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revision 1.796 by mlosch, Sun Apr 22 19:57:13 2007 UTC revision 1.1021 by mlosch, Tue Sep 9 07:26:01 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 fix a bug in diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
8    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
9      and rename:
10      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
11      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
12    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
13    
14    checkpoint61c
15    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
16      to add mass source/sink of fluid in the interior (3-D generalisation
17      of oceanic real-fresh water flux).
18    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
19    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
20    o new pkg: down_slope
21      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
22      - presently, modify T & S inland (dwnslp_calc_rho.F).
23        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
24      - implementation for ocean in P-coords not tested.
25      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
26    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
27      (to facilitate conversion of oceanic pkg to p-coordinate).
28    o change FIND_RHO to FIND_RHO_2D :
29      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
30    o new pkg: cheapaml
31    
32    checkpoint61b
33    o exch2:
34      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
35      - no longer depend on the order sequence (N,S,E,W).
36      - 3rd exchange no longer needed (tested with 24 tiles).
37      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
38      - exch_UV_A-grid readily available (but not yet tested).
39      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
40      (both are no longer needed) in exch_uv: no effect in forward run; but
41       get truncation error differences with adjoint exch.
42    o exch2:
43     - change index-bounds storage (moved from target to local tile,
44       more intuitive this way) ; rename/remove some variables.
45     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
46    
47    checkpoint61a
48    o exch2/matlab-topology-generator:
49      fix bug in index bounds for N-S internal exchange (hard to tell if this
50      had any effect on the solution).
51    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
52      is exceeded
53    o testreport: modify syntax of awk, so that it works also with
54      awk, and not only with nawk and gawk
55    
56    checkpoint61
57    o autodiff
58      Change default for TAF usage by removing argument '-nonew_arg'
59      This changes TAF subroutine argument list (ordering of active var.)
60      Omission of this flag leads to incompatibility w.r.t. TAMC
61      To restore TAMC-compatibility, need following modifs:
62      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
63      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
64      Tested TAF version is 1.9.22
65      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
66    
67    checkpoint60
68    --->>> This is the last checkpoint for which generating the adjoint
69    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
70    --->>> by default.
71    --->>> Future checkpoints will ommit this flag by default.
72    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
73    o pkg/grdchk: Add gradient check to etan0 perturbations.
74    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
75    o pkg/autodiff: more flexibility in zeroadj.
76      model/src: modifying do_oceanic_phys.F accordingly.
77    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
78    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
79      special setup of gmredi for which the adjoint is stable
80      enough for parameter optimization.
81    o bridging the gap between eddy stress and GM.
82      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
83          along with a change in CPP option (now ALLOW_EDDYPSI).
84      -> when using GM w/ GM_AdvForm:
85          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
86          is applied either in the tracer Eq. or in momentum Eq.
87          depending on data.gmredi (intro. GM_InMomAsStress).
88      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
89      The key modifications are in model/src/taueddy_external_forcing.F
90      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
91    
92    checkpoint59r
93    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
94      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
95      fix option to read coriolis(@ cell-corner) from files with CS-grid.
96    o pkg/mnc: add some attributes to standard 1D-coordinate variables
97    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
98      mass points, when using mnc for output
99      - add runtime parameter (missing_value, missing_value_int) to override
100        default (which is the value of getcon('UNDEF'))
101    o pkg/mnc: prepare mnc for the actual use of missing values with the
102      diagnostics package: small fix in mnc_cw_readwrite.template and more
103      initialisation of never used fields
104      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
105      versions
106    o pkg/thsice/thsice_ini_vars.F added default initial values so that
107      thermodynamics sea ice solver does not blow up when some initial fields
108      are missing.
109    o move from external_forcing_surf.F to ini_forcing.F
110      the p-coord. hack consisting in using pLoad to set phi0surf ;
111      update output of tutorial_global_oce_in_p (affected @ truncation level).
112    o Freshen up a bit hs94.1x64x5, notably:
113      remove rotationPeriod and tRef=5*0. (adjoint only), and add
114      exactConserv=.TRUE.
115    o pkg/generic_advdiff:
116      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
117      applies to files where Temperature & Salinity 2nd Order moments are used.
118    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
119      this uses a dynamically allocated internal state data structure
120      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
121      and requires a fortran 90 compiler
122    
123    checkpoint59q
124    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
125       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
126    o Refresh tutorial_global_oce_biogeo, notably:
127      - change bathymetry (put back seamounts in ACC, use hFacs)
128      - change EOS (POLY3 --> JMD95Z)
129      - use Bryan-Lewis vertical diffusivity
130      - use multidimensional advection
131      - remove old virtual virtual in dic pkg, now done through ptracer pkg
132      - change a couple of parameters in dic pkg
133    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
134    o pkg/obcs: change default to OBCSfixTopo = .true.,
135      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
136      - replace "debugMode" with "debugLevel .GE. debLevB"
137    o implementation of TAF directives for gchem,cfc,dic
138    o remove "exp5" (replaced by tutorial_deep_convection).
139    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
140      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
141      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
142      --> changes results in exp4, seaice_obcs
143    o tutorial_deep_convection :
144      update the set-up and increase resolution and domain size ; start
145      from pseudo initial conditions = output at t=120mn in order to see
146      something happening when running testreport.
147    o pkg/seaice: add os7mp as an advection scheme
148                  add check for advection schemes
149                  add a flag for restoring T and S underneath sea ice
150    o pkg/my82: add netcdf-support and diagnostics
151    o thsice pkg:
152      - Now hsMax limits snow height by turning it into ice following
153        flooding scheme (and now conserving energy)
154      - Slight rewriting of the formula in thsice_calc_thick.F
155      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
156      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
157    
158    checkpoint59p
159    o gchem / dic / cfc :
160      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
161      - add new parameter files: "data.dic" & "data.cfc" ;
162      - various re-arrangement in initialisation & header file ;
163      - fix tutorial_global_oce_biogeo for multi-threaded test.
164    o pkg/dic: test for "pickup_dic" file when restarting ;
165      if no pickup-file, can restart with a re-initialised pH (same as it did
166      before) providing pickupStrictlyMatch is set to False.
167    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
168      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
169    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
170      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
171    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
172     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
173       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
174    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
175       scheme to use for vorticty-term ;
176     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
177       (with default selectVortScheme, return to original discretisation)
178     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
179    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
180    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
181      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
182      also fix diagnostics VISCAHW & VISCA4W.
183    
184    checkpoint59o
185    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
186    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
187      move a few statemens out the main loop into separate loops
188    o pkg/shelfice:
189      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
190        (kg/m^2/s), does not break tests, because in verification/isomip,
191        rhoConstFresh=rhoConst (by accident)
192      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
193      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
194        new file model/src/seawater.F, so that they are available for all pkgs.
195      - convert potential temperature into in-situ temperature. This changes the
196        isomip tests => update tests
197    o add a flag writePickupAtEnd (default=true) to be able to suppress
198      writing a pickup at the last timestep
199    o tools/mpack-1.6 :
200      - disable automake (not working) and autoconf (not needed).
201      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
202        also cleaner with much less compilation warnings.
203    o pkg/profiles:
204      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
205      (for "less than 32 characters name" compiler requirement)
206    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
207      conditions that have a different sampling frequency than S/T/U/V obcs
208    o pkg/diagnostics (stats-diags):
209      - fix global Min/Max in case 1 processor get only empty tiles
210    o genmake2: replace (4 times)
211         make genmake_tc_1.o >> genmake_warnings 2>&1
212      with
213         COMM="$CC $CFLAGS -c genmake_tc_1.c"
214         echo $COMM >> genmake_warnings
215         $COMM >> genmake_warnings 2>&1
216      to make genmake2 always see the value of CC as specified in the optfile.
217    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
218      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
219      - modify verification advect_cs test to test SOM-advection on CS-grid.
220    o pkg/ctrl:
221      - Rewrite of ctrl_map_ini_ecco.F,
222        introducing a generic routine (ctrl_map_ini_gen.F).
223      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
224    
225    checkpoint59n
226    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
227      number in dedicate array "hdiag":
228      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
229        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
230      - many small changes (integer format) for large number of diagnostics
231      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
232        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
233    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
234      usingSphericalGrid, this allows to define the rotated grid coordinates
235      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
236      geographical coordinates according to the inverse of the rotation defined
237      by the Euler angles, so that Coriolis parameter and online-interpolation by
238      exf works with the geographical coordinates on XC/YC/XG/YG.
239      Naturally, this feature does not work with all packages, so some
240      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
241      profiles), because there the coordinates are assumed to be regular
242      spherical grid coordinates.
243    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
244      - introduce isopycnal diffusion coefficient control.
245    o tools/adjoint_options:
246      - additional control vector components.
247    o pkg/mnc: have mnc create marginally meaning full coordinate variables
248      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
249    o pkg/mypackage:
250      - add example of read/write pickup for state-var ;
251      - add entry points to the main code for state-vars diags & write-pickup.
252    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
253      transitions for useExfYearlyFields
254      - add new subroutine that determines the file to read from for
255        use*YearlyFields = .TRUE. and .FALSE.
256      - add a verification experiment to global_with_exf that tests
257        useExfYearlyFields with USE_EXF_INTERPOLATION defined
258    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
259      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
260      subroutines (which could be generated from a template, because they are
261      almost identical), for now they are included in obcs_prescribe_read.F for
262      simplicity
263    o pkg/exf:
264      - add a little more diagnostic to exf_interp_read (in analogy to
265        mds_read_field, can be turned off with debugLevel < debugLevA=1)
266      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
267        ugly but fast by unrolling short inner loops, inserting a unroll=8
268        directive in routine lagran, and splitting a loop and making do while the
269        outermost loop (the latter requires the intoduction of index arrays)
270    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
271    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
272      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
273    o verification/seaice_obcs: updated for restart test and latest options
274    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
275      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
276      for now this is only available for the C-grid code and also within
277      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
278    
279    checkpoint59m
280    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
281      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
282    o gad_som : fix flux output (& diagnostics) to have same units as other  
283      advection scheme fluxes (was previously multiplied by deltaT).  
284    o added verification/seaice_obcs both to test seaice open boundaries
285      and to provide an example matlab scrpt for generating them
286    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
287    o pkg/salt_plume: clean up salt_plume_frac.F to
288      remove redundancy in PlumeMethod 1 and 4
289    o pkg/kpp: added saltplume diagnostics
290    o pkg/obcs and pkg/seaice:
291      - do not set uice and vice to zero when OB*icefile are unspecified
292      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
293      - moved seaice tracer obcs after call to seaice_growth
294    o pkg/salt_plume: added various options for salt plume depth
295      criterion and for vertical distribution of the salt
296    
297    checkpoint59l
298    o pkg/ptracers: new version of ptracers pickup:
299      read meta file and write only fields which are needed to restart.
300      ( same logic as main pickup file ; also using pickupStrictlyMatch )
301    o pkg/seaice:
302      - add timescale for melting due to warm mixed layer as a means of
303        setting SEAICE_availHeatFrac more conveniently
304      - add a CPP-flag/runtime parameter check for flooding algorithm
305      - reformulated availHeat in seaice_growth.F to be independent of AREA
306    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
307      unit changes
308    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
309    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
310      SX vector computer.
311    o pkg/seaice:
312      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
313        seaice forcing fields can now be read only through pkg/exf
314      - removed some unused halos
315    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
316    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
317      or U/VICE from U/VWIND before computing U/VSTRESS
318    
319    checkpoint59k
320    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
321      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
322    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
323      all experiments pass when compile with un-initialised var. checking option.
324    o added pkg/salt_plume
325    o script to test restart (for now, in MITgcm_contrib/jmc_script)
326    o pkg/seaice: new read/write pickup version.
327      read meta file and write only fields which are needed to restart.
328      ( same logic as main pickup file ; also using pickupStrictlyMatch )
329    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
330    o lab_sea.hb87: modify the domain & update output.hb87.txt :
331      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
332      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
333      process. Fixed here by closing the domain at the Northern boundary.
334    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
335    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
336      a set of consecutive levels in/from a 3-D array.
337    o pkg/ptracers:
338      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
339      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
340    
341    checkpoint59j
342    o in pkgs: dic, obcs, offline, rbcs:
343      standard way to compute coeff. for time interpolation between 2 time reccords
344      which retains full precision (& make results less dependent on compiler).
345      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
346    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
347      packages instead of reading ice cover and wind speed separately
348    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
349     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
350      to allow to compile customized code before the update)
351    o cleaning-up:
352      - fix CPP instruction syntax in pkg/obcs
353      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
354        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
355      - fix some threads issue in IO parts.
356    o pkg/dic:
357      - add tons of "_d 0" (--> much better testreports !)
358       and then update outputs of tutorial_global_oce_biogeo
359    o pkg/mom_fluxform:
360      add a special version of momentum advection intended to conserve momentum
361      next to a bathymetry step or a coastline edge. (default = off = #undef)
362    o new read/write pickup version:
363      - for now, only implemented for main (mdsio) pickup file.
364      - write out only what is needed to restart; merge pickup_nh , pickup_ph
365        and main pickup together.
366      - read meta file; read only what is needed to restart; stop if a field
367        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
368        if it make sense (even if the restart is not perfect).
369      - if no meta file, assume that pickup to read corresponds exactly to
370        a pickup that would currently be written.
371      - read pickup written in the old format (until checkpoint59i) if it
372        recognizes an old meta file (no field-list).
373      - add a meta file in exp. which starts from a pickup: 2 cases:
374        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
375         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
376        b) a meta file describing the content of the associated pickup file
377         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
378    o pkg/mdsio & pkg/rw:
379      - new routine to read a meta file ; new set of routine to read
380        Multiple-fields file (with meta file).
381    o added open boundary conditions capability for seaice
382        HSNOW, HSALT, UICE, and VICE
383    
384    checkpoint59i
385    o adjoint:
386      * fix multiDimAdvection adjoint
387        (partial recomputation problem by TAF for fVerT(:,:,kDown)
388        and comlev1 size definition (maxpass vs. max. number of tracers)
389      * verification/global_ocean.90x45x15 adjoint now tests
390        NLFS and multiDimAdvection using DST3 (=30)
391      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
392    o pkg/kpp: add "_d 0" to real constant (if missing);
393      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
394      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
395    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
396      for internal parameters related to restart process (formerly from PARAMS.h)
397      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
398    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
399      as argument. (only atm2d & obcs write_pickup have not yet been updated)
400    o pkg/monitor:
401      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
402      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
403      - account for deep Atmosphere factor and density factor (anelastic)
404    o added open boundary conditions capability for seaice HEFF and AREA
405    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
406      thermodynamics
407      - requires a little reorganization, which affects the testreport results
408        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
409        so that now the conservative form is tested
410      - add a few comments
411    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
412    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
413    o add new diagnostics to seaice: advective, diffusive fluxes (only for
414      multidim-advection, for scheme 2 they are not filled) and transports,
415      thermodynamic growth rates
416    o change units of EmPmR (inside the code, + within coupling interface)
417      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
418      Affects results @ truncation level (cg2d match) and update output of
419       experiments: lab_sea(6), global_ocean.90x40x15(10),
420      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
421      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
422      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
423      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
424    
425    checkpoint59h
426    o pkg/exf:
427      - improve vectorization by moving if-statement out of loops in
428        exf_mapfields, exf_radiation
429      - exf_bulkformulae.F: introduce 2D fields and vectorize code
430    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
431    o testreport:
432      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
433        monitor & update offline_exf_seaice exp. output.
434      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
435    o pkg/seaice:
436      - bug fix in the evp solver: boundary conditions were affected be
437        masking of zMax/zMin (changes results)
438      - minor bug fix in boundary conditions in seaice_calc_strainrates
439        (changes results for no_slip)
440      - seaice_lsr.F: make interpolation of eta dependent on boundaries
441      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
442      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
443        stress formulation and no-slip boundary conditions
444    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
445      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
446    o pkg/seaice: a first HSALT time stepping equation has been checked in
447    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
448      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
449      without requiring DO-IF statements
450    o pkg/thsice:
451      use continuous power-law function for partition of energy between lateral
452      melting/freezing and thinning/thickening ; old code using step function
453      still available with #undef THSICE_FRACEN_POWERLAW
454      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
455    o testreport: change AD testing : check against results/output_adm.txt
456      using same scripts as for forward test.
457    
458    checkpoint59g
459    o adjoint testing: in preparation for changing testreport:
460      - output format: cost and grad written on separated lines
461      - ad output results in directory "results" (instead of "results_ad")
462    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
463    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
464    o pkg/ecco: allow user defined cost function contributions
465    o testreport:
466      Allow to choose (per experiment) the list of tested output variables
467       and the main variable (used to issue a pass/FAIL ) ;
468      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
469      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
470      Also modify printing of summary:
471       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
472       b) echo the list of tested variables in the individual summary.txt of
473          each experiment.
474    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
475      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
476      (but still depend on the tile decompostion of the domain).
477    o pkg/seaice: change a discretization detail to make the B-grid code
478      "more symmetric". This change is likely to remove all "ridges/leads" that
479      where quasi-aligned with the grid in B-grid solutions. It may also be
480      the solution to the stress coupling issues with the B-grid.
481    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
482      remove .cvsignore from input dir. (since testreport no longer run here).
483    o pkg/thsice:
484     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
485     - fix reshaping of sea-ice just after advection:
486       melt all the ice only if ice-volume is too small.
487     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
488       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
489     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
490    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
491      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
492    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
493      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
494      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
495      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
496      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
497      -> update output.txt
498    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
499     this affects truncation error: -> update output.txt of exp:
500      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
501      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
502    
503    checkpoint59f
504    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
505    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
506      a bounded range (in forward mode)
507    o pkg/ecco, ctrl, autodiff and mom_common:
508     internal parameter controls, completements of implementations
509    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
510    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
511      (not seem any difference in testing results).
512    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
513       at face corners.
514    o pkg/generic_advdiff:
515     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
516      loop range indices for computing vertical advection tendency
517      and do the calculation in the interior only (no overlap) ;
518      for now, only implemented for SOM advection (to save CPU time).
519     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
520    o exch2 adjoint
521      First set of changes:
522      - add exch2 hand-written adjoint templates
523      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
524        This will require cleanup in pkg/autodiff/*.F
525        (changed routines currently kept separate in verif. code/)
526      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
527        that used to hide exch2 or cubed-sphere specific code
528        (commented via 'cph-exch2')
529    o pkg/seaice
530      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
531    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
532       output of global_ocean.cs32x15.thsice .
533    
534    checkpoint59e
535    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
536      for B-grid vector (not yet tested) and C-grid vector (<- only used
537      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
538    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
539      (#ifdef ALLOW_SALT_PLUME)
540    o gather_2d/scatter_2d: removed halo regions
541    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
542      scheme and the corresponding test case (under front_relax dir). For now,
543      only available with Skew-flux form and not yet tested in realistic set-up.
544      adjoint: store directives updated, but gradient checks deteriorated,
545      so maybe GM/Redi adjoint is now broken.
546    o seaice adjoint
547      * add AREA, HEFF, HSNOW as control variable
548        (should not change lab_sea results)
549      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
550    o pkg/seaice:
551      * added computation of saltFlux in seaice_growth;
552        For time being, sea ice salinity is assumed constant
553        contribution of snow flooding to freshening of sea ice is neglected.
554        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
555        defaults to 0.0 in order to maintain backward compatibility.
556        Typical values for SEAICE_salinity are 4 to 10 g/kg.
557      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
558      * added SEAICE_availHeatFrac, which specifies fraction of surface level
559        heat content used to melt or grow ice
560      * commented out cap of HICE: it helps keep ice thinner
561      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
562      * applied OBCS T/S mask to HEFFM sea ice mask
563    
564    checkpoint59d
565    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
566     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
567     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
568    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
569     and change default value of parameter "GM_Small_Number";
570     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
571       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
572       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
573    o pkg/ecco: cost function when applying pkg/smooth to controls
574    o pkg/ctrl: add forcingPrecond run time parameter
575    o pkg/seaice:
576     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
577     - fix bug in metric terms of u-equation in LSR solver (implicit part),
578       changes verification/lab_sea
579     - rearrange implicit part of u-equation in LSR solver to make it easier to
580       read, understand, and debug. This causes changes at the truncation level.
581     - fix (serious) bug in the boundary conditions (sign error in the implicit
582       part) of the LSR solver. Changes all LSR results.
583     - fixed problem with HSNOW initialization to avoid thick snow when AREA
584       is initilized with small values - does not change lab_sea results.
585     - added HsnowFile initialization capability
586    o pkg/smooth: addition to model/src and pkg/ctrl so allow
587     initialization of pkg/smooth and application to control vector
588    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
589    o dependencies: pkg/profiles requires pkg/cal
590    o pkg/profiles:
591     - added option ALLOW_PROFILES_GENERICGRID
592         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
593         that interpolation information (grid points and coefficients) is provided
594         within the netcdf input files.
595         -> sample matlab scripts can be found in MITgcm_contrib/gael
596         that allow you to prepare netcdf input files.
597     - also modified: cleaner include statements, cleaner error print statements,
598       cleaner stops when error, and more tests of the netcdf input files consistency.
599    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
600    o pkg/seaice:
601     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
602       requires a new routine: seaice_diagnostics_fill.F
603     - make sure that seaice does not move if not forced (pressure replacement
604       method, Hibler and Ip, 1995), changes results
605     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
606     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
607       It is turned off by default (=-1.), because it changes the results.
608     - make it possible to read AREA from a file, too.
609    
610    checkpoint59c
611    o add S/R and diagnostics for oceanic mixed-layer depth
612    o move GMRedi call after all vertical mixing schemes (including KPP)
613    o pkg/thsice:
614     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
615      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
616    o pkg/obcs:
617     - bug fix for balance code
618    o pkg/seaice:
619      - allow values of SEAICE_elasticParm > 1
620      - add new parameter SEAICE_evpTauRelax as an alternative
621        to SEAICE_elasticParm
622      - make lsr boundary conditions free slip (by default), changes result
623      - add code for no slip boundary conditions for lsr
624      - set minimum of zeta to zero (and not 4e8) (changes results)
625      - add a cap on AREA after advecting AREA if seaice_growth is not called
626    o change calculation of Visbeck K:
627      - no longer depend on tapering scheme; instead, compute slope (limited
628        by GM_maxSlope). this is equivalent to what was comuted before with
629        clipping or linear tappering.
630      - fix vertical averaging (wrong by 1/2 level)
631      - leave the old version (but will not be maintained) within
632        #ifdef OLD_VISBECK_CALC / #endif
633      - update output of exp. ideal_2D_oce
634    o change error catch in calc_r_star to improve vectorization
635    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
636      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
637    o adjoint:
638      Re-organized adjoint checkpointing according to Matt Mazloff
639      (but with modifs/completions/cleanups)
640      Storing is now bundled into large arrays to optimized I/O
641      (and second step in cleanup of the_main_loop)
642    
643    checkpoint59b
644    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
645      - export/import (between ocean & coupler) fields needed for ocean DIC.
646    o pkg/seaice:
647      - get rid of three more exchanges seaice_calc_viscosities (required
648        different loop boundaries in seaice_lsr and seaice_ocean_stress)
649      - bug fix in seaice_ocean_stress (update of lab_sea required)
650      - reduce loop boundaries to necessary minimum also in seaice_evp
651      - go back to the old way of computing deltaC/Z as the adjoint likes that
652        better
653    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
654      passive tracer to an Age Tracer) + update output.txt
655    o pkg/exf:
656      - implement A-grid / C-grid selection for wind-stress input files.
657      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
658      for now, in exf_bulk_largeyeager04.F only :
659      - change implementation for case where windspeed + 2. components wind-stress
660        are read-in. AND use rhoConstFresh to convert evap.
661    o pkg/seaice:
662      - use correct EXCH_UV for wind-forcing (on A-grid).
663      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
664        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
665    o pkg/exf:
666      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
667      EXF_INTERPOLATION:
668      - merge global_with_exf/code version of exf_interp_read.F
669        to the main code ;
670      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
671        reading the file ; Important: This options needs to be defined to recover
672        previous code.
673        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
674      - no longer loose real*8 precision along the way when using exf_iprec=64.
675    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
676      - change discretisation of evp-solver in order to avoid another exchange
677        (changes lab_sea) and clean up a little
678      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
679        help the adjoint (this also changes the results slightly)
680      - add a few "_d 0" where they had been missing in seaice_evp.F
681      - cleaning up: remove unused seaice_calc_rhs.F
682    o pkg/exf: some cleaning-up:
683      - change various "constants" into runtime parameters
684      - cleaned-up Large&Yeager04 routine which should eventually
685        replace exf_bulkformulae.F (changed names of S/R and CPP)
686        and merged various ALLOW_ATM_WIND options
687     only used with thsice pkg (in thsice_get_exf.F):
688      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
689        which are used when useStabilityFct_overIce=TRUE (= the default)
690      - change default values of ice & snow emissivity and scale downward LW
691        by ice & snow emissivity.
692    o pkg/thsice:
693     fix few little problems, in thsice_calc_thickn.F:
694      - growth vertically (and not laterally) if iceFrac == iceMaskMax
695      - melt only laterally if hIce < hThinIce (as the comments say)
696      and in thsice_extend.F:
697      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
698      - start to form ice as soon as the minimum ice-volume is reachable.
699     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
700      and cpl_aim+ocn
701    o pkg/kpp
702     - move computation of surface related input fields to KPP into a new
703       subroutine kpp_forcing_surf.F
704     - remove wrong (within bi,bj loops) EXCH calls.
705     - little cleaning (add argument myThid in last position, cvs header ...)
706     - for now, fix conservation problem by exchanging KPPviscAz (may not
707       be the best fix)
708    o pkg/seaice
709     - check for inconsistent evp parameter/cpp-flag combination
710     - remove leftover errIO flat for obsolete name list error handling
711    o OpenAD
712     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
713    
714    checkpoint59a
715    o pkg/seaice: some parameter clarifications and a little bit of clean up
716    o pkg/thsice: rename run-time parameters:
717       himin       -> hIceMin
718       himin0      -> hThinIce
719       hihig       -> hThickIce
720       i0          -> i0swFrac
721       transCoef   -> bMeltCoef
722       frac_energy -> fracMelting
723      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
724       with default values (for now) that do not change the results.
725      remove old version of thsice vars advection in pkg/seaice.
726    o in FFIELDS.h:
727      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
728      - make pLoad & sIceLoad always available (but still only used if
729         ATMOSPHERIC_LOADING is #define).
730    o pkg/kpp: replaced _KPP_RL with _RL
731    o bug fixes for vertical diffusivity computations when both KPP and
732        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
733        are no longer updating the vertical diffusivity array
734        (passed as argument) but are (re-) setting those arrays.
735  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
736    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
737      cgrid-lsr and evp solver      cgrid-lsr and evp solver
# Line 15  o pkg/seaice: fix bug in evp solver, whi Line 743  o pkg/seaice: fix bug in evp solver, whi
743    - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp    - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
744      (to force the user to pick a time step since there is not "safe" way      (to force the user to pick a time step since there is not "safe" way
745      of choosing it)      of choosing it)
746      - add principal stress diagnostics
747      - rearrange fields for evp a little to avoid having to call a: too many
748        exchanges and b: exchanges for stress trensor components which we do
749        not have.
750      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
751        of evp, complete rewrite for lsr case (latter is does not yet work
752        in all cases)
753  o pkg/kpp: add code to have mixing in shelf ice caverns  o pkg/kpp: add code to have mixing in shelf ice caverns
754      - add myThid to all kpp routines (long overdue)
755    
756  checkpoint59  checkpoint59
757  o pkg/exf:  o pkg/exf:
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