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revision 1.871 by dimitri, Fri Sep 14 02:07:37 2007 UTC revision 1.1024 by jmc, Mon Sep 22 18:00:25 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 store 3-D (in-situ) density in commom block (DYNVARS.h)
8     - save 1 rho computation.
9     - no longer modify T & S inland when using down_slope pkg.
10    o gad_som : allow to switch to SOM advection for T & S without corresponding
11      pickup files (using new S/R: MDS_CHECK4FILE).
12    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
13      (for useSingleCpuIO to work in multi-threaded)
14    o pkg/shelfice:
15     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
16       with SHELFICEtopoFile in data.shelfice
17     - move code for reading ice shelf topography and modifying hFacC into separate
18       subroutines of the shelfice package
19     - separate initialisation of "fixed" and "variable" variables
20     - kTopC is not (yet) replaced by kSurfC, although this is possible
21    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
22    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
23      and rename:
24      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
25      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
26    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
27    
28    checkpoint61c
29    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
30      to add mass source/sink of fluid in the interior (3-D generalisation
31      of oceanic real-fresh water flux).
32    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
33    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
34    o new pkg: down_slope
35      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
36      - presently, modify T & S inland (dwnslp_calc_rho.F).
37        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
38      - implementation for ocean in P-coords not tested.
39      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
40    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
41      (to facilitate conversion of oceanic pkg to p-coordinate).
42    o change FIND_RHO to FIND_RHO_2D :
43      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
44    o new pkg: cheapaml
45    
46    checkpoint61b
47    o exch2:
48      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
49      - no longer depend on the order sequence (N,S,E,W).
50      - 3rd exchange no longer needed (tested with 24 tiles).
51      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
52      - exch_UV_A-grid readily available (but not yet tested).
53      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
54      (both are no longer needed) in exch_uv: no effect in forward run; but
55       get truncation error differences with adjoint exch.
56    o exch2:
57     - change index-bounds storage (moved from target to local tile,
58       more intuitive this way) ; rename/remove some variables.
59     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
60    
61    checkpoint61a
62    o exch2/matlab-topology-generator:
63      fix bug in index bounds for N-S internal exchange (hard to tell if this
64      had any effect on the solution).
65    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
66      is exceeded
67    o testreport: modify syntax of awk, so that it works also with
68      awk, and not only with nawk and gawk
69    
70    checkpoint61
71    o autodiff
72      Change default for TAF usage by removing argument '-nonew_arg'
73      This changes TAF subroutine argument list (ordering of active var.)
74      Omission of this flag leads to incompatibility w.r.t. TAMC
75      To restore TAMC-compatibility, need following modifs:
76      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
77      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
78      Tested TAF version is 1.9.22
79      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
80    
81    checkpoint60
82    --->>> This is the last checkpoint for which generating the adjoint
83    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
84    --->>> by default.
85    --->>> Future checkpoints will ommit this flag by default.
86    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
87    o pkg/grdchk: Add gradient check to etan0 perturbations.
88    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
89    o pkg/autodiff: more flexibility in zeroadj.
90      model/src: modifying do_oceanic_phys.F accordingly.
91    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
92    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
93      special setup of gmredi for which the adjoint is stable
94      enough for parameter optimization.
95    o bridging the gap between eddy stress and GM.
96      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
97          along with a change in CPP option (now ALLOW_EDDYPSI).
98      -> when using GM w/ GM_AdvForm:
99          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
100          is applied either in the tracer Eq. or in momentum Eq.
101          depending on data.gmredi (intro. GM_InMomAsStress).
102      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
103      The key modifications are in model/src/taueddy_external_forcing.F
104      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
105    
106    checkpoint59r
107    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
108      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
109      fix option to read coriolis(@ cell-corner) from files with CS-grid.
110    o pkg/mnc: add some attributes to standard 1D-coordinate variables
111    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
112      mass points, when using mnc for output
113      - add runtime parameter (missing_value, missing_value_int) to override
114        default (which is the value of getcon('UNDEF'))
115    o pkg/mnc: prepare mnc for the actual use of missing values with the
116      diagnostics package: small fix in mnc_cw_readwrite.template and more
117      initialisation of never used fields
118      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
119      versions
120    o pkg/thsice/thsice_ini_vars.F added default initial values so that
121      thermodynamics sea ice solver does not blow up when some initial fields
122      are missing.
123    o move from external_forcing_surf.F to ini_forcing.F
124      the p-coord. hack consisting in using pLoad to set phi0surf ;
125      update output of tutorial_global_oce_in_p (affected @ truncation level).
126    o Freshen up a bit hs94.1x64x5, notably:
127      remove rotationPeriod and tRef=5*0. (adjoint only), and add
128      exactConserv=.TRUE.
129    o pkg/generic_advdiff:
130      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
131      applies to files where Temperature & Salinity 2nd Order moments are used.
132    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
133      this uses a dynamically allocated internal state data structure
134      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
135      and requires a fortran 90 compiler
136    
137    checkpoint59q
138    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
139       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
140    o Refresh tutorial_global_oce_biogeo, notably:
141      - change bathymetry (put back seamounts in ACC, use hFacs)
142      - change EOS (POLY3 --> JMD95Z)
143      - use Bryan-Lewis vertical diffusivity
144      - use multidimensional advection
145      - remove old virtual virtual in dic pkg, now done through ptracer pkg
146      - change a couple of parameters in dic pkg
147    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
148    o pkg/obcs: change default to OBCSfixTopo = .true.,
149      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
150      - replace "debugMode" with "debugLevel .GE. debLevB"
151    o implementation of TAF directives for gchem,cfc,dic
152    o remove "exp5" (replaced by tutorial_deep_convection).
153    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
154      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
155      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
156      --> changes results in exp4, seaice_obcs
157    o tutorial_deep_convection :
158      update the set-up and increase resolution and domain size ; start
159      from pseudo initial conditions = output at t=120mn in order to see
160      something happening when running testreport.
161    o pkg/seaice: add os7mp as an advection scheme
162                  add check for advection schemes
163                  add a flag for restoring T and S underneath sea ice
164    o pkg/my82: add netcdf-support and diagnostics
165    o thsice pkg:
166      - Now hsMax limits snow height by turning it into ice following
167        flooding scheme (and now conserving energy)
168      - Slight rewriting of the formula in thsice_calc_thick.F
169      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
170      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
171    
172    checkpoint59p
173    o gchem / dic / cfc :
174      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
175      - add new parameter files: "data.dic" & "data.cfc" ;
176      - various re-arrangement in initialisation & header file ;
177      - fix tutorial_global_oce_biogeo for multi-threaded test.
178    o pkg/dic: test for "pickup_dic" file when restarting ;
179      if no pickup-file, can restart with a re-initialised pH (same as it did
180      before) providing pickupStrictlyMatch is set to False.
181    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
182      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
183    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
184      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
185    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
186     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
187       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
188    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
189       scheme to use for vorticty-term ;
190     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
191       (with default selectVortScheme, return to original discretisation)
192     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
193    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
194    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
195      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
196      also fix diagnostics VISCAHW & VISCA4W.
197    
198    checkpoint59o
199    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
200    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
201      move a few statemens out the main loop into separate loops
202    o pkg/shelfice:
203      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
204        (kg/m^2/s), does not break tests, because in verification/isomip,
205        rhoConstFresh=rhoConst (by accident)
206      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
207      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
208        new file model/src/seawater.F, so that they are available for all pkgs.
209      - convert potential temperature into in-situ temperature. This changes the
210        isomip tests => update tests
211    o add a flag writePickupAtEnd (default=true) to be able to suppress
212      writing a pickup at the last timestep
213    o tools/mpack-1.6 :
214      - disable automake (not working) and autoconf (not needed).
215      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
216        also cleaner with much less compilation warnings.
217    o pkg/profiles:
218      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
219      (for "less than 32 characters name" compiler requirement)
220    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
221      conditions that have a different sampling frequency than S/T/U/V obcs
222    o pkg/diagnostics (stats-diags):
223      - fix global Min/Max in case 1 processor get only empty tiles
224    o genmake2: replace (4 times)
225         make genmake_tc_1.o >> genmake_warnings 2>&1
226      with
227         COMM="$CC $CFLAGS -c genmake_tc_1.c"
228         echo $COMM >> genmake_warnings
229         $COMM >> genmake_warnings 2>&1
230      to make genmake2 always see the value of CC as specified in the optfile.
231    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
232      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
233      - modify verification advect_cs test to test SOM-advection on CS-grid.
234    o pkg/ctrl:
235      - Rewrite of ctrl_map_ini_ecco.F,
236        introducing a generic routine (ctrl_map_ini_gen.F).
237      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
238    
239    checkpoint59n
240    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
241      number in dedicate array "hdiag":
242      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
243        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
244      - many small changes (integer format) for large number of diagnostics
245      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
246        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
247    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
248      usingSphericalGrid, this allows to define the rotated grid coordinates
249      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
250      geographical coordinates according to the inverse of the rotation defined
251      by the Euler angles, so that Coriolis parameter and online-interpolation by
252      exf works with the geographical coordinates on XC/YC/XG/YG.
253      Naturally, this feature does not work with all packages, so some
254      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
255      profiles), because there the coordinates are assumed to be regular
256      spherical grid coordinates.
257    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
258      - introduce isopycnal diffusion coefficient control.
259    o tools/adjoint_options:
260      - additional control vector components.
261    o pkg/mnc: have mnc create marginally meaning full coordinate variables
262      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
263    o pkg/mypackage:
264      - add example of read/write pickup for state-var ;
265      - add entry points to the main code for state-vars diags & write-pickup.
266    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
267      transitions for useExfYearlyFields
268      - add new subroutine that determines the file to read from for
269        use*YearlyFields = .TRUE. and .FALSE.
270      - add a verification experiment to global_with_exf that tests
271        useExfYearlyFields with USE_EXF_INTERPOLATION defined
272    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
273      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
274      subroutines (which could be generated from a template, because they are
275      almost identical), for now they are included in obcs_prescribe_read.F for
276      simplicity
277    o pkg/exf:
278      - add a little more diagnostic to exf_interp_read (in analogy to
279        mds_read_field, can be turned off with debugLevel < debugLevA=1)
280      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
281        ugly but fast by unrolling short inner loops, inserting a unroll=8
282        directive in routine lagran, and splitting a loop and making do while the
283        outermost loop (the latter requires the intoduction of index arrays)
284    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
285    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
286      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
287    o verification/seaice_obcs: updated for restart test and latest options
288    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
289      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
290      for now this is only available for the C-grid code and also within
291      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
292    
293    checkpoint59m
294    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
295      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
296    o gad_som : fix flux output (& diagnostics) to have same units as other  
297      advection scheme fluxes (was previously multiplied by deltaT).  
298    o added verification/seaice_obcs both to test seaice open boundaries
299      and to provide an example matlab scrpt for generating them
300    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
301    o pkg/salt_plume: clean up salt_plume_frac.F to
302      remove redundancy in PlumeMethod 1 and 4
303    o pkg/kpp: added saltplume diagnostics
304    o pkg/obcs and pkg/seaice:
305      - do not set uice and vice to zero when OB*icefile are unspecified
306      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
307      - moved seaice tracer obcs after call to seaice_growth
308    o pkg/salt_plume: added various options for salt plume depth
309      criterion and for vertical distribution of the salt
310    
311    checkpoint59l
312    o pkg/ptracers: new version of ptracers pickup:
313      read meta file and write only fields which are needed to restart.
314      ( same logic as main pickup file ; also using pickupStrictlyMatch )
315    o pkg/seaice:
316      - add timescale for melting due to warm mixed layer as a means of
317        setting SEAICE_availHeatFrac more conveniently
318      - add a CPP-flag/runtime parameter check for flooding algorithm
319      - reformulated availHeat in seaice_growth.F to be independent of AREA
320    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
321      unit changes
322    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
323    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
324      SX vector computer.
325    o pkg/seaice:
326      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
327        seaice forcing fields can now be read only through pkg/exf
328      - removed some unused halos
329    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
330    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
331      or U/VICE from U/VWIND before computing U/VSTRESS
332    
333    checkpoint59k
334    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
335      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
336    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
337      all experiments pass when compile with un-initialised var. checking option.
338    o added pkg/salt_plume
339    o script to test restart (for now, in MITgcm_contrib/jmc_script)
340    o pkg/seaice: new read/write pickup version.
341      read meta file and write only fields which are needed to restart.
342      ( same logic as main pickup file ; also using pickupStrictlyMatch )
343    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
344    o lab_sea.hb87: modify the domain & update output.hb87.txt :
345      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
346      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
347      process. Fixed here by closing the domain at the Northern boundary.
348    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
349    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
350      a set of consecutive levels in/from a 3-D array.
351    o pkg/ptracers:
352      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
353      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
354    
355    checkpoint59j
356    o in pkgs: dic, obcs, offline, rbcs:
357      standard way to compute coeff. for time interpolation between 2 time reccords
358      which retains full precision (& make results less dependent on compiler).
359      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
360    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
361      packages instead of reading ice cover and wind speed separately
362    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
363     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
364      to allow to compile customized code before the update)
365    o cleaning-up:
366      - fix CPP instruction syntax in pkg/obcs
367      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
368        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
369      - fix some threads issue in IO parts.
370    o pkg/dic:
371      - add tons of "_d 0" (--> much better testreports !)
372       and then update outputs of tutorial_global_oce_biogeo
373    o pkg/mom_fluxform:
374      add a special version of momentum advection intended to conserve momentum
375      next to a bathymetry step or a coastline edge. (default = off = #undef)
376    o new read/write pickup version:
377      - for now, only implemented for main (mdsio) pickup file.
378      - write out only what is needed to restart; merge pickup_nh , pickup_ph
379        and main pickup together.
380      - read meta file; read only what is needed to restart; stop if a field
381        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
382        if it make sense (even if the restart is not perfect).
383      - if no meta file, assume that pickup to read corresponds exactly to
384        a pickup that would currently be written.
385      - read pickup written in the old format (until checkpoint59i) if it
386        recognizes an old meta file (no field-list).
387      - add a meta file in exp. which starts from a pickup: 2 cases:
388        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
389         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
390        b) a meta file describing the content of the associated pickup file
391         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
392    o pkg/mdsio & pkg/rw:
393      - new routine to read a meta file ; new set of routine to read
394        Multiple-fields file (with meta file).
395    o added open boundary conditions capability for seaice
396        HSNOW, HSALT, UICE, and VICE
397    
398    checkpoint59i
399    o adjoint:
400      * fix multiDimAdvection adjoint
401        (partial recomputation problem by TAF for fVerT(:,:,kDown)
402        and comlev1 size definition (maxpass vs. max. number of tracers)
403      * verification/global_ocean.90x45x15 adjoint now tests
404        NLFS and multiDimAdvection using DST3 (=30)
405      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
406    o pkg/kpp: add "_d 0" to real constant (if missing);
407      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
408      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
409    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
410      for internal parameters related to restart process (formerly from PARAMS.h)
411      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
412    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
413      as argument. (only atm2d & obcs write_pickup have not yet been updated)
414    o pkg/monitor:
415      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
416      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
417      - account for deep Atmosphere factor and density factor (anelastic)
418    o added open boundary conditions capability for seaice HEFF and AREA
419    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
420      thermodynamics
421      - requires a little reorganization, which affects the testreport results
422        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
423        so that now the conservative form is tested
424      - add a few comments
425    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
426    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
427    o add new diagnostics to seaice: advective, diffusive fluxes (only for
428      multidim-advection, for scheme 2 they are not filled) and transports,
429      thermodynamic growth rates
430    o change units of EmPmR (inside the code, + within coupling interface)
431      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
432      Affects results @ truncation level (cg2d match) and update output of
433       experiments: lab_sea(6), global_ocean.90x40x15(10),
434      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
435      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
436      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
437      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
438    
439    checkpoint59h
440    o pkg/exf:
441      - improve vectorization by moving if-statement out of loops in
442        exf_mapfields, exf_radiation
443      - exf_bulkformulae.F: introduce 2D fields and vectorize code
444    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
445    o testreport:
446      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
447        monitor & update offline_exf_seaice exp. output.
448      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
449    o pkg/seaice:
450      - bug fix in the evp solver: boundary conditions were affected be
451        masking of zMax/zMin (changes results)
452      - minor bug fix in boundary conditions in seaice_calc_strainrates
453        (changes results for no_slip)
454      - seaice_lsr.F: make interpolation of eta dependent on boundaries
455      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
456      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
457        stress formulation and no-slip boundary conditions
458    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
459      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
460    o pkg/seaice: a first HSALT time stepping equation has been checked in
461    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
462      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
463      without requiring DO-IF statements
464    o pkg/thsice:
465      use continuous power-law function for partition of energy between lateral
466      melting/freezing and thinning/thickening ; old code using step function
467      still available with #undef THSICE_FRACEN_POWERLAW
468      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
469    o testreport: change AD testing : check against results/output_adm.txt
470      using same scripts as for forward test.
471    
472    checkpoint59g
473    o adjoint testing: in preparation for changing testreport:
474      - output format: cost and grad written on separated lines
475      - ad output results in directory "results" (instead of "results_ad")
476    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
477  o pkg/seaice: changes for using pkg/seaice with pkg/obcs  o pkg/seaice: changes for using pkg/seaice with pkg/obcs
478  o pkg/ecco: allow user defined cost function contributions  o pkg/ecco: allow user defined cost function contributions
479  o testreport:  o testreport:
480    Allow to choose (per experiment) the list of tested output variables    Allow to choose (per experiment) the list of tested output variables
481     and the main variable (used to issue a pass/FAIL ) ;     and the main variable (used to issue a pass/FAIL ) ;
482    - 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
483    - 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] ;
484    Also modify printing of summary:    Also modify printing of summary:
485     a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)     a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
486     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 743  o in FFIELDS.h:
743       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
744  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
745  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
746      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
747        are no longer updating the vertical diffusivity array
748        (passed as argument) but are (re-) setting those arrays.
749  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
750    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
751      cgrid-lsr and evp solver      cgrid-lsr and evp solver
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