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revision 1.862 by jmc, Tue Aug 21 14:39:43 2007 UTC revision 1.1017 by jmc, Fri Aug 22 16:06:54 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 vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
8    o new pkg: down_slope
9      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
10      - presently, modify T & S inland (dwnslp_calc_rho.F).
11        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
12      - implementation for ocean in P-coords not tested.
13      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
14    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
15      (to facilitate conversion of oceanic pkg to p-coordinate).
16    o change FIND_RHO to FIND_RHO_2D :
17      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
18    o new pkg: cheapaml
19    
20    checkpoint61b
21    o exch2:
22      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
23      - no longer depend on the order sequence (N,S,E,W).
24      - 3rd exchange no longer needed (tested with 24 tiles).
25      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
26      - exch_UV_A-grid readily available (but not yet tested).
27      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
28      (both are no longer needed) in exch_uv: no effect in forward run; but
29       get truncation error differences with adjoint exch.
30    o exch2:
31     - change index-bounds storage (moved from target to local tile,
32       more intuitive this way) ; rename/remove some variables.
33     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
34    
35    checkpoint61a
36    o exch2/matlab-topology-generator:
37      fix bug in index bounds for N-S internal exchange (hard to tell if this
38      had any effect on the solution).
39    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
40      is exceeded
41    o testreport: modify syntax of awk, so that it works also with
42      awk, and not only with nawk and gawk
43    
44    checkpoint61
45    o autodiff
46      Change default for TAF usage by removing argument '-nonew_arg'
47      This changes TAF subroutine argument list (ordering of active var.)
48      Omission of this flag leads to incompatibility w.r.t. TAMC
49      To restore TAMC-compatibility, need following modifs:
50      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
51      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
52      Tested TAF version is 1.9.22
53      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
54    
55    checkpoint60
56    --->>> This is the last checkpoint for which generating the adjoint
57    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
58    --->>> by default.
59    --->>> Future checkpoints will ommit this flag by default.
60    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
61    o pkg/grdchk: Add gradient check to etan0 perturbations.
62    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
63    o pkg/autodiff: more flexibility in zeroadj.
64      model/src: modifying do_oceanic_phys.F accordingly.
65    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
66    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
67      special setup of gmredi for which the adjoint is stable
68      enough for parameter optimization.
69    o bridging the gap between eddy stress and GM.
70      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
71          along with a change in CPP option (now ALLOW_EDDYPSI).
72      -> when using GM w/ GM_AdvForm:
73          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
74          is applied either in the tracer Eq. or in momentum Eq.
75          depending on data.gmredi (intro. GM_InMomAsStress).
76      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
77      The key modifications are in model/src/taueddy_external_forcing.F
78      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
79    
80    checkpoint59r
81    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
82      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
83      fix option to read coriolis(@ cell-corner) from files with CS-grid.
84    o pkg/mnc: add some attributes to standard 1D-coordinate variables
85    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
86      mass points, when using mnc for output
87      - add runtime parameter (missing_value, missing_value_int) to override
88        default (which is the value of getcon('UNDEF'))
89    o pkg/mnc: prepare mnc for the actual use of missing values with the
90      diagnostics package: small fix in mnc_cw_readwrite.template and more
91      initialisation of never used fields
92      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
93      versions
94    o pkg/thsice/thsice_ini_vars.F added default initial values so that
95      thermodynamics sea ice solver does not blow up when some initial fields
96      are missing.
97    o move from external_forcing_surf.F to ini_forcing.F
98      the p-coord. hack consisting in using pLoad to set phi0surf ;
99      update output of tutorial_global_oce_in_p (affected @ truncation level).
100    o Freshen up a bit hs94.1x64x5, notably:
101      remove rotationPeriod and tRef=5*0. (adjoint only), and add
102      exactConserv=.TRUE.
103    o pkg/generic_advdiff:
104      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
105      applies to files where Temperature & Salinity 2nd Order moments are used.
106    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
107      this uses a dynamically allocated internal state data structure
108      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
109      and requires a fortran 90 compiler
110    
111    checkpoint59q
112    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
113       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
114    o Refresh tutorial_global_oce_biogeo, notably:
115      - change bathymetry (put back seamounts in ACC, use hFacs)
116      - change EOS (POLY3 --> JMD95Z)
117      - use Bryan-Lewis vertical diffusivity
118      - use multidimensional advection
119      - remove old virtual virtual in dic pkg, now done through ptracer pkg
120      - change a couple of parameters in dic pkg
121    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
122    o pkg/obcs: change default to OBCSfixTopo = .true.,
123      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
124      - replace "debugMode" with "debugLevel .GE. debLevB"
125    o implementation of TAF directives for gchem,cfc,dic
126    o remove "exp5" (replaced by tutorial_deep_convection).
127    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
128      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
129      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
130      --> changes results in exp4, seaice_obcs
131    o tutorial_deep_convection :
132      update the set-up and increase resolution and domain size ; start
133      from pseudo initial conditions = output at t=120mn in order to see
134      something happening when running testreport.
135    o pkg/seaice: add os7mp as an advection scheme
136                  add check for advection schemes
137                  add a flag for restoring T and S underneath sea ice
138    o pkg/my82: add netcdf-support and diagnostics
139    o thsice pkg:
140      - Now hsMax limits snow height by turning it into ice following
141        flooding scheme (and now conserving energy)
142      - Slight rewriting of the formula in thsice_calc_thick.F
143      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
144      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
145    
146    checkpoint59p
147    o gchem / dic / cfc :
148      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
149      - add new parameter files: "data.dic" & "data.cfc" ;
150      - various re-arrangement in initialisation & header file ;
151      - fix tutorial_global_oce_biogeo for multi-threaded test.
152    o pkg/dic: test for "pickup_dic" file when restarting ;
153      if no pickup-file, can restart with a re-initialised pH (same as it did
154      before) providing pickupStrictlyMatch is set to False.
155    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
156      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
157    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
158      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
159    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
160     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
161       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
162    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
163       scheme to use for vorticty-term ;
164     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
165       (with default selectVortScheme, return to original discretisation)
166     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
167    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
168    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
169      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
170      also fix diagnostics VISCAHW & VISCA4W.
171    
172    checkpoint59o
173    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
174    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
175      move a few statemens out the main loop into separate loops
176    o pkg/shelfice:
177      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
178        (kg/m^2/s), does not break tests, because in verification/isomip,
179        rhoConstFresh=rhoConst (by accident)
180      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
181      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
182        new file model/src/seawater.F, so that they are available for all pkgs.
183      - convert potential temperature into in-situ temperature. This changes the
184        isomip tests => update tests
185    o add a flag writePickupAtEnd (default=true) to be able to suppress
186      writing a pickup at the last timestep
187    o tools/mpack-1.6 :
188      - disable automake (not working) and autoconf (not needed).
189      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
190        also cleaner with much less compilation warnings.
191    o pkg/profiles:
192      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
193      (for "less than 32 characters name" compiler requirement)
194    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
195      conditions that have a different sampling frequency than S/T/U/V obcs
196    o pkg/diagnostics (stats-diags):
197      - fix global Min/Max in case 1 processor get only empty tiles
198    o genmake2: replace (4 times)
199         make genmake_tc_1.o >> genmake_warnings 2>&1
200      with
201         COMM="$CC $CFLAGS -c genmake_tc_1.c"
202         echo $COMM >> genmake_warnings
203         $COMM >> genmake_warnings 2>&1
204      to make genmake2 always see the value of CC as specified in the optfile.
205    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
206      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
207      - modify verification advect_cs test to test SOM-advection on CS-grid.
208    o pkg/ctrl:
209      - Rewrite of ctrl_map_ini_ecco.F,
210        introducing a generic routine (ctrl_map_ini_gen.F).
211      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
212    
213    checkpoint59n
214    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
215      number in dedicate array "hdiag":
216      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
217        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
218      - many small changes (integer format) for large number of diagnostics
219      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
220        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
221    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
222      usingSphericalGrid, this allows to define the rotated grid coordinates
223      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
224      geographical coordinates according to the inverse of the rotation defined
225      by the Euler angles, so that Coriolis parameter and online-interpolation by
226      exf works with the geographical coordinates on XC/YC/XG/YG.
227      Naturally, this feature does not work with all packages, so some
228      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
229      profiles), because there the coordinates are assumed to be regular
230      spherical grid coordinates.
231    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
232      - introduce isopycnal diffusion coefficient control.
233    o tools/adjoint_options:
234      - additional control vector components.
235    o pkg/mnc: have mnc create marginally meaning full coordinate variables
236      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
237    o pkg/mypackage:
238      - add example of read/write pickup for state-var ;
239      - add entry points to the main code for state-vars diags & write-pickup.
240    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
241      transitions for useExfYearlyFields
242      - add new subroutine that determines the file to read from for
243        use*YearlyFields = .TRUE. and .FALSE.
244      - add a verification experiment to global_with_exf that tests
245        useExfYearlyFields with USE_EXF_INTERPOLATION defined
246    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
247      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
248      subroutines (which could be generated from a template, because they are
249      almost identical), for now they are included in obcs_prescribe_read.F for
250      simplicity
251    o pkg/exf:
252      - add a little more diagnostic to exf_interp_read (in analogy to
253        mds_read_field, can be turned off with debugLevel < debugLevA=1)
254      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
255        ugly but fast by unrolling short inner loops, inserting a unroll=8
256        directive in routine lagran, and splitting a loop and making do while the
257        outermost loop (the latter requires the intoduction of index arrays)
258    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
259    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
260      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
261    o verification/seaice_obcs: updated for restart test and latest options
262    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
263      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
264      for now this is only available for the C-grid code and also within
265      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
266    
267    checkpoint59m
268    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
269      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
270    o gad_som : fix flux output (& diagnostics) to have same units as other  
271      advection scheme fluxes (was previously multiplied by deltaT).  
272    o added verification/seaice_obcs both to test seaice open boundaries
273      and to provide an example matlab scrpt for generating them
274    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
275    o pkg/salt_plume: clean up salt_plume_frac.F to
276      remove redundancy in PlumeMethod 1 and 4
277    o pkg/kpp: added saltplume diagnostics
278    o pkg/obcs and pkg/seaice:
279      - do not set uice and vice to zero when OB*icefile are unspecified
280      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
281      - moved seaice tracer obcs after call to seaice_growth
282    o pkg/salt_plume: added various options for salt plume depth
283      criterion and for vertical distribution of the salt
284    
285    checkpoint59l
286    o pkg/ptracers: new version of ptracers pickup:
287      read meta file and write only fields which are needed to restart.
288      ( same logic as main pickup file ; also using pickupStrictlyMatch )
289    o pkg/seaice:
290      - add timescale for melting due to warm mixed layer as a means of
291        setting SEAICE_availHeatFrac more conveniently
292      - add a CPP-flag/runtime parameter check for flooding algorithm
293      - reformulated availHeat in seaice_growth.F to be independent of AREA
294    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
295      unit changes
296    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
297    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
298      SX vector computer.
299    o pkg/seaice:
300      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
301        seaice forcing fields can now be read only through pkg/exf
302      - removed some unused halos
303    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
304    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
305      or U/VICE from U/VWIND before computing U/VSTRESS
306    
307    checkpoint59k
308    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
309      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
310    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
311      all experiments pass when compile with un-initialised var. checking option.
312    o added pkg/salt_plume
313    o script to test restart (for now, in MITgcm_contrib/jmc_script)
314    o pkg/seaice: new read/write pickup version.
315      read meta file and write only fields which are needed to restart.
316      ( same logic as main pickup file ; also using pickupStrictlyMatch )
317    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
318    o lab_sea.hb87: modify the domain & update output.hb87.txt :
319      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
320      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
321      process. Fixed here by closing the domain at the Northern boundary.
322    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
323    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
324      a set of consecutive levels in/from a 3-D array.
325    o pkg/ptracers:
326      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
327      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
328    
329    checkpoint59j
330    o in pkgs: dic, obcs, offline, rbcs:
331      standard way to compute coeff. for time interpolation between 2 time reccords
332      which retains full precision (& make results less dependent on compiler).
333      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
334    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
335      packages instead of reading ice cover and wind speed separately
336    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
337     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
338      to allow to compile customized code before the update)
339    o cleaning-up:
340      - fix CPP instruction syntax in pkg/obcs
341      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
342        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
343      - fix some threads issue in IO parts.
344    o pkg/dic:
345      - add tons of "_d 0" (--> much better testreports !)
346       and then update outputs of tutorial_global_oce_biogeo
347    o pkg/mom_fluxform:
348      add a special version of momentum advection intended to conserve momentum
349      next to a bathymetry step or a coastline edge. (default = off = #undef)
350    o new read/write pickup version:
351      - for now, only implemented for main (mdsio) pickup file.
352      - write out only what is needed to restart; merge pickup_nh , pickup_ph
353        and main pickup together.
354      - read meta file; read only what is needed to restart; stop if a field
355        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
356        if it make sense (even if the restart is not perfect).
357      - if no meta file, assume that pickup to read corresponds exactly to
358        a pickup that would currently be written.
359      - read pickup written in the old format (until checkpoint59i) if it
360        recognizes an old meta file (no field-list).
361      - add a meta file in exp. which starts from a pickup: 2 cases:
362        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
363         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
364        b) a meta file describing the content of the associated pickup file
365         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
366    o pkg/mdsio & pkg/rw:
367      - new routine to read a meta file ; new set of routine to read
368        Multiple-fields file (with meta file).
369    o added open boundary conditions capability for seaice
370        HSNOW, HSALT, UICE, and VICE
371    
372    checkpoint59i
373    o adjoint:
374      * fix multiDimAdvection adjoint
375        (partial recomputation problem by TAF for fVerT(:,:,kDown)
376        and comlev1 size definition (maxpass vs. max. number of tracers)
377      * verification/global_ocean.90x45x15 adjoint now tests
378        NLFS and multiDimAdvection using DST3 (=30)
379      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
380    o pkg/kpp: add "_d 0" to real constant (if missing);
381      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
382      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
383    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
384      for internal parameters related to restart process (formerly from PARAMS.h)
385      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
386    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
387      as argument. (only atm2d & obcs write_pickup have not yet been updated)
388    o pkg/monitor:
389      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
390      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
391      - account for deep Atmosphere factor and density factor (anelastic)
392    o added open boundary conditions capability for seaice HEFF and AREA
393    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
394      thermodynamics
395      - requires a little reorganization, which affects the testreport results
396        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
397        so that now the conservative form is tested
398      - add a few comments
399    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
400    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
401    o add new diagnostics to seaice: advective, diffusive fluxes (only for
402      multidim-advection, for scheme 2 they are not filled) and transports,
403      thermodynamic growth rates
404    o change units of EmPmR (inside the code, + within coupling interface)
405      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
406      Affects results @ truncation level (cg2d match) and update output of
407       experiments: lab_sea(6), global_ocean.90x40x15(10),
408      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
409      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
410      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
411      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
412    
413    checkpoint59h
414    o pkg/exf:
415      - improve vectorization by moving if-statement out of loops in
416        exf_mapfields, exf_radiation
417      - exf_bulkformulae.F: introduce 2D fields and vectorize code
418    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
419    o testreport:
420      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
421        monitor & update offline_exf_seaice exp. output.
422      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
423    o pkg/seaice:
424      - bug fix in the evp solver: boundary conditions were affected be
425        masking of zMax/zMin (changes results)
426      - minor bug fix in boundary conditions in seaice_calc_strainrates
427        (changes results for no_slip)
428      - seaice_lsr.F: make interpolation of eta dependent on boundaries
429      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
430      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
431        stress formulation and no-slip boundary conditions
432    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
433      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
434    o pkg/seaice: a first HSALT time stepping equation has been checked in
435    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
436      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
437      without requiring DO-IF statements
438    o pkg/thsice:
439      use continuous power-law function for partition of energy between lateral
440      melting/freezing and thinning/thickening ; old code using step function
441      still available with #undef THSICE_FRACEN_POWERLAW
442      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
443    o testreport: change AD testing : check against results/output_adm.txt
444      using same scripts as for forward test.
445    
446    checkpoint59g
447    o adjoint testing: in preparation for changing testreport:
448      - output format: cost and grad written on separated lines
449      - ad output results in directory "results" (instead of "results_ad")
450    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
451    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
452    o pkg/ecco: allow user defined cost function contributions
453    o testreport:
454      Allow to choose (per experiment) the list of tested output variables
455       and the main variable (used to issue a pass/FAIL ) ;
456      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
457      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
458      Also modify printing of summary:
459       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
460       b) echo the list of tested variables in the individual summary.txt of
461          each experiment.
462    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
463      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
464      (but still depend on the tile decompostion of the domain).
465    o pkg/seaice: change a discretization detail to make the B-grid code
466      "more symmetric". This change is likely to remove all "ridges/leads" that
467      where quasi-aligned with the grid in B-grid solutions. It may also be
468      the solution to the stress coupling issues with the B-grid.
469    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
470      remove .cvsignore from input dir. (since testreport no longer run here).
471    o pkg/thsice:
472     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
473     - fix reshaping of sea-ice just after advection:
474       melt all the ice only if ice-volume is too small.
475     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
476       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
477     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
478    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
479      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
480    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
481      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
482      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
483      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
484      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
485      -> update output.txt
486    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
487     this affects truncation error: -> update output.txt of exp:
488      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
489      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
490    
491  checkpoint59f  checkpoint59f
492  o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)  o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
493  o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in  o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
# Line 233  o in FFIELDS.h: Line 717  o in FFIELDS.h:
717       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
718  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
719  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
720      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
721        are no longer updating the vertical diffusivity array
722        (passed as argument) but are (re-) setting those arrays.
723  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
724    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
725      cgrid-lsr and evp solver      cgrid-lsr and evp solver
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