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revision 1.871 by dimitri, Fri Sep 14 02:07:37 2007 UTC revision 1.1027 by jmc, Tue Oct 7 20:59:20 2008 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o gmredi(fm07):
8      - add lower limit on Transition layer thickness D + lower limit on D/lambda
9      - allow to set few more params from data.gmredi
10    o pkg ggl90:
11          - add missing sqrt(2) factor in computation of mixing length
12            scale in ggl90_calc.F
13            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
14    
15    checkpoint61d
16    o adjoint modifs
17      - adapt to new field rhoInSitu
18      - allow to revert from StoreDynVars2D, StoreDynVars3D
19        to individual fields
20        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
21    o store 3-D (in-situ) density in commom block (DYNVARS.h)
22     - save 1 rho computation.
23     - no longer modify T & S inland when using down_slope pkg.
24    o gad_som : allow to switch to SOM advection for T & S without corresponding
25      pickup files (using new S/R: MDS_CHECK4FILE).
26    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
27      (for useSingleCpuIO to work in multi-threaded)
28    o pkg/shelfice:
29     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
30       with SHELFICEtopoFile in data.shelfice
31     - move code for reading ice shelf topography and modifying hFacC into separate
32       subroutines of the shelfice package
33     - separate initialisation of "fixed" and "variable" variables
34     - kTopC is not (yet) replaced by kSurfC, although this is possible
35    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
36    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
37      and rename:
38      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
39      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
40    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
41    
42    checkpoint61c
43    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
44      to add mass source/sink of fluid in the interior (3-D generalisation
45      of oceanic real-fresh water flux).
46    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
47    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
48    o new pkg: down_slope
49      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
50      - presently, modify T & S inland (dwnslp_calc_rho.F).
51        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
52      - implementation for ocean in P-coords not tested.
53      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
54    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
55      (to facilitate conversion of oceanic pkg to p-coordinate).
56    o change FIND_RHO to FIND_RHO_2D :
57      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
58    o new pkg: cheapaml
59    
60    checkpoint61b
61    o exch2:
62      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
63      - no longer depend on the order sequence (N,S,E,W).
64      - 3rd exchange no longer needed (tested with 24 tiles).
65      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
66      - exch_UV_A-grid readily available (but not yet tested).
67      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
68      (both are no longer needed) in exch_uv: no effect in forward run; but
69       get truncation error differences with adjoint exch.
70    o exch2:
71     - change index-bounds storage (moved from target to local tile,
72       more intuitive this way) ; rename/remove some variables.
73     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
74    
75    checkpoint61a
76    o exch2/matlab-topology-generator:
77      fix bug in index bounds for N-S internal exchange (hard to tell if this
78      had any effect on the solution).
79    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
80      is exceeded
81    o testreport: modify syntax of awk, so that it works also with
82      awk, and not only with nawk and gawk
83    
84    checkpoint61
85    o autodiff
86      Change default for TAF usage by removing argument '-nonew_arg'
87      This changes TAF subroutine argument list (ordering of active var.)
88      Omission of this flag leads to incompatibility w.r.t. TAMC
89      To restore TAMC-compatibility, need following modifs:
90      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
91      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
92      Tested TAF version is 1.9.22
93      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
94    
95    checkpoint60
96    --->>> This is the last checkpoint for which generating the adjoint
97    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
98    --->>> by default.
99    --->>> Future checkpoints will ommit this flag by default.
100    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
101    o pkg/grdchk: Add gradient check to etan0 perturbations.
102    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
103    o pkg/autodiff: more flexibility in zeroadj.
104      model/src: modifying do_oceanic_phys.F accordingly.
105    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
106    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
107      special setup of gmredi for which the adjoint is stable
108      enough for parameter optimization.
109    o bridging the gap between eddy stress and GM.
110      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
111          along with a change in CPP option (now ALLOW_EDDYPSI).
112      -> when using GM w/ GM_AdvForm:
113          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
114          is applied either in the tracer Eq. or in momentum Eq.
115          depending on data.gmredi (intro. GM_InMomAsStress).
116      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
117      The key modifications are in model/src/taueddy_external_forcing.F
118      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
119    
120    checkpoint59r
121    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
122      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
123      fix option to read coriolis(@ cell-corner) from files with CS-grid.
124    o pkg/mnc: add some attributes to standard 1D-coordinate variables
125    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
126      mass points, when using mnc for output
127      - add runtime parameter (missing_value, missing_value_int) to override
128        default (which is the value of getcon('UNDEF'))
129    o pkg/mnc: prepare mnc for the actual use of missing values with the
130      diagnostics package: small fix in mnc_cw_readwrite.template and more
131      initialisation of never used fields
132      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
133      versions
134    o pkg/thsice/thsice_ini_vars.F added default initial values so that
135      thermodynamics sea ice solver does not blow up when some initial fields
136      are missing.
137    o move from external_forcing_surf.F to ini_forcing.F
138      the p-coord. hack consisting in using pLoad to set phi0surf ;
139      update output of tutorial_global_oce_in_p (affected @ truncation level).
140    o Freshen up a bit hs94.1x64x5, notably:
141      remove rotationPeriod and tRef=5*0. (adjoint only), and add
142      exactConserv=.TRUE.
143    o pkg/generic_advdiff:
144      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
145      applies to files where Temperature & Salinity 2nd Order moments are used.
146    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
147      this uses a dynamically allocated internal state data structure
148      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
149      and requires a fortran 90 compiler
150    
151    checkpoint59q
152    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
153       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
154    o Refresh tutorial_global_oce_biogeo, notably:
155      - change bathymetry (put back seamounts in ACC, use hFacs)
156      - change EOS (POLY3 --> JMD95Z)
157      - use Bryan-Lewis vertical diffusivity
158      - use multidimensional advection
159      - remove old virtual virtual in dic pkg, now done through ptracer pkg
160      - change a couple of parameters in dic pkg
161    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
162    o pkg/obcs: change default to OBCSfixTopo = .true.,
163      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
164      - replace "debugMode" with "debugLevel .GE. debLevB"
165    o implementation of TAF directives for gchem,cfc,dic
166    o remove "exp5" (replaced by tutorial_deep_convection).
167    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
168      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
169      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
170      --> changes results in exp4, seaice_obcs
171    o tutorial_deep_convection :
172      update the set-up and increase resolution and domain size ; start
173      from pseudo initial conditions = output at t=120mn in order to see
174      something happening when running testreport.
175    o pkg/seaice: add os7mp as an advection scheme
176                  add check for advection schemes
177                  add a flag for restoring T and S underneath sea ice
178    o pkg/my82: add netcdf-support and diagnostics
179    o thsice pkg:
180      - Now hsMax limits snow height by turning it into ice following
181        flooding scheme (and now conserving energy)
182      - Slight rewriting of the formula in thsice_calc_thick.F
183      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
184      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
185    
186    checkpoint59p
187    o gchem / dic / cfc :
188      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
189      - add new parameter files: "data.dic" & "data.cfc" ;
190      - various re-arrangement in initialisation & header file ;
191      - fix tutorial_global_oce_biogeo for multi-threaded test.
192    o pkg/dic: test for "pickup_dic" file when restarting ;
193      if no pickup-file, can restart with a re-initialised pH (same as it did
194      before) providing pickupStrictlyMatch is set to False.
195    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
196      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
197    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
198      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
199    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
200     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
201       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
202    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
203       scheme to use for vorticty-term ;
204     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
205       (with default selectVortScheme, return to original discretisation)
206     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
207    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
208    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
209      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
210      also fix diagnostics VISCAHW & VISCA4W.
211    
212    checkpoint59o
213    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
214    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
215      move a few statemens out the main loop into separate loops
216    o pkg/shelfice:
217      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
218        (kg/m^2/s), does not break tests, because in verification/isomip,
219        rhoConstFresh=rhoConst (by accident)
220      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
221      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
222        new file model/src/seawater.F, so that they are available for all pkgs.
223      - convert potential temperature into in-situ temperature. This changes the
224        isomip tests => update tests
225    o add a flag writePickupAtEnd (default=true) to be able to suppress
226      writing a pickup at the last timestep
227    o tools/mpack-1.6 :
228      - disable automake (not working) and autoconf (not needed).
229      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
230        also cleaner with much less compilation warnings.
231    o pkg/profiles:
232      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
233      (for "less than 32 characters name" compiler requirement)
234    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
235      conditions that have a different sampling frequency than S/T/U/V obcs
236    o pkg/diagnostics (stats-diags):
237      - fix global Min/Max in case 1 processor get only empty tiles
238    o genmake2: replace (4 times)
239         make genmake_tc_1.o >> genmake_warnings 2>&1
240      with
241         COMM="$CC $CFLAGS -c genmake_tc_1.c"
242         echo $COMM >> genmake_warnings
243         $COMM >> genmake_warnings 2>&1
244      to make genmake2 always see the value of CC as specified in the optfile.
245    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
246      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
247      - modify verification advect_cs test to test SOM-advection on CS-grid.
248    o pkg/ctrl:
249      - Rewrite of ctrl_map_ini_ecco.F,
250        introducing a generic routine (ctrl_map_ini_gen.F).
251      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
252    
253    checkpoint59n
254    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
255      number in dedicate array "hdiag":
256      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
257        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
258      - many small changes (integer format) for large number of diagnostics
259      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
260        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
261    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
262      usingSphericalGrid, this allows to define the rotated grid coordinates
263      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
264      geographical coordinates according to the inverse of the rotation defined
265      by the Euler angles, so that Coriolis parameter and online-interpolation by
266      exf works with the geographical coordinates on XC/YC/XG/YG.
267      Naturally, this feature does not work with all packages, so some
268      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
269      profiles), because there the coordinates are assumed to be regular
270      spherical grid coordinates.
271    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
272      - introduce isopycnal diffusion coefficient control.
273    o tools/adjoint_options:
274      - additional control vector components.
275    o pkg/mnc: have mnc create marginally meaning full coordinate variables
276      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
277    o pkg/mypackage:
278      - add example of read/write pickup for state-var ;
279      - add entry points to the main code for state-vars diags & write-pickup.
280    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
281      transitions for useExfYearlyFields
282      - add new subroutine that determines the file to read from for
283        use*YearlyFields = .TRUE. and .FALSE.
284      - add a verification experiment to global_with_exf that tests
285        useExfYearlyFields with USE_EXF_INTERPOLATION defined
286    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
287      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
288      subroutines (which could be generated from a template, because they are
289      almost identical), for now they are included in obcs_prescribe_read.F for
290      simplicity
291    o pkg/exf:
292      - add a little more diagnostic to exf_interp_read (in analogy to
293        mds_read_field, can be turned off with debugLevel < debugLevA=1)
294      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
295        ugly but fast by unrolling short inner loops, inserting a unroll=8
296        directive in routine lagran, and splitting a loop and making do while the
297        outermost loop (the latter requires the intoduction of index arrays)
298    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
299    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
300      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
301    o verification/seaice_obcs: updated for restart test and latest options
302    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
303      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
304      for now this is only available for the C-grid code and also within
305      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
306    
307    checkpoint59m
308    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
309      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
310    o gad_som : fix flux output (& diagnostics) to have same units as other  
311      advection scheme fluxes (was previously multiplied by deltaT).  
312    o added verification/seaice_obcs both to test seaice open boundaries
313      and to provide an example matlab scrpt for generating them
314    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
315    o pkg/salt_plume: clean up salt_plume_frac.F to
316      remove redundancy in PlumeMethod 1 and 4
317    o pkg/kpp: added saltplume diagnostics
318    o pkg/obcs and pkg/seaice:
319      - do not set uice and vice to zero when OB*icefile are unspecified
320      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
321      - moved seaice tracer obcs after call to seaice_growth
322    o pkg/salt_plume: added various options for salt plume depth
323      criterion and for vertical distribution of the salt
324    
325    checkpoint59l
326    o pkg/ptracers: new version of ptracers pickup:
327      read meta file and write only fields which are needed to restart.
328      ( same logic as main pickup file ; also using pickupStrictlyMatch )
329    o pkg/seaice:
330      - add timescale for melting due to warm mixed layer as a means of
331        setting SEAICE_availHeatFrac more conveniently
332      - add a CPP-flag/runtime parameter check for flooding algorithm
333      - reformulated availHeat in seaice_growth.F to be independent of AREA
334    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
335      unit changes
336    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
337    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
338      SX vector computer.
339    o pkg/seaice:
340      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
341        seaice forcing fields can now be read only through pkg/exf
342      - removed some unused halos
343    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
344    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
345      or U/VICE from U/VWIND before computing U/VSTRESS
346    
347    checkpoint59k
348    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
349      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
350    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
351      all experiments pass when compile with un-initialised var. checking option.
352    o added pkg/salt_plume
353    o script to test restart (for now, in MITgcm_contrib/jmc_script)
354    o pkg/seaice: new read/write pickup version.
355      read meta file and write only fields which are needed to restart.
356      ( same logic as main pickup file ; also using pickupStrictlyMatch )
357    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
358    o lab_sea.hb87: modify the domain & update output.hb87.txt :
359      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
360      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
361      process. Fixed here by closing the domain at the Northern boundary.
362    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
363    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
364      a set of consecutive levels in/from a 3-D array.
365    o pkg/ptracers:
366      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
367      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
368    
369    checkpoint59j
370    o in pkgs: dic, obcs, offline, rbcs:
371      standard way to compute coeff. for time interpolation between 2 time reccords
372      which retains full precision (& make results less dependent on compiler).
373      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
374    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
375      packages instead of reading ice cover and wind speed separately
376    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
377     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
378      to allow to compile customized code before the update)
379    o cleaning-up:
380      - fix CPP instruction syntax in pkg/obcs
381      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
382        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
383      - fix some threads issue in IO parts.
384    o pkg/dic:
385      - add tons of "_d 0" (--> much better testreports !)
386       and then update outputs of tutorial_global_oce_biogeo
387    o pkg/mom_fluxform:
388      add a special version of momentum advection intended to conserve momentum
389      next to a bathymetry step or a coastline edge. (default = off = #undef)
390    o new read/write pickup version:
391      - for now, only implemented for main (mdsio) pickup file.
392      - write out only what is needed to restart; merge pickup_nh , pickup_ph
393        and main pickup together.
394      - read meta file; read only what is needed to restart; stop if a field
395        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
396        if it make sense (even if the restart is not perfect).
397      - if no meta file, assume that pickup to read corresponds exactly to
398        a pickup that would currently be written.
399      - read pickup written in the old format (until checkpoint59i) if it
400        recognizes an old meta file (no field-list).
401      - add a meta file in exp. which starts from a pickup: 2 cases:
402        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
403         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
404        b) a meta file describing the content of the associated pickup file
405         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
406    o pkg/mdsio & pkg/rw:
407      - new routine to read a meta file ; new set of routine to read
408        Multiple-fields file (with meta file).
409    o added open boundary conditions capability for seaice
410        HSNOW, HSALT, UICE, and VICE
411    
412    checkpoint59i
413    o adjoint:
414      * fix multiDimAdvection adjoint
415        (partial recomputation problem by TAF for fVerT(:,:,kDown)
416        and comlev1 size definition (maxpass vs. max. number of tracers)
417      * verification/global_ocean.90x45x15 adjoint now tests
418        NLFS and multiDimAdvection using DST3 (=30)
419      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
420    o pkg/kpp: add "_d 0" to real constant (if missing);
421      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
422      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
423    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
424      for internal parameters related to restart process (formerly from PARAMS.h)
425      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
426    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
427      as argument. (only atm2d & obcs write_pickup have not yet been updated)
428    o pkg/monitor:
429      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
430      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
431      - account for deep Atmosphere factor and density factor (anelastic)
432    o added open boundary conditions capability for seaice HEFF and AREA
433    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
434      thermodynamics
435      - requires a little reorganization, which affects the testreport results
436        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
437        so that now the conservative form is tested
438      - add a few comments
439    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
440    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
441    o add new diagnostics to seaice: advective, diffusive fluxes (only for
442      multidim-advection, for scheme 2 they are not filled) and transports,
443      thermodynamic growth rates
444    o change units of EmPmR (inside the code, + within coupling interface)
445      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
446      Affects results @ truncation level (cg2d match) and update output of
447       experiments: lab_sea(6), global_ocean.90x40x15(10),
448      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
449      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
450      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
451      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
452    
453    checkpoint59h
454    o pkg/exf:
455      - improve vectorization by moving if-statement out of loops in
456        exf_mapfields, exf_radiation
457      - exf_bulkformulae.F: introduce 2D fields and vectorize code
458    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
459    o testreport:
460      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
461        monitor & update offline_exf_seaice exp. output.
462      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
463    o pkg/seaice:
464      - bug fix in the evp solver: boundary conditions were affected be
465        masking of zMax/zMin (changes results)
466      - minor bug fix in boundary conditions in seaice_calc_strainrates
467        (changes results for no_slip)
468      - seaice_lsr.F: make interpolation of eta dependent on boundaries
469      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
470      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
471        stress formulation and no-slip boundary conditions
472    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
473      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
474    o pkg/seaice: a first HSALT time stepping equation has been checked in
475    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
476      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
477      without requiring DO-IF statements
478    o pkg/thsice:
479      use continuous power-law function for partition of energy between lateral
480      melting/freezing and thinning/thickening ; old code using step function
481      still available with #undef THSICE_FRACEN_POWERLAW
482      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
483    o testreport: change AD testing : check against results/output_adm.txt
484      using same scripts as for forward test.
485    
486    checkpoint59g
487    o adjoint testing: in preparation for changing testreport:
488      - output format: cost and grad written on separated lines
489      - ad output results in directory "results" (instead of "results_ad")
490    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
491  o pkg/seaice: changes for using pkg/seaice with pkg/obcs  o pkg/seaice: changes for using pkg/seaice with pkg/obcs
492  o pkg/ecco: allow user defined cost function contributions  o pkg/ecco: allow user defined cost function contributions
493  o testreport:  o testreport:
494    Allow to choose (per experiment) the list of tested output variables    Allow to choose (per experiment) the list of tested output variables
495     and the main variable (used to issue a pass/FAIL ) ;     and the main variable (used to issue a pass/FAIL ) ;
496    - for now, done by adding the specific list in file: [exp]/input/tr_checklist    - for now, done by adding the specific list in file: [exp]/input/tr_checklist
497    - default is unchange: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;    - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
498    Also modify printing of summary:    Also modify printing of summary:
499     a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)     a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
500     b) echo the list of tested variables in the individual summary.txt of     b) echo the list of tested variables in the individual summary.txt of
# Line 273  o in FFIELDS.h: Line 757  o in FFIELDS.h:
757       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
758  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
759  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
760      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
761        are no longer updating the vertical diffusivity array
762        (passed as argument) but are (re-) setting those arrays.
763  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
764    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
765      cgrid-lsr and evp solver      cgrid-lsr and evp solver
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