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revision 1.826 by mlosch, Fri Jun 1 12:57:48 2007 UTC revision 1.1022 by mlosch, Wed Sep 10 09:20:47 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 pkg/shelfice:
8     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
9       with SHELFICEtopoFile in data.shelfice
10     - move code for reading ice shelf topography and modifying hFacC into separate
11       subroutines of the shelfice package
12     - separate initialisation of "fixed" and "variable" variables
13     - kTopC is not (yet) replaced by kSurfC, although this is possible
14    o fix a bug in diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
15    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
16      and rename:
17      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
18      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
19    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
20    
21    checkpoint61c
22    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
23      to add mass source/sink of fluid in the interior (3-D generalisation
24      of oceanic real-fresh water flux).
25    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
26    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
27    o new pkg: down_slope
28      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
29      - presently, modify T & S inland (dwnslp_calc_rho.F).
30        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
31      - implementation for ocean in P-coords not tested.
32      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
33    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
34      (to facilitate conversion of oceanic pkg to p-coordinate).
35    o change FIND_RHO to FIND_RHO_2D :
36      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
37    o new pkg: cheapaml
38    
39    checkpoint61b
40    o exch2:
41      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
42      - no longer depend on the order sequence (N,S,E,W).
43      - 3rd exchange no longer needed (tested with 24 tiles).
44      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
45      - exch_UV_A-grid readily available (but not yet tested).
46      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
47      (both are no longer needed) in exch_uv: no effect in forward run; but
48       get truncation error differences with adjoint exch.
49    o exch2:
50     - change index-bounds storage (moved from target to local tile,
51       more intuitive this way) ; rename/remove some variables.
52     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
53    
54    checkpoint61a
55    o exch2/matlab-topology-generator:
56      fix bug in index bounds for N-S internal exchange (hard to tell if this
57      had any effect on the solution).
58    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
59      is exceeded
60    o testreport: modify syntax of awk, so that it works also with
61      awk, and not only with nawk and gawk
62    
63    checkpoint61
64    o autodiff
65      Change default for TAF usage by removing argument '-nonew_arg'
66      This changes TAF subroutine argument list (ordering of active var.)
67      Omission of this flag leads to incompatibility w.r.t. TAMC
68      To restore TAMC-compatibility, need following modifs:
69      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
70      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
71      Tested TAF version is 1.9.22
72      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
73    
74    checkpoint60
75    --->>> This is the last checkpoint for which generating the adjoint
76    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
77    --->>> by default.
78    --->>> Future checkpoints will ommit this flag by default.
79    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
80    o pkg/grdchk: Add gradient check to etan0 perturbations.
81    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
82    o pkg/autodiff: more flexibility in zeroadj.
83      model/src: modifying do_oceanic_phys.F accordingly.
84    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
85    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
86      special setup of gmredi for which the adjoint is stable
87      enough for parameter optimization.
88    o bridging the gap between eddy stress and GM.
89      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
90          along with a change in CPP option (now ALLOW_EDDYPSI).
91      -> when using GM w/ GM_AdvForm:
92          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
93          is applied either in the tracer Eq. or in momentum Eq.
94          depending on data.gmredi (intro. GM_InMomAsStress).
95      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
96      The key modifications are in model/src/taueddy_external_forcing.F
97      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
98    
99    checkpoint59r
100    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
101      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
102      fix option to read coriolis(@ cell-corner) from files with CS-grid.
103    o pkg/mnc: add some attributes to standard 1D-coordinate variables
104    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
105      mass points, when using mnc for output
106      - add runtime parameter (missing_value, missing_value_int) to override
107        default (which is the value of getcon('UNDEF'))
108    o pkg/mnc: prepare mnc for the actual use of missing values with the
109      diagnostics package: small fix in mnc_cw_readwrite.template and more
110      initialisation of never used fields
111      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
112      versions
113    o pkg/thsice/thsice_ini_vars.F added default initial values so that
114      thermodynamics sea ice solver does not blow up when some initial fields
115      are missing.
116    o move from external_forcing_surf.F to ini_forcing.F
117      the p-coord. hack consisting in using pLoad to set phi0surf ;
118      update output of tutorial_global_oce_in_p (affected @ truncation level).
119    o Freshen up a bit hs94.1x64x5, notably:
120      remove rotationPeriod and tRef=5*0. (adjoint only), and add
121      exactConserv=.TRUE.
122    o pkg/generic_advdiff:
123      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
124      applies to files where Temperature & Salinity 2nd Order moments are used.
125    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
126      this uses a dynamically allocated internal state data structure
127      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
128      and requires a fortran 90 compiler
129    
130    checkpoint59q
131    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
132       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
133    o Refresh tutorial_global_oce_biogeo, notably:
134      - change bathymetry (put back seamounts in ACC, use hFacs)
135      - change EOS (POLY3 --> JMD95Z)
136      - use Bryan-Lewis vertical diffusivity
137      - use multidimensional advection
138      - remove old virtual virtual in dic pkg, now done through ptracer pkg
139      - change a couple of parameters in dic pkg
140    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
141    o pkg/obcs: change default to OBCSfixTopo = .true.,
142      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
143      - replace "debugMode" with "debugLevel .GE. debLevB"
144    o implementation of TAF directives for gchem,cfc,dic
145    o remove "exp5" (replaced by tutorial_deep_convection).
146    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
147      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
148      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
149      --> changes results in exp4, seaice_obcs
150    o tutorial_deep_convection :
151      update the set-up and increase resolution and domain size ; start
152      from pseudo initial conditions = output at t=120mn in order to see
153      something happening when running testreport.
154    o pkg/seaice: add os7mp as an advection scheme
155                  add check for advection schemes
156                  add a flag for restoring T and S underneath sea ice
157    o pkg/my82: add netcdf-support and diagnostics
158    o thsice pkg:
159      - Now hsMax limits snow height by turning it into ice following
160        flooding scheme (and now conserving energy)
161      - Slight rewriting of the formula in thsice_calc_thick.F
162      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
163      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
164    
165    checkpoint59p
166    o gchem / dic / cfc :
167      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
168      - add new parameter files: "data.dic" & "data.cfc" ;
169      - various re-arrangement in initialisation & header file ;
170      - fix tutorial_global_oce_biogeo for multi-threaded test.
171    o pkg/dic: test for "pickup_dic" file when restarting ;
172      if no pickup-file, can restart with a re-initialised pH (same as it did
173      before) providing pickupStrictlyMatch is set to False.
174    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
175      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
176    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
177      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
178    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
179     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
180       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
181    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
182       scheme to use for vorticty-term ;
183     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
184       (with default selectVortScheme, return to original discretisation)
185     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
186    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
187    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
188      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
189      also fix diagnostics VISCAHW & VISCA4W.
190    
191    checkpoint59o
192    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
193    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
194      move a few statemens out the main loop into separate loops
195    o pkg/shelfice:
196      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
197        (kg/m^2/s), does not break tests, because in verification/isomip,
198        rhoConstFresh=rhoConst (by accident)
199      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
200      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
201        new file model/src/seawater.F, so that they are available for all pkgs.
202      - convert potential temperature into in-situ temperature. This changes the
203        isomip tests => update tests
204    o add a flag writePickupAtEnd (default=true) to be able to suppress
205      writing a pickup at the last timestep
206    o tools/mpack-1.6 :
207      - disable automake (not working) and autoconf (not needed).
208      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
209        also cleaner with much less compilation warnings.
210    o pkg/profiles:
211      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
212      (for "less than 32 characters name" compiler requirement)
213    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
214      conditions that have a different sampling frequency than S/T/U/V obcs
215    o pkg/diagnostics (stats-diags):
216      - fix global Min/Max in case 1 processor get only empty tiles
217    o genmake2: replace (4 times)
218         make genmake_tc_1.o >> genmake_warnings 2>&1
219      with
220         COMM="$CC $CFLAGS -c genmake_tc_1.c"
221         echo $COMM >> genmake_warnings
222         $COMM >> genmake_warnings 2>&1
223      to make genmake2 always see the value of CC as specified in the optfile.
224    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
225      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
226      - modify verification advect_cs test to test SOM-advection on CS-grid.
227    o pkg/ctrl:
228      - Rewrite of ctrl_map_ini_ecco.F,
229        introducing a generic routine (ctrl_map_ini_gen.F).
230      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
231    
232    checkpoint59n
233    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
234      number in dedicate array "hdiag":
235      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
236        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
237      - many small changes (integer format) for large number of diagnostics
238      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
239        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
240    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
241      usingSphericalGrid, this allows to define the rotated grid coordinates
242      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
243      geographical coordinates according to the inverse of the rotation defined
244      by the Euler angles, so that Coriolis parameter and online-interpolation by
245      exf works with the geographical coordinates on XC/YC/XG/YG.
246      Naturally, this feature does not work with all packages, so some
247      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
248      profiles), because there the coordinates are assumed to be regular
249      spherical grid coordinates.
250    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
251      - introduce isopycnal diffusion coefficient control.
252    o tools/adjoint_options:
253      - additional control vector components.
254    o pkg/mnc: have mnc create marginally meaning full coordinate variables
255      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
256    o pkg/mypackage:
257      - add example of read/write pickup for state-var ;
258      - add entry points to the main code for state-vars diags & write-pickup.
259    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
260      transitions for useExfYearlyFields
261      - add new subroutine that determines the file to read from for
262        use*YearlyFields = .TRUE. and .FALSE.
263      - add a verification experiment to global_with_exf that tests
264        useExfYearlyFields with USE_EXF_INTERPOLATION defined
265    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
266      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
267      subroutines (which could be generated from a template, because they are
268      almost identical), for now they are included in obcs_prescribe_read.F for
269      simplicity
270    o pkg/exf:
271      - add a little more diagnostic to exf_interp_read (in analogy to
272        mds_read_field, can be turned off with debugLevel < debugLevA=1)
273      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
274        ugly but fast by unrolling short inner loops, inserting a unroll=8
275        directive in routine lagran, and splitting a loop and making do while the
276        outermost loop (the latter requires the intoduction of index arrays)
277    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
278    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
279      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
280    o verification/seaice_obcs: updated for restart test and latest options
281    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
282      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
283      for now this is only available for the C-grid code and also within
284      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
285    
286    checkpoint59m
287    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
288      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
289    o gad_som : fix flux output (& diagnostics) to have same units as other  
290      advection scheme fluxes (was previously multiplied by deltaT).  
291    o added verification/seaice_obcs both to test seaice open boundaries
292      and to provide an example matlab scrpt for generating them
293    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
294    o pkg/salt_plume: clean up salt_plume_frac.F to
295      remove redundancy in PlumeMethod 1 and 4
296    o pkg/kpp: added saltplume diagnostics
297    o pkg/obcs and pkg/seaice:
298      - do not set uice and vice to zero when OB*icefile are unspecified
299      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
300      - moved seaice tracer obcs after call to seaice_growth
301    o pkg/salt_plume: added various options for salt plume depth
302      criterion and for vertical distribution of the salt
303    
304    checkpoint59l
305    o pkg/ptracers: new version of ptracers pickup:
306      read meta file and write only fields which are needed to restart.
307      ( same logic as main pickup file ; also using pickupStrictlyMatch )
308    o pkg/seaice:
309      - add timescale for melting due to warm mixed layer as a means of
310        setting SEAICE_availHeatFrac more conveniently
311      - add a CPP-flag/runtime parameter check for flooding algorithm
312      - reformulated availHeat in seaice_growth.F to be independent of AREA
313    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
314      unit changes
315    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
316    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
317      SX vector computer.
318    o pkg/seaice:
319      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
320        seaice forcing fields can now be read only through pkg/exf
321      - removed some unused halos
322    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
323    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
324      or U/VICE from U/VWIND before computing U/VSTRESS
325    
326    checkpoint59k
327    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
328      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
329    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
330      all experiments pass when compile with un-initialised var. checking option.
331    o added pkg/salt_plume
332    o script to test restart (for now, in MITgcm_contrib/jmc_script)
333    o pkg/seaice: new read/write pickup version.
334      read meta file and write only fields which are needed to restart.
335      ( same logic as main pickup file ; also using pickupStrictlyMatch )
336    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
337    o lab_sea.hb87: modify the domain & update output.hb87.txt :
338      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
339      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
340      process. Fixed here by closing the domain at the Northern boundary.
341    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
342    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
343      a set of consecutive levels in/from a 3-D array.
344    o pkg/ptracers:
345      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
346      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
347    
348    checkpoint59j
349    o in pkgs: dic, obcs, offline, rbcs:
350      standard way to compute coeff. for time interpolation between 2 time reccords
351      which retains full precision (& make results less dependent on compiler).
352      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
353    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
354      packages instead of reading ice cover and wind speed separately
355    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
356     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
357      to allow to compile customized code before the update)
358    o cleaning-up:
359      - fix CPP instruction syntax in pkg/obcs
360      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
361        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
362      - fix some threads issue in IO parts.
363    o pkg/dic:
364      - add tons of "_d 0" (--> much better testreports !)
365       and then update outputs of tutorial_global_oce_biogeo
366    o pkg/mom_fluxform:
367      add a special version of momentum advection intended to conserve momentum
368      next to a bathymetry step or a coastline edge. (default = off = #undef)
369    o new read/write pickup version:
370      - for now, only implemented for main (mdsio) pickup file.
371      - write out only what is needed to restart; merge pickup_nh , pickup_ph
372        and main pickup together.
373      - read meta file; read only what is needed to restart; stop if a field
374        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
375        if it make sense (even if the restart is not perfect).
376      - if no meta file, assume that pickup to read corresponds exactly to
377        a pickup that would currently be written.
378      - read pickup written in the old format (until checkpoint59i) if it
379        recognizes an old meta file (no field-list).
380      - add a meta file in exp. which starts from a pickup: 2 cases:
381        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
382         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
383        b) a meta file describing the content of the associated pickup file
384         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
385    o pkg/mdsio & pkg/rw:
386      - new routine to read a meta file ; new set of routine to read
387        Multiple-fields file (with meta file).
388    o added open boundary conditions capability for seaice
389        HSNOW, HSALT, UICE, and VICE
390    
391    checkpoint59i
392    o adjoint:
393      * fix multiDimAdvection adjoint
394        (partial recomputation problem by TAF for fVerT(:,:,kDown)
395        and comlev1 size definition (maxpass vs. max. number of tracers)
396      * verification/global_ocean.90x45x15 adjoint now tests
397        NLFS and multiDimAdvection using DST3 (=30)
398      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
399    o pkg/kpp: add "_d 0" to real constant (if missing);
400      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
401      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
402    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
403      for internal parameters related to restart process (formerly from PARAMS.h)
404      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
405    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
406      as argument. (only atm2d & obcs write_pickup have not yet been updated)
407    o pkg/monitor:
408      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
409      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
410      - account for deep Atmosphere factor and density factor (anelastic)
411    o added open boundary conditions capability for seaice HEFF and AREA
412    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
413      thermodynamics
414      - requires a little reorganization, which affects the testreport results
415        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
416        so that now the conservative form is tested
417      - add a few comments
418    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
419    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
420    o add new diagnostics to seaice: advective, diffusive fluxes (only for
421      multidim-advection, for scheme 2 they are not filled) and transports,
422      thermodynamic growth rates
423    o change units of EmPmR (inside the code, + within coupling interface)
424      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
425      Affects results @ truncation level (cg2d match) and update output of
426       experiments: lab_sea(6), global_ocean.90x40x15(10),
427      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
428      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
429      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
430      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
431    
432    checkpoint59h
433    o pkg/exf:
434      - improve vectorization by moving if-statement out of loops in
435        exf_mapfields, exf_radiation
436      - exf_bulkformulae.F: introduce 2D fields and vectorize code
437    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
438    o testreport:
439      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
440        monitor & update offline_exf_seaice exp. output.
441      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
442    o pkg/seaice:
443      - bug fix in the evp solver: boundary conditions were affected be
444        masking of zMax/zMin (changes results)
445      - minor bug fix in boundary conditions in seaice_calc_strainrates
446        (changes results for no_slip)
447      - seaice_lsr.F: make interpolation of eta dependent on boundaries
448      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
449      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
450        stress formulation and no-slip boundary conditions
451    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
452      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
453    o pkg/seaice: a first HSALT time stepping equation has been checked in
454    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
455      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
456      without requiring DO-IF statements
457    o pkg/thsice:
458      use continuous power-law function for partition of energy between lateral
459      melting/freezing and thinning/thickening ; old code using step function
460      still available with #undef THSICE_FRACEN_POWERLAW
461      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
462    o testreport: change AD testing : check against results/output_adm.txt
463      using same scripts as for forward test.
464    
465    checkpoint59g
466    o adjoint testing: in preparation for changing testreport:
467      - output format: cost and grad written on separated lines
468      - ad output results in directory "results" (instead of "results_ad")
469    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
470    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
471    o pkg/ecco: allow user defined cost function contributions
472    o testreport:
473      Allow to choose (per experiment) the list of tested output variables
474       and the main variable (used to issue a pass/FAIL ) ;
475      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
476      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
477      Also modify printing of summary:
478       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
479       b) echo the list of tested variables in the individual summary.txt of
480          each experiment.
481    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
482      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
483      (but still depend on the tile decompostion of the domain).
484    o pkg/seaice: change a discretization detail to make the B-grid code
485      "more symmetric". This change is likely to remove all "ridges/leads" that
486      where quasi-aligned with the grid in B-grid solutions. It may also be
487      the solution to the stress coupling issues with the B-grid.
488    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
489      remove .cvsignore from input dir. (since testreport no longer run here).
490    o pkg/thsice:
491     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
492     - fix reshaping of sea-ice just after advection:
493       melt all the ice only if ice-volume is too small.
494     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
495       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
496     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
497    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
498      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
499    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
500      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
501      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
502      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
503      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
504      -> update output.txt
505    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
506     this affects truncation error: -> update output.txt of exp:
507      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
508      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
509    
510    checkpoint59f
511    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
512    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
513      a bounded range (in forward mode)
514    o pkg/ecco, ctrl, autodiff and mom_common:
515     internal parameter controls, completements of implementations
516    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
517    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
518      (not seem any difference in testing results).
519    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
520       at face corners.
521    o pkg/generic_advdiff:
522     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
523      loop range indices for computing vertical advection tendency
524      and do the calculation in the interior only (no overlap) ;
525      for now, only implemented for SOM advection (to save CPU time).
526     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
527    o exch2 adjoint
528      First set of changes:
529      - add exch2 hand-written adjoint templates
530      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
531        This will require cleanup in pkg/autodiff/*.F
532        (changed routines currently kept separate in verif. code/)
533      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
534        that used to hide exch2 or cubed-sphere specific code
535        (commented via 'cph-exch2')
536    o pkg/seaice
537      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
538    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
539       output of global_ocean.cs32x15.thsice .
540    
541    checkpoint59e
542    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
543      for B-grid vector (not yet tested) and C-grid vector (<- only used
544      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
545    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
546      (#ifdef ALLOW_SALT_PLUME)
547    o gather_2d/scatter_2d: removed halo regions
548    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
549      scheme and the corresponding test case (under front_relax dir). For now,
550      only available with Skew-flux form and not yet tested in realistic set-up.
551      adjoint: store directives updated, but gradient checks deteriorated,
552      so maybe GM/Redi adjoint is now broken.
553    o seaice adjoint
554      * add AREA, HEFF, HSNOW as control variable
555        (should not change lab_sea results)
556      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
557    o pkg/seaice:
558      * added computation of saltFlux in seaice_growth;
559        For time being, sea ice salinity is assumed constant
560        contribution of snow flooding to freshening of sea ice is neglected.
561        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
562        defaults to 0.0 in order to maintain backward compatibility.
563        Typical values for SEAICE_salinity are 4 to 10 g/kg.
564      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
565      * added SEAICE_availHeatFrac, which specifies fraction of surface level
566        heat content used to melt or grow ice
567      * commented out cap of HICE: it helps keep ice thinner
568      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
569      * applied OBCS T/S mask to HEFFM sea ice mask
570    
571    checkpoint59d
572    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
573     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
574     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
575    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
576     and change default value of parameter "GM_Small_Number";
577     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
578       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
579       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
580    o pkg/ecco: cost function when applying pkg/smooth to controls
581    o pkg/ctrl: add forcingPrecond run time parameter
582    o pkg/seaice:
583     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
584     - fix bug in metric terms of u-equation in LSR solver (implicit part),
585       changes verification/lab_sea
586     - rearrange implicit part of u-equation in LSR solver to make it easier to
587       read, understand, and debug. This causes changes at the truncation level.
588     - fix (serious) bug in the boundary conditions (sign error in the implicit
589       part) of the LSR solver. Changes all LSR results.
590     - fixed problem with HSNOW initialization to avoid thick snow when AREA
591       is initilized with small values - does not change lab_sea results.
592     - added HsnowFile initialization capability
593    o pkg/smooth: addition to model/src and pkg/ctrl so allow
594     initialization of pkg/smooth and application to control vector
595    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
596    o dependencies: pkg/profiles requires pkg/cal
597    o pkg/profiles:
598     - added option ALLOW_PROFILES_GENERICGRID
599         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
600         that interpolation information (grid points and coefficients) is provided
601         within the netcdf input files.
602         -> sample matlab scripts can be found in MITgcm_contrib/gael
603         that allow you to prepare netcdf input files.
604     - also modified: cleaner include statements, cleaner error print statements,
605       cleaner stops when error, and more tests of the netcdf input files consistency.
606    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
607    o pkg/seaice:
608     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
609       requires a new routine: seaice_diagnostics_fill.F
610     - make sure that seaice does not move if not forced (pressure replacement
611       method, Hibler and Ip, 1995), changes results
612     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
613     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
614       It is turned off by default (=-1.), because it changes the results.
615     - make it possible to read AREA from a file, too.
616    
617    checkpoint59c
618    o add S/R and diagnostics for oceanic mixed-layer depth
619    o move GMRedi call after all vertical mixing schemes (including KPP)
620    o pkg/thsice:
621     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
622      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
623  o pkg/obcs:  o pkg/obcs:
624   - bug fix for balance code   - bug fix for balance code
625  o pkg/seaice:  o pkg/seaice:
# Line 18  o change calculation of Visbeck K: Line 634  o change calculation of Visbeck K:
634    - no longer depend on tapering scheme; instead, compute slope (limited    - no longer depend on tapering scheme; instead, compute slope (limited
635      by GM_maxSlope). this is equivalent to what was comuted before with      by GM_maxSlope). this is equivalent to what was comuted before with
636      clipping or linear tappering.      clipping or linear tappering.
637    - fix vertical averaging (wrong by 1 level)    - fix vertical averaging (wrong by 1/2 level)
638    - leave the old version (but will not be maintained) within    - leave the old version (but will not be maintained) within
639      #ifdef OLD_VISBECK_CALC / #endif      #ifdef OLD_VISBECK_CALC / #endif
640      - update output of exp. ideal_2D_oce
641  o change error catch in calc_r_star to improve vectorization  o change error catch in calc_r_star to improve vectorization
642  o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and  o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
643    add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).    add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
644    o adjoint:
645      Re-organized adjoint checkpointing according to Matt Mazloff
646      (but with modifs/completions/cleanups)
647      Storing is now bundled into large arrays to optimized I/O
648      (and second step in cleanup of the_main_loop)
649    
650  checkpoint59b  checkpoint59b
651  o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):  o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
# Line 77  o pkg/exf: some cleaning-up: Line 699  o pkg/exf: some cleaning-up:
699  o pkg/thsice:  o pkg/thsice:
700   fix few little problems, in thsice_calc_thickn.F:   fix few little problems, in thsice_calc_thickn.F:
701    - growth vertically (and not laterally) if iceFrac == iceMaskMax    - growth vertically (and not laterally) if iceFrac == iceMaskMax
702    - melt laterally only if hIce < hThinIce (as the comments say)    - melt only laterally if hIce < hThinIce (as the comments say)
703    and in thsice_extend.F:    and in thsice_extend.F:
704    - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)    - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
705    - start to form ice as soon as the minimum ice-volume is reachable.    - start to form ice as soon as the minimum ice-volume is reachable.
# Line 114  o in FFIELDS.h: Line 736  o in FFIELDS.h:
736       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
737  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
738  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
739      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
740        are no longer updating the vertical diffusivity array
741        (passed as argument) but are (re-) setting those arrays.
742  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
743    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
744      cgrid-lsr and evp solver      cgrid-lsr and evp solver
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