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revision 1.859 by jmc, Fri Aug 17 20:51:27 2007 UTC revision 1.1053 by jmc, Tue Jan 20 00:34:15 2009 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
8    o pkg/obcs: fix loop ranges for balancing code
9    o pkg/flt:
10     - improve criteria for finding which tile owns a float.
11     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
12    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
13      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
14      with ocean biogeo)
15    o pkg/flt:
16     - do some cleaning and fix the restart ;
17     - add output.txt in flt_example/results to get this pkg tested.
18    o genmake2: add an EXTENDED_SRC option and flag.
19       for now, cannot be turned on on command line (only through genmake_local)
20    o pkg/mdsio: read/write vector:
21     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
22     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
23       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
24     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
25      (drop to 4 digits matching for grad). But this test does not look very
26      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
27    
28    checkpoint61g
29    o pkg/flt:
30      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
31       + make OPTIONS file more standard.
32      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
33      - fix _BYTESWAPIO CPP-Flag
34      - standard reading of file-parameter "data.flt"
35      - fix argument list of S/R FLT_RESTART
36      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
37    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
38    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
39      a still unfixed compiler/optimization bug
40    
41    checkpoint61f
42    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
43      update results of global_ocean.cs32x15.icedyn test.
44    o move getcon.F from model/src to pkg/fizhi.
45    o pkg/exf: add parameter for extrapolation of temp up to the surface
46       and option to prevent negative evap (in bulk_largeyeager04 only).
47    o Prather Advection scheme: fix tracer conservation for divergent flow
48      (e.g., when using NonLin Free-Surface).
49    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
50    o gmredi (Visbeck-variable-K):
51     - add more parameters to Visbeck-variable-K.
52     - use a 5 points average for dSigmaR in Visbeck-K calculation
53       (more "homogenous": same stencil and same weights as in dSigmaH)
54     - update output of ideal_2D_oce experiment.
55    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
56      (#undef REAL4_IS_SLOW)
57     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
58       coordinate variable
59     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
60       (surface forcing fields), removes some of the functionality
61     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
62     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
63       probably not all: copy _RS surface flux fields to RL field before
64       calling DIAGNOSTICS_FILL
65     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
66       real*4 (CALL EXCH_*_RS) versions.
67     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
68       (generate new output).
69    
70    checkpoint61e
71    o gmredi (Visbeck-variable-K):
72      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
73      - change computation of Visbeck-K where Slope > Smax :        
74        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
75        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
76    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
77      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
78    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
79    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
80      does not become too large (to avoid precision problems in implicit-diffusion
81      solver); update ideal_2D_oce output.
82    o pkg ggl90:
83      - in ggl90_cal.F: compute only one set of visc/diff, used to
84        step forward TKE/T/S/momentum
85      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
86        have Prandlt =1)
87    o gmredi (fm07):
88      - add lower limit on Transition layer thickness + lower limit on 1/lambda
89      - allow to set few more params from data.gmredi
90    o pkg ggl90:
91          - add missing sqrt(2) factor in computation of mixing length
92            scale in ggl90_calc.F
93            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
94    
95    checkpoint61d
96    o adjoint modifs
97      - adapt to new field rhoInSitu
98      - allow to revert from StoreDynVars2D, StoreDynVars3D
99        to individual fields
100        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
101    o store 3-D (in-situ) density in commom block (DYNVARS.h)
102     - save 1 rho computation.
103     - no longer modify T & S inland when using down_slope pkg.
104    o gad_som : allow to switch to SOM advection for T & S without corresponding
105      pickup files (using new S/R: MDS_CHECK4FILE).
106    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
107      (for useSingleCpuIO to work in multi-threaded)
108    o pkg/shelfice:
109     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
110       with SHELFICEtopoFile in data.shelfice
111     - move code for reading ice shelf topography and modifying hFacC into separate
112       subroutines of the shelfice package
113     - separate initialisation of "fixed" and "variable" variables
114     - kTopC is not (yet) replaced by kSurfC, although this is possible
115    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
116    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
117      and rename:
118      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
119      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
120    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
121    
122    checkpoint61c
123    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
124      to add mass source/sink of fluid in the interior (3-D generalisation
125      of oceanic real-fresh water flux).
126    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
127    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
128    o new pkg: down_slope
129      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
130      - presently, modify T & S inland (dwnslp_calc_rho.F).
131        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
132      - implementation for ocean in P-coords not tested.
133      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
134    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
135      (to facilitate conversion of oceanic pkg to p-coordinate).
136    o change FIND_RHO to FIND_RHO_2D :
137      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
138    o new pkg: cheapaml
139    
140    checkpoint61b
141    o exch2:
142      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
143      - no longer depend on the order sequence (N,S,E,W).
144      - 3rd exchange no longer needed (tested with 24 tiles).
145      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
146      - exch_UV_A-grid readily available (but not yet tested).
147      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
148      (both are no longer needed) in exch_uv: no effect in forward run; but
149       get truncation error differences with adjoint exch.
150    o exch2:
151     - change index-bounds storage (moved from target to local tile,
152       more intuitive this way) ; rename/remove some variables.
153     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
154    
155    checkpoint61a
156    o exch2/matlab-topology-generator:
157      fix bug in index bounds for N-S internal exchange (hard to tell if this
158      had any effect on the solution).
159    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
160      is exceeded
161    o testreport: modify syntax of awk, so that it works also with
162      awk, and not only with nawk and gawk
163    
164    checkpoint61
165    o autodiff
166      Change default for TAF usage by removing argument '-nonew_arg'
167      This changes TAF subroutine argument list (ordering of active var.)
168      Omission of this flag leads to incompatibility w.r.t. TAMC
169      To restore TAMC-compatibility, need following modifs:
170      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
171      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
172      Tested TAF version is 1.9.22
173      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
174    
175    checkpoint60
176    --->>> This is the last checkpoint for which generating the adjoint
177    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
178    --->>> by default.
179    --->>> Future checkpoints will ommit this flag by default.
180    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
181    o pkg/grdchk: Add gradient check to etan0 perturbations.
182    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
183    o pkg/autodiff: more flexibility in zeroadj.
184      model/src: modifying do_oceanic_phys.F accordingly.
185    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
186    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
187      special setup of gmredi for which the adjoint is stable
188      enough for parameter optimization.
189    o bridging the gap between eddy stress and GM.
190      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
191          along with a change in CPP option (now ALLOW_EDDYPSI).
192      -> when using GM w/ GM_AdvForm:
193          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
194          is applied either in the tracer Eq. or in momentum Eq.
195          depending on data.gmredi (intro. GM_InMomAsStress).
196      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
197      The key modifications are in model/src/taueddy_external_forcing.F
198      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
199    
200    checkpoint59r
201    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
202      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
203      fix option to read coriolis(@ cell-corner) from files with CS-grid.
204    o pkg/mnc: add some attributes to standard 1D-coordinate variables
205    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
206      mass points, when using mnc for output
207      - add runtime parameter (missing_value, missing_value_int) to override
208        default (which is the value of getcon('UNDEF'))
209    o pkg/mnc: prepare mnc for the actual use of missing values with the
210      diagnostics package: small fix in mnc_cw_readwrite.template and more
211      initialisation of never used fields
212      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
213      versions
214    o pkg/thsice/thsice_ini_vars.F added default initial values so that
215      thermodynamics sea ice solver does not blow up when some initial fields
216      are missing.
217    o move from external_forcing_surf.F to ini_forcing.F
218      the p-coord. hack consisting in using pLoad to set phi0surf ;
219      update output of tutorial_global_oce_in_p (affected @ truncation level).
220    o Freshen up a bit hs94.1x64x5, notably:
221      remove rotationPeriod and tRef=5*0. (adjoint only), and add
222      exactConserv=.TRUE.
223    o pkg/generic_advdiff:
224      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
225      applies to files where Temperature & Salinity 2nd Order moments are used.
226    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
227      this uses a dynamically allocated internal state data structure
228      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
229      and requires a fortran 90 compiler
230    
231    checkpoint59q
232    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
233       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
234    o Refresh tutorial_global_oce_biogeo, notably:
235      - change bathymetry (put back seamounts in ACC, use hFacs)
236      - change EOS (POLY3 --> JMD95Z)
237      - use Bryan-Lewis vertical diffusivity
238      - use multidimensional advection
239      - remove old virtual virtual in dic pkg, now done through ptracer pkg
240      - change a couple of parameters in dic pkg
241    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
242    o pkg/obcs: change default to OBCSfixTopo = .true.,
243      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
244      - replace "debugMode" with "debugLevel .GE. debLevB"
245    o implementation of TAF directives for gchem,cfc,dic
246    o remove "exp5" (replaced by tutorial_deep_convection).
247    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
248      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
249      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
250      --> changes results in exp4, seaice_obcs
251    o tutorial_deep_convection :
252      update the set-up and increase resolution and domain size ; start
253      from pseudo initial conditions = output at t=120mn in order to see
254      something happening when running testreport.
255    o pkg/seaice: add os7mp as an advection scheme
256                  add check for advection schemes
257                  add a flag for restoring T and S underneath sea ice
258    o pkg/my82: add netcdf-support and diagnostics
259    o thsice pkg:
260      - Now hsMax limits snow height by turning it into ice following
261        flooding scheme (and now conserving energy)
262      - Slight rewriting of the formula in thsice_calc_thick.F
263      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
264      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
265    
266    checkpoint59p
267    o gchem / dic / cfc :
268      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
269      - add new parameter files: "data.dic" & "data.cfc" ;
270      - various re-arrangement in initialisation & header file ;
271      - fix tutorial_global_oce_biogeo for multi-threaded test.
272    o pkg/dic: test for "pickup_dic" file when restarting ;
273      if no pickup-file, can restart with a re-initialised pH (same as it did
274      before) providing pickupStrictlyMatch is set to False.
275    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
276      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
277    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
278      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
279    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
280     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
281       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
282    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
283       scheme to use for vorticty-term ;
284     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
285       (with default selectVortScheme, return to original discretisation)
286     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
287    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
288    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
289      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
290      also fix diagnostics VISCAHW & VISCA4W.
291    
292    checkpoint59o
293    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
294    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
295      move a few statemens out the main loop into separate loops
296    o pkg/shelfice:
297      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
298        (kg/m^2/s), does not break tests, because in verification/isomip,
299        rhoConstFresh=rhoConst (by accident)
300      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
301      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
302        new file model/src/seawater.F, so that they are available for all pkgs.
303      - convert potential temperature into in-situ temperature. This changes the
304        isomip tests => update tests
305    o add a flag writePickupAtEnd (default=true) to be able to suppress
306      writing a pickup at the last timestep
307    o tools/mpack-1.6 :
308      - disable automake (not working) and autoconf (not needed).
309      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
310        also cleaner with much less compilation warnings.
311    o pkg/profiles:
312      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
313      (for "less than 32 characters name" compiler requirement)
314    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
315      conditions that have a different sampling frequency than S/T/U/V obcs
316    o pkg/diagnostics (stats-diags):
317      - fix global Min/Max in case 1 processor get only empty tiles
318    o genmake2: replace (4 times)
319         make genmake_tc_1.o >> genmake_warnings 2>&1
320      with
321         COMM="$CC $CFLAGS -c genmake_tc_1.c"
322         echo $COMM >> genmake_warnings
323         $COMM >> genmake_warnings 2>&1
324      to make genmake2 always see the value of CC as specified in the optfile.
325    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
326      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
327      - modify verification advect_cs test to test SOM-advection on CS-grid.
328    o pkg/ctrl:
329      - Rewrite of ctrl_map_ini_ecco.F,
330        introducing a generic routine (ctrl_map_ini_gen.F).
331      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
332    
333    checkpoint59n
334    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
335      number in dedicate array "hdiag":
336      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
337        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
338      - many small changes (integer format) for large number of diagnostics
339      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
340        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
341    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
342      usingSphericalGrid, this allows to define the rotated grid coordinates
343      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
344      geographical coordinates according to the inverse of the rotation defined
345      by the Euler angles, so that Coriolis parameter and online-interpolation by
346      exf works with the geographical coordinates on XC/YC/XG/YG.
347      Naturally, this feature does not work with all packages, so some
348      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
349      profiles), because there the coordinates are assumed to be regular
350      spherical grid coordinates.
351    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
352      - introduce isopycnal diffusion coefficient control.
353    o tools/adjoint_options:
354      - additional control vector components.
355    o pkg/mnc: have mnc create marginally meaning full coordinate variables
356      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
357    o pkg/mypackage:
358      - add example of read/write pickup for state-var ;
359      - add entry points to the main code for state-vars diags & write-pickup.
360    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
361      transitions for useExfYearlyFields
362      - add new subroutine that determines the file to read from for
363        use*YearlyFields = .TRUE. and .FALSE.
364      - add a verification experiment to global_with_exf that tests
365        useExfYearlyFields with USE_EXF_INTERPOLATION defined
366    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
367      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
368      subroutines (which could be generated from a template, because they are
369      almost identical), for now they are included in obcs_prescribe_read.F for
370      simplicity
371    o pkg/exf:
372      - add a little more diagnostic to exf_interp_read (in analogy to
373        mds_read_field, can be turned off with debugLevel < debugLevA=1)
374      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
375        ugly but fast by unrolling short inner loops, inserting a unroll=8
376        directive in routine lagran, and splitting a loop and making do while the
377        outermost loop (the latter requires the intoduction of index arrays)
378    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
379    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
380      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
381    o verification/seaice_obcs: updated for restart test and latest options
382    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
383      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
384      for now this is only available for the C-grid code and also within
385      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
386    
387    checkpoint59m
388    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
389      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
390    o gad_som : fix flux output (& diagnostics) to have same units as other  
391      advection scheme fluxes (was previously multiplied by deltaT).  
392    o added verification/seaice_obcs both to test seaice open boundaries
393      and to provide an example matlab scrpt for generating them
394    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
395    o pkg/salt_plume: clean up salt_plume_frac.F to
396      remove redundancy in PlumeMethod 1 and 4
397    o pkg/kpp: added saltplume diagnostics
398    o pkg/obcs and pkg/seaice:
399      - do not set uice and vice to zero when OB*icefile are unspecified
400      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
401      - moved seaice tracer obcs after call to seaice_growth
402    o pkg/salt_plume: added various options for salt plume depth
403      criterion and for vertical distribution of the salt
404    
405    checkpoint59l
406    o pkg/ptracers: new version of ptracers pickup:
407      read meta file and write only fields which are needed to restart.
408      ( same logic as main pickup file ; also using pickupStrictlyMatch )
409    o pkg/seaice:
410      - add timescale for melting due to warm mixed layer as a means of
411        setting SEAICE_availHeatFrac more conveniently
412      - add a CPP-flag/runtime parameter check for flooding algorithm
413      - reformulated availHeat in seaice_growth.F to be independent of AREA
414    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
415      unit changes
416    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
417    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
418      SX vector computer.
419    o pkg/seaice:
420      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
421        seaice forcing fields can now be read only through pkg/exf
422      - removed some unused halos
423    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
424    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
425      or U/VICE from U/VWIND before computing U/VSTRESS
426    
427    checkpoint59k
428    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
429      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
430    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
431      all experiments pass when compile with un-initialised var. checking option.
432    o added pkg/salt_plume
433    o script to test restart (for now, in MITgcm_contrib/jmc_script)
434    o pkg/seaice: new read/write pickup version.
435      read meta file and write only fields which are needed to restart.
436      ( same logic as main pickup file ; also using pickupStrictlyMatch )
437    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
438    o lab_sea.hb87: modify the domain & update output.hb87.txt :
439      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
440      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
441      process. Fixed here by closing the domain at the Northern boundary.
442    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
443    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
444      a set of consecutive levels in/from a 3-D array.
445    o pkg/ptracers:
446      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
447      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
448    
449    checkpoint59j
450    o in pkgs: dic, obcs, offline, rbcs:
451      standard way to compute coeff. for time interpolation between 2 time reccords
452      which retains full precision (& make results less dependent on compiler).
453      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
454    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
455      packages instead of reading ice cover and wind speed separately
456    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
457     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
458      to allow to compile customized code before the update)
459    o cleaning-up:
460      - fix CPP instruction syntax in pkg/obcs
461      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
462        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
463      - fix some threads issue in IO parts.
464    o pkg/dic:
465      - add tons of "_d 0" (--> much better testreports !)
466       and then update outputs of tutorial_global_oce_biogeo
467    o pkg/mom_fluxform:
468      add a special version of momentum advection intended to conserve momentum
469      next to a bathymetry step or a coastline edge. (default = off = #undef)
470    o new read/write pickup version:
471      - for now, only implemented for main (mdsio) pickup file.
472      - write out only what is needed to restart; merge pickup_nh , pickup_ph
473        and main pickup together.
474      - read meta file; read only what is needed to restart; stop if a field
475        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
476        if it make sense (even if the restart is not perfect).
477      - if no meta file, assume that pickup to read corresponds exactly to
478        a pickup that would currently be written.
479      - read pickup written in the old format (until checkpoint59i) if it
480        recognizes an old meta file (no field-list).
481      - add a meta file in exp. which starts from a pickup: 2 cases:
482        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
483         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
484        b) a meta file describing the content of the associated pickup file
485         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
486    o pkg/mdsio & pkg/rw:
487      - new routine to read a meta file ; new set of routine to read
488        Multiple-fields file (with meta file).
489    o added open boundary conditions capability for seaice
490        HSNOW, HSALT, UICE, and VICE
491    
492    checkpoint59i
493    o adjoint:
494      * fix multiDimAdvection adjoint
495        (partial recomputation problem by TAF for fVerT(:,:,kDown)
496        and comlev1 size definition (maxpass vs. max. number of tracers)
497      * verification/global_ocean.90x45x15 adjoint now tests
498        NLFS and multiDimAdvection using DST3 (=30)
499      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
500    o pkg/kpp: add "_d 0" to real constant (if missing);
501      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
502      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
503    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
504      for internal parameters related to restart process (formerly from PARAMS.h)
505      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
506    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
507      as argument. (only atm2d & obcs write_pickup have not yet been updated)
508    o pkg/monitor:
509      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
510      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
511      - account for deep Atmosphere factor and density factor (anelastic)
512    o added open boundary conditions capability for seaice HEFF and AREA
513    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
514      thermodynamics
515      - requires a little reorganization, which affects the testreport results
516        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
517        so that now the conservative form is tested
518      - add a few comments
519    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
520    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
521    o add new diagnostics to seaice: advective, diffusive fluxes (only for
522      multidim-advection, for scheme 2 they are not filled) and transports,
523      thermodynamic growth rates
524    o change units of EmPmR (inside the code, + within coupling interface)
525      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
526      Affects results @ truncation level (cg2d match) and update output of
527       experiments: lab_sea(6), global_ocean.90x40x15(10),
528      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
529      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
530      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
531      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
532    
533    checkpoint59h
534    o pkg/exf:
535      - improve vectorization by moving if-statement out of loops in
536        exf_mapfields, exf_radiation
537      - exf_bulkformulae.F: introduce 2D fields and vectorize code
538    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
539    o testreport:
540      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
541        monitor & update offline_exf_seaice exp. output.
542      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
543    o pkg/seaice:
544      - bug fix in the evp solver: boundary conditions were affected be
545        masking of zMax/zMin (changes results)
546      - minor bug fix in boundary conditions in seaice_calc_strainrates
547        (changes results for no_slip)
548      - seaice_lsr.F: make interpolation of eta dependent on boundaries
549      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
550      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
551        stress formulation and no-slip boundary conditions
552    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
553      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
554    o pkg/seaice: a first HSALT time stepping equation has been checked in
555    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
556      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
557      without requiring DO-IF statements
558    o pkg/thsice:
559      use continuous power-law function for partition of energy between lateral
560      melting/freezing and thinning/thickening ; old code using step function
561      still available with #undef THSICE_FRACEN_POWERLAW
562      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
563    o testreport: change AD testing : check against results/output_adm.txt
564      using same scripts as for forward test.
565    
566    checkpoint59g
567    o adjoint testing: in preparation for changing testreport:
568      - output format: cost and grad written on separated lines
569      - ad output results in directory "results" (instead of "results_ad")
570    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
571    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
572    o pkg/ecco: allow user defined cost function contributions
573    o testreport:
574      Allow to choose (per experiment) the list of tested output variables
575       and the main variable (used to issue a pass/FAIL ) ;
576      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
577      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
578      Also modify printing of summary:
579       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
580       b) echo the list of tested variables in the individual summary.txt of
581          each experiment.
582    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
583      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
584      (but still depend on the tile decompostion of the domain).
585    o pkg/seaice: change a discretization detail to make the B-grid code
586      "more symmetric". This change is likely to remove all "ridges/leads" that
587      where quasi-aligned with the grid in B-grid solutions. It may also be
588      the solution to the stress coupling issues with the B-grid.
589    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
590      remove .cvsignore from input dir. (since testreport no longer run here).
591    o pkg/thsice:
592     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
593     - fix reshaping of sea-ice just after advection:
594       melt all the ice only if ice-volume is too small.
595     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
596       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
597     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
598    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
599      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
600    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
601      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
602      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
603      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
604      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
605      -> update output.txt
606    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
607     this affects truncation error: -> update output.txt of exp:
608      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
609      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
610    
611    checkpoint59f
612    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
613    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
614      a bounded range (in forward mode)
615    o pkg/ecco, ctrl, autodiff and mom_common:
616     internal parameter controls, completements of implementations
617  o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.  o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
618    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
619      (not seem any difference in testing results).
620  o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains  o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
621     at face corners.     at face corners.
622  o pkg/generic_advdiff:  o pkg/generic_advdiff:
# Line 225  o in FFIELDS.h: Line 837  o in FFIELDS.h:
837       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
838  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
839  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
840      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
841        are no longer updating the vertical diffusivity array
842        (passed as argument) but are (re-) setting those arrays.
843  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
844    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
845      cgrid-lsr and evp solver      cgrid-lsr and evp solver

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