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revision 1.850 by dimitri, Wed Jul 18 22:53:34 2007 UTC revision 1.1031 by jmc, Tue Oct 21 18:07:02 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 bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
8      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
9    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
10    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
11      does not become too large (to avoid precision problems in implicit-diffusion
12      solver); update ideal_2D_oce output.
13    o pkg ggl90:
14      - in ggl90_cal.F: compute only one set of visc/diff, used to
15        step forward TKE/T/S/momentum
16      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
17        have Prandlt =1)
18    o gmredi(fm07):
19      - add lower limit on Transition layer thickness + lower limit on 1/lambda
20      - allow to set few more params from data.gmredi
21    o pkg ggl90:
22          - add missing sqrt(2) factor in computation of mixing length
23            scale in ggl90_calc.F
24            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
25    
26    checkpoint61d
27    o adjoint modifs
28      - adapt to new field rhoInSitu
29      - allow to revert from StoreDynVars2D, StoreDynVars3D
30        to individual fields
31        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
32    o store 3-D (in-situ) density in commom block (DYNVARS.h)
33     - save 1 rho computation.
34     - no longer modify T & S inland when using down_slope pkg.
35    o gad_som : allow to switch to SOM advection for T & S without corresponding
36      pickup files (using new S/R: MDS_CHECK4FILE).
37    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
38      (for useSingleCpuIO to work in multi-threaded)
39    o pkg/shelfice:
40     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
41       with SHELFICEtopoFile in data.shelfice
42     - move code for reading ice shelf topography and modifying hFacC into separate
43       subroutines of the shelfice package
44     - separate initialisation of "fixed" and "variable" variables
45     - kTopC is not (yet) replaced by kSurfC, although this is possible
46    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
47    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
48      and rename:
49      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
50      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
51    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
52    
53    checkpoint61c
54    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
55      to add mass source/sink of fluid in the interior (3-D generalisation
56      of oceanic real-fresh water flux).
57    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
58    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
59    o new pkg: down_slope
60      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
61      - presently, modify T & S inland (dwnslp_calc_rho.F).
62        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
63      - implementation for ocean in P-coords not tested.
64      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
65    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
66      (to facilitate conversion of oceanic pkg to p-coordinate).
67    o change FIND_RHO to FIND_RHO_2D :
68      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
69    o new pkg: cheapaml
70    
71    checkpoint61b
72    o exch2:
73      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
74      - no longer depend on the order sequence (N,S,E,W).
75      - 3rd exchange no longer needed (tested with 24 tiles).
76      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
77      - exch_UV_A-grid readily available (but not yet tested).
78      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
79      (both are no longer needed) in exch_uv: no effect in forward run; but
80       get truncation error differences with adjoint exch.
81    o exch2:
82     - change index-bounds storage (moved from target to local tile,
83       more intuitive this way) ; rename/remove some variables.
84     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
85    
86    checkpoint61a
87    o exch2/matlab-topology-generator:
88      fix bug in index bounds for N-S internal exchange (hard to tell if this
89      had any effect on the solution).
90    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
91      is exceeded
92    o testreport: modify syntax of awk, so that it works also with
93      awk, and not only with nawk and gawk
94    
95    checkpoint61
96    o autodiff
97      Change default for TAF usage by removing argument '-nonew_arg'
98      This changes TAF subroutine argument list (ordering of active var.)
99      Omission of this flag leads to incompatibility w.r.t. TAMC
100      To restore TAMC-compatibility, need following modifs:
101      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
102      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
103      Tested TAF version is 1.9.22
104      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
105    
106    checkpoint60
107    --->>> This is the last checkpoint for which generating the adjoint
108    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
109    --->>> by default.
110    --->>> Future checkpoints will ommit this flag by default.
111    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
112    o pkg/grdchk: Add gradient check to etan0 perturbations.
113    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
114    o pkg/autodiff: more flexibility in zeroadj.
115      model/src: modifying do_oceanic_phys.F accordingly.
116    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
117    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
118      special setup of gmredi for which the adjoint is stable
119      enough for parameter optimization.
120    o bridging the gap between eddy stress and GM.
121      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
122          along with a change in CPP option (now ALLOW_EDDYPSI).
123      -> when using GM w/ GM_AdvForm:
124          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
125          is applied either in the tracer Eq. or in momentum Eq.
126          depending on data.gmredi (intro. GM_InMomAsStress).
127      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
128      The key modifications are in model/src/taueddy_external_forcing.F
129      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
130    
131    checkpoint59r
132    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
133      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
134      fix option to read coriolis(@ cell-corner) from files with CS-grid.
135    o pkg/mnc: add some attributes to standard 1D-coordinate variables
136    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
137      mass points, when using mnc for output
138      - add runtime parameter (missing_value, missing_value_int) to override
139        default (which is the value of getcon('UNDEF'))
140    o pkg/mnc: prepare mnc for the actual use of missing values with the
141      diagnostics package: small fix in mnc_cw_readwrite.template and more
142      initialisation of never used fields
143      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
144      versions
145    o pkg/thsice/thsice_ini_vars.F added default initial values so that
146      thermodynamics sea ice solver does not blow up when some initial fields
147      are missing.
148    o move from external_forcing_surf.F to ini_forcing.F
149      the p-coord. hack consisting in using pLoad to set phi0surf ;
150      update output of tutorial_global_oce_in_p (affected @ truncation level).
151    o Freshen up a bit hs94.1x64x5, notably:
152      remove rotationPeriod and tRef=5*0. (adjoint only), and add
153      exactConserv=.TRUE.
154    o pkg/generic_advdiff:
155      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
156      applies to files where Temperature & Salinity 2nd Order moments are used.
157    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
158      this uses a dynamically allocated internal state data structure
159      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
160      and requires a fortran 90 compiler
161    
162    checkpoint59q
163    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
164       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
165    o Refresh tutorial_global_oce_biogeo, notably:
166      - change bathymetry (put back seamounts in ACC, use hFacs)
167      - change EOS (POLY3 --> JMD95Z)
168      - use Bryan-Lewis vertical diffusivity
169      - use multidimensional advection
170      - remove old virtual virtual in dic pkg, now done through ptracer pkg
171      - change a couple of parameters in dic pkg
172    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
173    o pkg/obcs: change default to OBCSfixTopo = .true.,
174      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
175      - replace "debugMode" with "debugLevel .GE. debLevB"
176    o implementation of TAF directives for gchem,cfc,dic
177    o remove "exp5" (replaced by tutorial_deep_convection).
178    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
179      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
180      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
181      --> changes results in exp4, seaice_obcs
182    o tutorial_deep_convection :
183      update the set-up and increase resolution and domain size ; start
184      from pseudo initial conditions = output at t=120mn in order to see
185      something happening when running testreport.
186    o pkg/seaice: add os7mp as an advection scheme
187                  add check for advection schemes
188                  add a flag for restoring T and S underneath sea ice
189    o pkg/my82: add netcdf-support and diagnostics
190    o thsice pkg:
191      - Now hsMax limits snow height by turning it into ice following
192        flooding scheme (and now conserving energy)
193      - Slight rewriting of the formula in thsice_calc_thick.F
194      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
195      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
196    
197    checkpoint59p
198    o gchem / dic / cfc :
199      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
200      - add new parameter files: "data.dic" & "data.cfc" ;
201      - various re-arrangement in initialisation & header file ;
202      - fix tutorial_global_oce_biogeo for multi-threaded test.
203    o pkg/dic: test for "pickup_dic" file when restarting ;
204      if no pickup-file, can restart with a re-initialised pH (same as it did
205      before) providing pickupStrictlyMatch is set to False.
206    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
207      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
208    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
209      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
210    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
211     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
212       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
213    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
214       scheme to use for vorticty-term ;
215     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
216       (with default selectVortScheme, return to original discretisation)
217     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
218    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
219    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
220      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
221      also fix diagnostics VISCAHW & VISCA4W.
222    
223    checkpoint59o
224    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
225    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
226      move a few statemens out the main loop into separate loops
227    o pkg/shelfice:
228      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
229        (kg/m^2/s), does not break tests, because in verification/isomip,
230        rhoConstFresh=rhoConst (by accident)
231      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
232      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
233        new file model/src/seawater.F, so that they are available for all pkgs.
234      - convert potential temperature into in-situ temperature. This changes the
235        isomip tests => update tests
236    o add a flag writePickupAtEnd (default=true) to be able to suppress
237      writing a pickup at the last timestep
238    o tools/mpack-1.6 :
239      - disable automake (not working) and autoconf (not needed).
240      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
241        also cleaner with much less compilation warnings.
242    o pkg/profiles:
243      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
244      (for "less than 32 characters name" compiler requirement)
245    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
246      conditions that have a different sampling frequency than S/T/U/V obcs
247    o pkg/diagnostics (stats-diags):
248      - fix global Min/Max in case 1 processor get only empty tiles
249    o genmake2: replace (4 times)
250         make genmake_tc_1.o >> genmake_warnings 2>&1
251      with
252         COMM="$CC $CFLAGS -c genmake_tc_1.c"
253         echo $COMM >> genmake_warnings
254         $COMM >> genmake_warnings 2>&1
255      to make genmake2 always see the value of CC as specified in the optfile.
256    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
257      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
258      - modify verification advect_cs test to test SOM-advection on CS-grid.
259    o pkg/ctrl:
260      - Rewrite of ctrl_map_ini_ecco.F,
261        introducing a generic routine (ctrl_map_ini_gen.F).
262      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
263    
264    checkpoint59n
265    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
266      number in dedicate array "hdiag":
267      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
268        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
269      - many small changes (integer format) for large number of diagnostics
270      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
271        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
272    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
273      usingSphericalGrid, this allows to define the rotated grid coordinates
274      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
275      geographical coordinates according to the inverse of the rotation defined
276      by the Euler angles, so that Coriolis parameter and online-interpolation by
277      exf works with the geographical coordinates on XC/YC/XG/YG.
278      Naturally, this feature does not work with all packages, so some
279      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
280      profiles), because there the coordinates are assumed to be regular
281      spherical grid coordinates.
282    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
283      - introduce isopycnal diffusion coefficient control.
284    o tools/adjoint_options:
285      - additional control vector components.
286    o pkg/mnc: have mnc create marginally meaning full coordinate variables
287      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
288    o pkg/mypackage:
289      - add example of read/write pickup for state-var ;
290      - add entry points to the main code for state-vars diags & write-pickup.
291    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
292      transitions for useExfYearlyFields
293      - add new subroutine that determines the file to read from for
294        use*YearlyFields = .TRUE. and .FALSE.
295      - add a verification experiment to global_with_exf that tests
296        useExfYearlyFields with USE_EXF_INTERPOLATION defined
297    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
298      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
299      subroutines (which could be generated from a template, because they are
300      almost identical), for now they are included in obcs_prescribe_read.F for
301      simplicity
302    o pkg/exf:
303      - add a little more diagnostic to exf_interp_read (in analogy to
304        mds_read_field, can be turned off with debugLevel < debugLevA=1)
305      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
306        ugly but fast by unrolling short inner loops, inserting a unroll=8
307        directive in routine lagran, and splitting a loop and making do while the
308        outermost loop (the latter requires the intoduction of index arrays)
309    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
310    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
311      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
312    o verification/seaice_obcs: updated for restart test and latest options
313    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
314      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
315      for now this is only available for the C-grid code and also within
316      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
317    
318    checkpoint59m
319    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
320      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
321    o gad_som : fix flux output (& diagnostics) to have same units as other  
322      advection scheme fluxes (was previously multiplied by deltaT).  
323    o added verification/seaice_obcs both to test seaice open boundaries
324      and to provide an example matlab scrpt for generating them
325    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
326    o pkg/salt_plume: clean up salt_plume_frac.F to
327      remove redundancy in PlumeMethod 1 and 4
328    o pkg/kpp: added saltplume diagnostics
329    o pkg/obcs and pkg/seaice:
330      - do not set uice and vice to zero when OB*icefile are unspecified
331      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
332      - moved seaice tracer obcs after call to seaice_growth
333    o pkg/salt_plume: added various options for salt plume depth
334      criterion and for vertical distribution of the salt
335    
336    checkpoint59l
337    o pkg/ptracers: new version of ptracers pickup:
338      read meta file and write only fields which are needed to restart.
339      ( same logic as main pickup file ; also using pickupStrictlyMatch )
340    o pkg/seaice:
341      - add timescale for melting due to warm mixed layer as a means of
342        setting SEAICE_availHeatFrac more conveniently
343      - add a CPP-flag/runtime parameter check for flooding algorithm
344      - reformulated availHeat in seaice_growth.F to be independent of AREA
345    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
346      unit changes
347    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
348    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
349      SX vector computer.
350    o pkg/seaice:
351      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
352        seaice forcing fields can now be read only through pkg/exf
353      - removed some unused halos
354    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
355    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
356      or U/VICE from U/VWIND before computing U/VSTRESS
357    
358    checkpoint59k
359    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
360      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
361    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
362      all experiments pass when compile with un-initialised var. checking option.
363    o added pkg/salt_plume
364    o script to test restart (for now, in MITgcm_contrib/jmc_script)
365    o pkg/seaice: new read/write pickup version.
366      read meta file and write only fields which are needed to restart.
367      ( same logic as main pickup file ; also using pickupStrictlyMatch )
368    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
369    o lab_sea.hb87: modify the domain & update output.hb87.txt :
370      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
371      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
372      process. Fixed here by closing the domain at the Northern boundary.
373    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
374    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
375      a set of consecutive levels in/from a 3-D array.
376    o pkg/ptracers:
377      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
378      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
379    
380    checkpoint59j
381    o in pkgs: dic, obcs, offline, rbcs:
382      standard way to compute coeff. for time interpolation between 2 time reccords
383      which retains full precision (& make results less dependent on compiler).
384      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
385    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
386      packages instead of reading ice cover and wind speed separately
387    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
388     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
389      to allow to compile customized code before the update)
390    o cleaning-up:
391      - fix CPP instruction syntax in pkg/obcs
392      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
393        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
394      - fix some threads issue in IO parts.
395    o pkg/dic:
396      - add tons of "_d 0" (--> much better testreports !)
397       and then update outputs of tutorial_global_oce_biogeo
398    o pkg/mom_fluxform:
399      add a special version of momentum advection intended to conserve momentum
400      next to a bathymetry step or a coastline edge. (default = off = #undef)
401    o new read/write pickup version:
402      - for now, only implemented for main (mdsio) pickup file.
403      - write out only what is needed to restart; merge pickup_nh , pickup_ph
404        and main pickup together.
405      - read meta file; read only what is needed to restart; stop if a field
406        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
407        if it make sense (even if the restart is not perfect).
408      - if no meta file, assume that pickup to read corresponds exactly to
409        a pickup that would currently be written.
410      - read pickup written in the old format (until checkpoint59i) if it
411        recognizes an old meta file (no field-list).
412      - add a meta file in exp. which starts from a pickup: 2 cases:
413        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
414         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
415        b) a meta file describing the content of the associated pickup file
416         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
417    o pkg/mdsio & pkg/rw:
418      - new routine to read a meta file ; new set of routine to read
419        Multiple-fields file (with meta file).
420    o added open boundary conditions capability for seaice
421        HSNOW, HSALT, UICE, and VICE
422    
423    checkpoint59i
424    o adjoint:
425      * fix multiDimAdvection adjoint
426        (partial recomputation problem by TAF for fVerT(:,:,kDown)
427        and comlev1 size definition (maxpass vs. max. number of tracers)
428      * verification/global_ocean.90x45x15 adjoint now tests
429        NLFS and multiDimAdvection using DST3 (=30)
430      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
431    o pkg/kpp: add "_d 0" to real constant (if missing);
432      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
433      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
434    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
435      for internal parameters related to restart process (formerly from PARAMS.h)
436      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
437    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
438      as argument. (only atm2d & obcs write_pickup have not yet been updated)
439    o pkg/monitor:
440      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
441      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
442      - account for deep Atmosphere factor and density factor (anelastic)
443    o added open boundary conditions capability for seaice HEFF and AREA
444    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
445      thermodynamics
446      - requires a little reorganization, which affects the testreport results
447        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
448        so that now the conservative form is tested
449      - add a few comments
450    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
451    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
452    o add new diagnostics to seaice: advective, diffusive fluxes (only for
453      multidim-advection, for scheme 2 they are not filled) and transports,
454      thermodynamic growth rates
455    o change units of EmPmR (inside the code, + within coupling interface)
456      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
457      Affects results @ truncation level (cg2d match) and update output of
458       experiments: lab_sea(6), global_ocean.90x40x15(10),
459      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
460      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
461      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
462      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
463    
464    checkpoint59h
465    o pkg/exf:
466      - improve vectorization by moving if-statement out of loops in
467        exf_mapfields, exf_radiation
468      - exf_bulkformulae.F: introduce 2D fields and vectorize code
469    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
470    o testreport:
471      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
472        monitor & update offline_exf_seaice exp. output.
473      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
474    o pkg/seaice:
475      - bug fix in the evp solver: boundary conditions were affected be
476        masking of zMax/zMin (changes results)
477      - minor bug fix in boundary conditions in seaice_calc_strainrates
478        (changes results for no_slip)
479      - seaice_lsr.F: make interpolation of eta dependent on boundaries
480      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
481      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
482        stress formulation and no-slip boundary conditions
483    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
484      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
485    o pkg/seaice: a first HSALT time stepping equation has been checked in
486    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
487      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
488      without requiring DO-IF statements
489    o pkg/thsice:
490      use continuous power-law function for partition of energy between lateral
491      melting/freezing and thinning/thickening ; old code using step function
492      still available with #undef THSICE_FRACEN_POWERLAW
493      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
494    o testreport: change AD testing : check against results/output_adm.txt
495      using same scripts as for forward test.
496    
497    checkpoint59g
498    o adjoint testing: in preparation for changing testreport:
499      - output format: cost and grad written on separated lines
500      - ad output results in directory "results" (instead of "results_ad")
501    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
502    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
503    o pkg/ecco: allow user defined cost function contributions
504    o testreport:
505      Allow to choose (per experiment) the list of tested output variables
506       and the main variable (used to issue a pass/FAIL ) ;
507      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
508      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
509      Also modify printing of summary:
510       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
511       b) echo the list of tested variables in the individual summary.txt of
512          each experiment.
513    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
514      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
515      (but still depend on the tile decompostion of the domain).
516    o pkg/seaice: change a discretization detail to make the B-grid code
517      "more symmetric". This change is likely to remove all "ridges/leads" that
518      where quasi-aligned with the grid in B-grid solutions. It may also be
519      the solution to the stress coupling issues with the B-grid.
520    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
521      remove .cvsignore from input dir. (since testreport no longer run here).
522    o pkg/thsice:
523     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
524     - fix reshaping of sea-ice just after advection:
525       melt all the ice only if ice-volume is too small.
526     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
527       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
528     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
529    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
530      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
531    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
532      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
533      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
534      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
535      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
536      -> update output.txt
537    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
538     this affects truncation error: -> update output.txt of exp:
539      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
540      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
541    
542    checkpoint59f
543    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
544    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
545      a bounded range (in forward mode)
546    o pkg/ecco, ctrl, autodiff and mom_common:
547     internal parameter controls, completements of implementations
548    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
549    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
550      (not seem any difference in testing results).
551    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
552       at face corners.
553    o pkg/generic_advdiff:
554     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
555      loop range indices for computing vertical advection tendency
556      and do the calculation in the interior only (no overlap) ;
557      for now, only implemented for SOM advection (to save CPU time).
558     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
559    o exch2 adjoint
560      First set of changes:
561      - add exch2 hand-written adjoint templates
562      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
563        This will require cleanup in pkg/autodiff/*.F
564        (changed routines currently kept separate in verif. code/)
565      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
566        that used to hide exch2 or cubed-sphere specific code
567        (commented via 'cph-exch2')
568    o pkg/seaice
569      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
570    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
571       output of global_ocean.cs32x15.thsice .
572    
573    checkpoint59e
574    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
575      for B-grid vector (not yet tested) and C-grid vector (<- only used
576      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
577    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
578      (#ifdef ALLOW_SALT_PLUME)
579    o gather_2d/scatter_2d: removed halo regions
580  o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007  o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
581    scheme and the corresponding test case (under front_relax dir). For now,    scheme and the corresponding test case (under front_relax dir). For now,
582    only available with Skew-flux form and not yet tested in realistic set-up.    only available with Skew-flux form and not yet tested in realistic set-up.
# Line 195  o in FFIELDS.h: Line 768  o in FFIELDS.h:
768       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
769  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
770  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
771      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
772        are no longer updating the vertical diffusivity array
773        (passed as argument) but are (re-) setting those arrays.
774  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
775    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
776      cgrid-lsr and evp solver      cgrid-lsr and evp solver
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