'oceTAUX '/g
501      s/'TAUY    '/'oceTAUY '/g
502      s/'SWFLUX  '/'oceQsw  '/g
503      s/DIFx/DFxE/g
504      s/DIFy/DFyE/g
505      and add few ocean-forcing diagnostics:
506      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
507    o modifications to pkg/seaice/growth.F and budget.F, which change results of
508      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
509      as actual snow thickness.  It now refers everywhere to effective snow
510      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
511    
512    checkpoint58r_post
513    o modifications to pkg/seaice/growth.F, which change results of
514      lab_sea experiment: fixes pertain to melting snow over open water, to
515      masking EVAP under sea ice, and to using the correct AREA variable for
516      computations of EVAP, PRECIP, HSNOW, and GHEFF
517    o add ability to read bathy, salt, and theta using MNC (off by def)
518    o add flooding algorithm and advection of HSNOW for pkg/seaice;
519      both are turned off by default and do no change any results
520    o seaice advection with pkg/thsice: a step toward the use of non-linear
521      advection scheme, but #ifdef or commented out for now (requires more EXCH).
522    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
523      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
524      in natl_box (affects results @ truncation level: update output.txt)
525    o multi-threading and IO:
526      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
527      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
528        (needed to work with SingleCpuIO): tested in all verif. exp.
529    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
530      affects the results (but none of the verification test uses this scheme).
531    o Adding some pkg/diagnostics capability to pkg/seaice
532      (will certainly be subject to changes)
533    o ctrl: adding new control variables:
534      lwflux, lwdown, evap, snowprecip, apressure, runoff
535    
536    checkpoint58q_post
537    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
538      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
539      high_res_cube configuration by 4% on Columbia.
540    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
541      add (in global_with_exf/code) a version of EXF_INTERP_READ without
542      dynamical allocation (seems to work in multi-threaded).
543    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
544      single CPU io) so that TAF does not have to see EESUPPORT.h
545    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
546    
547    checkpoint58p_post
548    o obcs: stop if obcs is used with useCDscheme = .true.
549    o shelfice:
550     - fix a sign error so that no slip at shelfice interface works
551     - remove stop for combination non-hydrostatic code and shelfice. That does
552       not mean, that the results are correct, but at least they are numerically
553       stable
554    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
555    o added adjoint exch routined for all exch*3d* routines
556      and updated flow directives
557    
558    checkpoint58o_post
559    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
560      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
561    o change controling S/R for writing pickup file (new S/R do_write_pickup)
562      and clean-up reading/writing of pickup files.
563    o fix local version of read/write pickup (NH part) in rotating_tank/code
564    o simplify EXCH interface:
565     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
566     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
567    o added the regrid package
568    o shelfice:
569     - add a simple boundary layer scheme to reduce noise
570     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
571    
572    checkpoint58n_post
573    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
574       local variable (not in common block).
575    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
576      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
577      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
578        to work with SingleCpuIO.
579    o add "_d 0" to real constant of pkg/cfc subroutines ;
580       update exp. cfc_exemple & tutorial_cfc_offline output files.
581    o multi-threading and IO:
582      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
583        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
584      - barrier before and after reading.
585      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
586      - avoid using MDS_WRITELOCAL for LAND pkg output.
587      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
588        common-block variables ; Allows multi-threading with master-thread IO.
589    o change default MAX_NO_THREADS from 32 to 4 ;
590      and stop cleanly when MAX_NO_THREADS is too small.
591    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
592    
593    checkpoint58m_post
594    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
595       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
596    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
597       keep global_ocean.90x40x15 (for AD testing) with former secondary test
598       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
599    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
600        add MITgcm_tutorials (= code + all the tutorials)
601    o ecco, option to compute cost for total ssh (mean+anom)
602    o consistent with addition of ptracer and ssh in pkg/profiles
603    o profiles: adding ptracer and ssh
604    o testreport: change multi-test output-file name
605      (from output.txt.{name} to output.{name}.txt)
606    o profiles: now ok for mutli-tiles case
607    o seaice: add 4 parameters for different advection schemes for area,
608      (effective) seaice thickness, enthalphy, and snow height. Their default
609      is the standard parameter SEAICEadvScheme
610    o calc_gw:
611     - add cosFacU in zonal viscous flux (harmonic.visc.).
612     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
613       of tutorial_plume_on_slope.
614    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
615    o calc_gw: true flux-form, account for horizontal grid spacing.
616      update rotating_tank results, but not plume_on_slope (affected at
617      truncation level, 11 digits).
618    
619    checkpoint58l_post
620    o calc_gw:
621     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
622     - remove side-drag for now (need to fix it); update plume_on_slope results.
623     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
624    o commit code to make SST/SSS weights spatially variable
625      (based on either variable in-situ or variable initial T/S weights)
626    o pkg/ecco:
627      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
628        now based on horizontally varying weights wthetaLev, wsaltLev
629      * cost_averagesflags now returns year indices in addition to day, month
630      * sflux balance is performed on annual basis
631        (sflxumm, sfluxmm2, bal_sfluxmm)
632      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
633        including separate counting and multipliers
634    o pkg/rbcs
635      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
636    
637    checkpoint58k_post
638    o testreport:
639     - always build in dir. "build" (if not there, mkdir build instead of building
640       & running in input)
641     - run in dir run (if it exists), in build otherwise.
642     - call prepare_run (if input/prepare_run exists)
643     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
644    o pkg/exf modifications to interpolation and rotation routines for more
645       reasonable treatment of North Pole singularity: for tracers North Pole
646       value is set to northernmost zonal-mean value, for zonal velocity it is
647       set to zero, and for meridional velocity it is set to northernmost value.
648    o pkg/exf/exf_check_range.F
649     - add tile index to diagnostics and move stop statement to the very
650       end of the routine.
651    o pkg/diagnostics: (diagnostics_main_init.F)
652      define title of isomorphic variables according to the current config.
653    o pkg/thsice with pkg/seaice dynamics:
654    - fix domain of computation (interior only, required for exf) and do exchanges
655    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
656    o towards a standard way of dealing with multi-threading in MONITOR
657      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
658    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
659       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
660    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
661    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
662    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
663       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
664    o tracer advection:
665     - clean-up and simplify calc_common_factors.F
666     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
667       advection subroutine (but still not used within DST advection S/R)
668    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
669    
670    checkpoint58j_post
671    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
672      from file (collects calls previously in FORWARD_STEP)
673    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
674    o adjoint store dir. adjusted accordingly
675    o genmake2
676      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
677    
678    checkpoint58i_post
679    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
680      on wind stress (SEAICEstressFactor defaults to 1.)
681    o Total number of Timers is finite (<=40): comment out 2 non-essential one
682      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
683    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
684      on CS-grid: no longer loosing mass.
685    o exf & curvilinear-grid: no longer modify longitude xC & xG.
686    o pkg/ggl90: fix sloppy output and fix a bug
687    o pkg/seaice: added SEAICEuseEVPpickup parameter
688      - Set to false in order to start EVP solver with
689        non-EVP pickup files when using SEAICEuseEVP
690      - fix sign error in diffusion in seaice_calc_rhs
691    
692    checkpoint58h_post
693    * Modifications for bottom topography control
694      o replace hFacC by _hFacC at various places
695      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
696      o add non-self-adjoint cg2d_nsa
697      o update autodiff support routines
698      o re-initialise hfac after ctrl_depth_ini
699      o works for 5x5 box, doesnt work for global_ocean.90x40x15
700    * Adding verification for 5x5 box (4-layer) bottom topography control
701    
702    checkpoint58g_post
703    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
704       used for mean seasonal cycle, mean diurnal cycle); add an example
705       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
706    o pkg/ggl90:
707      - add parameter (minimum surface kinetic energy)
708      - fix bug (avoiding division by zero)
709    o couple pkg/thsice to pkg/seaice:
710      - modify advection in seaice to accomodate new scalar fields to be advected
711      - only muliDimAdection scheme work with seaice/thsice
712      - mapping of thsice-variables to seaice-variables, back and forth
713      - does not break the verification experiments, but does not give the
714        desired results either
715    o pkg/seaice
716      - make (default) second order advection a bit less confusing?
717    
718    checkpoint58f_post
719    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
720      to pkg/seaice):
721      - new routines thsice_map_exf and thsice_get_exf provide the interface
722      - add an additional formal parameter to thsice_solve4temp
723    o pkg/exf:
724      - add new fields wspeed, snowprecip (to be able to couple to thsice)
725      - correct Stefan-Boltzmann constant
726      - new parameter for longwave surface emittance
727      - separate some stuff from exf_bulkformulae into new routines  
728        exf_radiation, exf_wind
729      - add new parameters and constants: longwave emissivity for ocean, ice
730        and snow, evaporation parameters over ice
731      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
732        either wind from stress or stress from wind
733    o pkg/thSIce:
734    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
735    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
736       and THSICE_CALC_THICKN
737    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
738    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
739      to make debugging easier.
740    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
741    o pkg/bulk_force:
742      - clean-up comments and parameters ;
743      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
744    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
745      generate new output for test-experiment: aim.5l_cs.thSI
746    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
747      testreport accordingly
748    
749    checkpoint58e_post
750    o SEAICE_CGRID adjoint done
751    o R_STAR adjoint implemented.
752      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
753      * need to sort out init. of h0facc, etc.
754    o Make pkg/profile fully independent of ecco,cost, etc. stuff
755      to be able to use it in pure forward.
756    
757    checkpoint58d_post
758    o upgrade simple test-experiment to tutorial example:
759     step.1: duplicate the experiment and (step.2) will remove the old copy.
760      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
761      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
762      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
763      tutorial_global_oce_biogeo    <- copy of dic_example
764      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
765      tutorial_plume_on_slope       <- copy of plume_on_slope
766      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
767      tutorial_global_oce_optim     <- empty for now (David ?)
768      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
769     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
770    o correct a sign problem in cost_scat.F
771    o obcs and ptracers: fix boundary conditions for advections schemes
772      with larger stencil
773    o thsice adjoint: start
774    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
775      completeness
776    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
777      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
778    o ptracers adjoint:
779      * avoid extensive recomputatations
780      * fix missing re-init. of gptr (missed by TAF)
781    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
782      me to turn off the excessive output to STDOUT that this package produces
783    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
784      and add those terms in Vector-Invariant formulation.
785    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
786      if the control period (xx_hfluxperiod etc) is 0
787    o in profiles pkg, clean routines and fix details
788    o in ecco pkg, reading ssh data:
789      fix problem in case the model does not start at iter0=0
790    o fix mnc-pickup/restart for ptracers
791    o new package prifiles:
792      code to compute profile-based cost by Gael Forget
793      (modifs in ecco, ctrl, autodiff)
794    o Benign bug fix in initialization (spotted by M. Mazloff) of
795      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
796    
797    checkpoint58c_post
798    o adjoint: finish NLFS adjoint and provide reference output in
799      verification/global_ocean.90x40x15/results_ad_nlfs
800    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
801      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
802      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
803      with SEAICE_CGRID defined.
804    o move calendarDumps from "data" to "data.cal" and clean-up the code
805      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
806    o add useEXF & useCAL flags (for now, set in hard-coded way)
807    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
808      (were missing in NH mode, and wrong in quasihydrostatic mode).
809      waiting for Chris updated version of calc_gw to add those CALLs.
810    o fix bug in quasihydrostatic S/R ;
811      add a test for this option: global_ocean.90x40x15.qshyd
812    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
813      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
814    o add on/off flag useOffLine for package OFFLINE
815    o seaice:
816      - modify advection so that it works also on the C-grid
817      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
818        problem in multi-tile runs with C-grid
819      - add flags for clipping ice velocities and/or masking solver forcing
820      - fix drag (ocean on ice) formulation and a bug that caused noise in the
821        C-grid solver
822      - added a few comments to seaice_diffusion.F
823      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
824        are now exclusive)
825      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
826        required re-ordering the code a little:
827       + make DAIRN global variable (defined in SEAICE)
828       + move computation of the viscosities eta and zeta into a new separate
829         routine (because I need to recompute them in seaice_ocean_stress.F)
830    
831    checkpoint58b_post
832    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
833      update output.txt of exp. aim.5l_cs.thSI
834    o various mnc cleanups and improvements:
835      + shrink lookup tables by factor of ~4
836      + better error reporting when running out of lookup space
837      + able to handle longer path/file names (up to 500 chars)
838    o adjoint:
839      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
840      - TBD: "hidden" mom_vecinv recomp. in dynamics
841    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
842     (allow to differentiate between forcing components using new integer flags:
843      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
844     and add new flag to put Dissipation tendency out of Adams-Bashforth.
845    o ecco
846      - enable trend removal from SSH anomaly obs.
847    o adjoint
848      - a fix for PmEpR when #undef EXACT_CONSERV
849      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
850      - try to fix "hidden" recomp. in forward_step for NLFS
851        (NLFS seems broken sometimes after I checked it in)
852    o seaice:
853     - add c-grid version of the dynamic solver:
854       + three new routines that are the c-grid substitute lsr, dynsolver
855         and ostres
856       + put a few fields that were local to dynsolver into global common
857         blocks, so that I can move the computation of stresses etc into
858         seaice_lsr (saves coding but may break the adjoint).
859     - replace more hardwired parameters by runtime parameters
860     - add ice masks that mask the rhs of the implicit solvers where there
861       is no ice (commented out in seaice_dynsolver, because i am not sure
862       if this works properly), eventually this should replace the clipping
863       of ice velocities in seaice_dynsolver to +/-40cm/s.
864    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
865      include it only where its needed
866    o move balancing of fluxes before the call of external_forcing_surf
867    o seaice:
868      - correct units of turning angles (now they are really in degrees)
869      - move computation of GWATX/Y out of main routine into dynsolver
870      - initialize GWATX/Y in seaice_init
871    o Apply mask on Fresh-Water flux (needed for SSH forcing).
872      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
873    o seaice: add runtime flags for turning angles (default to zero)
874    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
875      and trend from exf forcing and ctrl control adjustments
876    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
877      (since checkpoint57x_post)
878    o change the default rotation period to 86164.s = the Earth rotation
879    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
880      and based on a reference stratification. Tested within hs94.cs-32x32x5.
881    o seaice advection: add code for choosing between the default (2nd order
882      central differences) and multiDim advection schemes provided by
883      pkg/generic_advdiff
884    o seaice:
885      - removed all references to SEAICE_GRID.h fields from
886        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
887        (cubed-sphere configuration will change a little)
888      - grid computations in seaice_init are obsolete now.
889      - cleaned up code a little so that is easier to read (hopefully).
890      - added new (better?) discretizations of default advection and diffusion
891        (turn on with SEAICEuseFluxForm)
892      - replace 1 in 3d global fields by kSurface in growth.F
893      
894    checkpoint58a_post
895    o seaice:
896      - bug fix in advect.F
897    o shelfice:
898      - separate shelfice load anomaly from pload (breaks with time
899        dependent forcing), => introduce constant field shelficeLoadAnomaly.
900        Its default is 0., but it may be computed more cleverly from (unknown)
901        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
902        done offline. A good approximation of the pressure load anomaly is
903        necessary to avoid large initial adjustment processes underneath
904        deep-reaching shelfice.
905      - small fix in ISOMIP shelfice_thermodynamics
906      - add more sophisticated thermodynamics of Hellmer (1989), this is
907        now the default
908      - give a few constants more intuitive names
909    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
910      if bulk formulae are used in long integration (especially EmPmR). Turn
911      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
912      if balancePrintMean, the imbalance that is substracted is printed to
913      STDOUT.
914    o fix bug (typo) in obcs_apply_eta.F
915    o add a new package shelfice which enables us to model the circulation
916      underneath shelf-ice with draughts of hundreds of meters.
917     - works
918     - to do: + include improved thermodynamics
919              + check whether kSurfC (from model/inc/SURFACE.h) can be used
920                instead of new field kTopC
921              + can we use topoFile, Ro_surf and existing code in ini_depth.F
922                instead of new field R_shelfIce and new code in ini_depth.F
923                and ini_mask_etc.F?
924              + adjust vertical mixing schemes?
925    o seaice pkg:
926     - add a cpp-flag to include a simple formula for a salinity dependent
927       freezing point of sea water at the surface
928     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
929       meridional stresses are now different (and hopefully correct)
930    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
931       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
932       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
933    o pkg/diagnostics: add options and parameters for regional-statistics
934       diagnostics ; define regions by reading a region-mask from a file
935       (might add other options later)
936    o pkg/bulk_force:
937     - add option and parameters to use AIM surface-flux formulae.
938     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
939       others forcing fields (defined in PARM05, parameter file "data") are loaded
940       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
941     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
942     - use the right EXCH call for uwind,vwind (to work on CS-grid).
943     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
944       and parameters (note: calcWindStress replaces .NOT.readwindstress).
945     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
946    
947    checkpoint58
948    o add "--embed-source" option to genmake2 which, when the supporting
949      tools can be compiled (as determined by genmake2) will turn on the
950      embed_files package which then embeds the entire MITgcm source code
951      (*.[fFhc] + Makefile) used for the build within the executable
952      - requested by CNH but off by default
953      - adds a paltry <9MB to the mitgcmuv executable in most cases
954      - only writes the output when useEMBEDSRC in eedata is true
955    o clean up 3-dim. relaxation codes:
956      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
957      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
958      * Thanks to Tom Haine for testing!
959    
960    checkpoint57z_post
961    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
962      affects output (@ truncation level) of exp. plume_on_slope ; updated.
963    o fix the pickup behavior for obcs in combination with ptracers
964    o fix a bug in ptracers_external_fields_load
965    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
966      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
967    o transfered surface NH pressure to eta field (if exactConserv).
968    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
969         and update lab_sea output.txt file.
970    o completing 3-dim. relaxation code: additional term
971         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
972      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
973      * At compile time, in "EXF_OPTIONS.h" set
974          #define  ALLOW_CLIMTEMP_RELAXATION
975          #define  ALLOW_CLIMSALT_RELAXATION
976      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
977          tauThetaClimRelax3Dim = 15552000.0,
978          tauSaltClimRelax3Dim  = 15552000.0,
979      * 3 cases:
980          1) Use a constant-in-time 3-dim. field
981          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
982          3) Real-time relax. to time-evolving prescribed field
983    o Adding Laplacian-type smoothness constraint on
984      initial and boundary (forcing) controls (ic, bc)
985      * enable at compile-time via
986        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
987      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
988      * Absolute scale somewhat unclear so far
989      * no area weighting was included since no other cost term does so far
990    
991    checkpoint57y_post
992    First step for a NLFS adjoint
993    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
994    o new init. routines for calc_r_star, calc_surf_dr
995    o still need to deal with ini_masks_etc
996    o testreport seemed happy
997    checkpoint57y_pre
998    
999    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
1000    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
1001    o add new offset feature to offline pkg (plus minor cleanup)
1002    o cfc fixes for final year of integration
1003    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
1004      be in GCHEM_OPTIONS).
1005    
1006    checkpoint57x_post
1007    o fix testreport Pb in multiple test experiment.
1008    o cleanup our namelist syntax in verification:
1009      - make it more F95 standards compliant (some work still needed)
1010      - allows the vast majority of our tests to work with gfortran
1011    o Non-Hydrostatic:
1012     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
1013     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
1014    o Allow to apply AB on T,S rather than on AB(gT,gS):
1015     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
1016     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
1017       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
1018     - need a "clever" read_pickup to restart from the other AB formulation
1019    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
1020    o remove some unused variables (reduces number of compiler warnings)
1021    o adjoint
1022      * Disable useVariableViscosity for adjoint for time being
1023        (there are a number of extensive recomputations)
1024      * Initialize certain variables needed for adjoint
1025    
1026    checkpoint57w_post
1027    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
1028                 fix the singleCpuIO RS version of MDSWRITEFIELD
1029       and add a WARNING if using globalFiles=T with multi-processors.
1030    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
1031      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
1032    o tracer advection scheme:
1033      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
1034       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
1035       was not very convenient).
1036      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
1037       (further tests needed for the implicit DST & Flux-Limiter schemes).
1038    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
1039      and sRef for convenience, handy, when you want to initialize
1040      ptracers in a large domain with a constant non-zero value. Also,
1041      untangle ptracers_init.F a little.
1042    
1043    checkpoint57v_post
1044    o change dome exp. to use variable viscosity in side-drag terms.
1045    o remove all the files from the cfc_offline test since they are now
1046      incorporated into tutorial_cfc_offline which has been producing
1047      identical results for a few days of testing
1048    o add new parameter: sideDragFactor to enable half-slip-side BC
1049      and change side-drag S/R to use viscosity from mom_calc_visc
1050      (can switch back by setting sideDragFactor=0.); affects results at
1051      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
1052       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
1053    o vorticity & strain are now computed without masking, to account for
1054      no-slip-side BC in variable viscosity calculation ; mask is applied
1055      anyway later on, before computing advection/coriolis terms.
1056    o modify exp4 to test new obcs support for reading from external files
1057      and for passive tracers
1058    o fix behavior of ptracers_monitor when monitor output is written to a
1059      netcdf-file; still not independent of monitor.F (writes in the same
1060      file).
1061    o change default value of tRef (put a uniform, meaningful value for ocean
1062      & atmos) and initialize sRef (was missing, as Martin mentioned).
1063    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
1064      to be proportional to enstrophy dissipation length.  Thus,
1065       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
1066      This is now consistent with Smagorinsky and with the manual.
1067    
1068    checkpoint57u_post
1069    o OBCS and PTRACERS: add open boundary support for passive tracers
1070      - either use homogenous (pseudo) v.Neumann conditions or prescribe
1071        OB-values from file; this is not different from the way theta and salinity
1072        are treated
1073      - however, Orlanski-radiation conditions are not supported, and the model
1074        will stop if you use pTracers and Orlanski at the same time.
1075      - beefed up the rountine obcs_external_fields_load: now only those open
1076        boundary values are overwritten with values from files for which there
1077        are really files, otherwise the OB-fields remain untouched. This makes
1078        it possible to use different OBs at different ends of the domain (as
1079        with EXF)
1080    o reduce number of exch calls in shap_filt (s2).
1081    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
1082      truncation level) 4/5 MLAdjust test results (11&12 digits match).
1083    
1084    checkpoint57t_post
1085    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
1086    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
1087      same truncation, independent of the face number: affects affects several
1088      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
1089    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
1090      note that biharmonic viscosity + no-slip was not tested in any experiment.
1091    o fix bug in non-linear free-surf side-drag ; generate new output for
1092      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
1093    o make mnc honor the writeBinaryPrec flag for most kinds of output
1094    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
1095    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
1096      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
1097    o add brackets in multi-terms sum to get same truncation, independent of
1098      the face number (manage to get exactly same value of gU,gV at the cs-edge)
1099      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
1100    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
1101      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
1102      a maximum grid-scale Reynolds number.  Also, changes all length calculations
1103      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
1104      Suggested values of viscosity parameters found in mom_calc_visc.
1105      Many new viscosity diagnostics available.
1106    
1107    checkpoint57s_post
1108    o Add clearing-house for viscosity calculations, mom_calc_visc and
1109      correct numerous bugs in LeithD and Smagorinsky discretizations.  
1110      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
1111      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
1112      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
1113      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
1114      The Strain-Tension form is now called with useStrainTensonVisc=.true.
1115      ViscAhStrain and viscAhTension are now retired.
1116    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
1117    o In response to JMC's bug report, genmake2 now ignores any soft-links
1118      that it finds in the *current* directory when searching for files.
1119      Soft-links found in any other source directories will still work as
1120      they did before.
1121    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
1122      a C routine to unlimit the stack size
1123    o mnc-ify pkg/aim snapshot vars
1124    o mnc-ify pkg/land as requested by Daniel
1125    o various changes to mnc including:
1126      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
1127      - output can now be grouped so that all files within a group
1128          change the ITER portion of their names in lock-step together
1129      - can now read ("global") PER-FACE (in addition to PER-TILE) files
1130          and works with both EXCH1 and EXCH2 (but needs more testing)
1131      - writing works for all verification test cases w/ g77 on Linux
1132    
1133    checkpoint57r_post
1134    o make MNC variable initialization happen earlier
1135    o add diagnostics for (almost) each term of the momentum Eq.
1136    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
1137    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
1138    o remove MINIMAL_TAVE_OUTPUT option ;
1139      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
1140    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
1141      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
1142    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
1143    o add time-dependent SST, SSS control
1144    o cost terms in ecco/ modularized (new cost_generic.F)
1145    o cost_averages routines are modularized (new cost_averagesgeneric.F)
1146    o new infrastructure for seaice model vs. obs misfits in seaice/
1147      * driver from the_main_loop.F is seaice_cost_driver.F
1148      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
1149      * gradient check in Exp. 6a of natl_box_adjoint/
1150    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
1151      (see README file)
1152    
1153    checkpoint57q_post
1154    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
1155    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
1156      - bug was reported by Jean-Michel and Ian Fenty
1157    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
1158      update exp. cpl_aim+ocn output.
1159    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
1160      Needed for high-res. runs with large global files
1161      to be able to limit tapelev size
1162    o Changed some tests for adjoint:
1163      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
1164      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
1165      * global_ocean.90x40x15/ back to default 3-level checkpointing
1166    o Modifications to enable scripted COMMON to MODULE conversion
1167      * verification/OpenAD/code/ has necessary scripts and description;
1168      * converts, compiles and runs successfully;
1169    
1170    checkpoint57p_post
1171    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
1172    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
1173      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
1174    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
1175    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
1176      (was already the case for dissipation with mom_vecinv,
1177       and also the case for grad.PhiHyd when staggered-timeStep)
1178      This will allow to put dissipation out-off the AB time-stepping.
1179     Unfortunately, affects truncation error. Update output of exp. that "fails"
1180      (cg2d matching number) and leave the others for later: front_relax(10),
1181      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
1182      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
1183    
1184    checkpoint57o_post
1185    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
1186      (2) its ready to be documented during the 20050801 DocFest
1187    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
1188      for ideal_2D_oce and lab_sea on linux_ia32_g77
1189    o set to #undef CTRL_SET_OLD_MAXCVARS_30
1190      in global1x1_tot/code_seaice_adj to access indices 32, 33
1191      (worth another tag)
1192    
1193    checkpoint57n_post
1194    o adding precip control xx_precip 32
1195    o adding swflux control xx_swflux 33
1196    o Replacing 10 forcing penalty cost routines by 1 generic.
1197    o Implementing partitioning in time-mean and variable adjustment
1198      for atmos. state.
1199    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
1200  o in natl_box_adjoint:  o in natl_box_adjoint:
1201    * updated: results_bulk/    * updated exp 1 to 10
1202    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
1203    o updated global1x1/*_seaice_adj/
1204      to incorporate latest changes
1205    o enable useSingleCpuIO for mdsio vector routines
1206      (applies in particular to tapelev I/O)
1207    o removed inefficient K-loop in all active_file*control*.F
1208    
1209  checkpoint57m_post  checkpoint57m_post
1210  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.1.880
  ViewVC Help
Powered by ViewVC 1.1.22