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revision 1.740 by heimbach, Fri Oct 27 05:19:42 2006 UTC revision 1.1019 by jmc, Sat Aug 30 16:37:48 2008 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint61c
8    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
9      to add mass source/sink of fluid in the interior (3-D generalisation
10      of oceanic real-fresh water flux).
11    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
12    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
13    o new pkg: down_slope
14      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
15      - presently, modify T & S inland (dwnslp_calc_rho.F).
16        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
17      - implementation for ocean in P-coords not tested.
18      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
19    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
20      (to facilitate conversion of oceanic pkg to p-coordinate).
21    o change FIND_RHO to FIND_RHO_2D :
22      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
23    o new pkg: cheapaml
24    
25    checkpoint61b
26    o exch2:
27      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
28      - no longer depend on the order sequence (N,S,E,W).
29      - 3rd exchange no longer needed (tested with 24 tiles).
30      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
31      - exch_UV_A-grid readily available (but not yet tested).
32      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
33      (both are no longer needed) in exch_uv: no effect in forward run; but
34       get truncation error differences with adjoint exch.
35    o exch2:
36     - change index-bounds storage (moved from target to local tile,
37       more intuitive this way) ; rename/remove some variables.
38     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
39    
40    checkpoint61a
41    o exch2/matlab-topology-generator:
42      fix bug in index bounds for N-S internal exchange (hard to tell if this
43      had any effect on the solution).
44    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
45      is exceeded
46    o testreport: modify syntax of awk, so that it works also with
47      awk, and not only with nawk and gawk
48    
49    checkpoint61
50    o autodiff
51      Change default for TAF usage by removing argument '-nonew_arg'
52      This changes TAF subroutine argument list (ordering of active var.)
53      Omission of this flag leads to incompatibility w.r.t. TAMC
54      To restore TAMC-compatibility, need following modifs:
55      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
56      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
57      Tested TAF version is 1.9.22
58      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
59    
60    checkpoint60
61    --->>> This is the last checkpoint for which generating the adjoint
62    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
63    --->>> by default.
64    --->>> Future checkpoints will ommit this flag by default.
65    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
66    o pkg/grdchk: Add gradient check to etan0 perturbations.
67    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
68    o pkg/autodiff: more flexibility in zeroadj.
69      model/src: modifying do_oceanic_phys.F accordingly.
70    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
71    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
72      special setup of gmredi for which the adjoint is stable
73      enough for parameter optimization.
74    o bridging the gap between eddy stress and GM.
75      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
76          along with a change in CPP option (now ALLOW_EDDYPSI).
77      -> when using GM w/ GM_AdvForm:
78          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
79          is applied either in the tracer Eq. or in momentum Eq.
80          depending on data.gmredi (intro. GM_InMomAsStress).
81      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
82      The key modifications are in model/src/taueddy_external_forcing.F
83      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
84    
85    checkpoint59r
86    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
87      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
88      fix option to read coriolis(@ cell-corner) from files with CS-grid.
89    o pkg/mnc: add some attributes to standard 1D-coordinate variables
90    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
91      mass points, when using mnc for output
92      - add runtime parameter (missing_value, missing_value_int) to override
93        default (which is the value of getcon('UNDEF'))
94    o pkg/mnc: prepare mnc for the actual use of missing values with the
95      diagnostics package: small fix in mnc_cw_readwrite.template and more
96      initialisation of never used fields
97      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
98      versions
99    o pkg/thsice/thsice_ini_vars.F added default initial values so that
100      thermodynamics sea ice solver does not blow up when some initial fields
101      are missing.
102    o move from external_forcing_surf.F to ini_forcing.F
103      the p-coord. hack consisting in using pLoad to set phi0surf ;
104      update output of tutorial_global_oce_in_p (affected @ truncation level).
105    o Freshen up a bit hs94.1x64x5, notably:
106      remove rotationPeriod and tRef=5*0. (adjoint only), and add
107      exactConserv=.TRUE.
108    o pkg/generic_advdiff:
109      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
110      applies to files where Temperature & Salinity 2nd Order moments are used.
111    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
112      this uses a dynamically allocated internal state data structure
113      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
114      and requires a fortran 90 compiler
115    
116    checkpoint59q
117    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
118       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
119    o Refresh tutorial_global_oce_biogeo, notably:
120      - change bathymetry (put back seamounts in ACC, use hFacs)
121      - change EOS (POLY3 --> JMD95Z)
122      - use Bryan-Lewis vertical diffusivity
123      - use multidimensional advection
124      - remove old virtual virtual in dic pkg, now done through ptracer pkg
125      - change a couple of parameters in dic pkg
126    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
127    o pkg/obcs: change default to OBCSfixTopo = .true.,
128      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
129      - replace "debugMode" with "debugLevel .GE. debLevB"
130    o implementation of TAF directives for gchem,cfc,dic
131    o remove "exp5" (replaced by tutorial_deep_convection).
132    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
133      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
134      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
135      --> changes results in exp4, seaice_obcs
136    o tutorial_deep_convection :
137      update the set-up and increase resolution and domain size ; start
138      from pseudo initial conditions = output at t=120mn in order to see
139      something happening when running testreport.
140    o pkg/seaice: add os7mp as an advection scheme
141                  add check for advection schemes
142                  add a flag for restoring T and S underneath sea ice
143    o pkg/my82: add netcdf-support and diagnostics
144    o thsice pkg:
145      - Now hsMax limits snow height by turning it into ice following
146        flooding scheme (and now conserving energy)
147      - Slight rewriting of the formula in thsice_calc_thick.F
148      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
149      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
150    
151    checkpoint59p
152    o gchem / dic / cfc :
153      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
154      - add new parameter files: "data.dic" & "data.cfc" ;
155      - various re-arrangement in initialisation & header file ;
156      - fix tutorial_global_oce_biogeo for multi-threaded test.
157    o pkg/dic: test for "pickup_dic" file when restarting ;
158      if no pickup-file, can restart with a re-initialised pH (same as it did
159      before) providing pickupStrictlyMatch is set to False.
160    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
161      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
162    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
163      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
164    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
165     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
166       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
167    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
168       scheme to use for vorticty-term ;
169     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
170       (with default selectVortScheme, return to original discretisation)
171     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
172    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
173    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
174      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
175      also fix diagnostics VISCAHW & VISCA4W.
176    
177    checkpoint59o
178    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
179    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
180      move a few statemens out the main loop into separate loops
181    o pkg/shelfice:
182      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
183        (kg/m^2/s), does not break tests, because in verification/isomip,
184        rhoConstFresh=rhoConst (by accident)
185      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
186      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
187        new file model/src/seawater.F, so that they are available for all pkgs.
188      - convert potential temperature into in-situ temperature. This changes the
189        isomip tests => update tests
190    o add a flag writePickupAtEnd (default=true) to be able to suppress
191      writing a pickup at the last timestep
192    o tools/mpack-1.6 :
193      - disable automake (not working) and autoconf (not needed).
194      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
195        also cleaner with much less compilation warnings.
196    o pkg/profiles:
197      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
198      (for "less than 32 characters name" compiler requirement)
199    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
200      conditions that have a different sampling frequency than S/T/U/V obcs
201    o pkg/diagnostics (stats-diags):
202      - fix global Min/Max in case 1 processor get only empty tiles
203    o genmake2: replace (4 times)
204         make genmake_tc_1.o >> genmake_warnings 2>&1
205      with
206         COMM="$CC $CFLAGS -c genmake_tc_1.c"
207         echo $COMM >> genmake_warnings
208         $COMM >> genmake_warnings 2>&1
209      to make genmake2 always see the value of CC as specified in the optfile.
210    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
211      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
212      - modify verification advect_cs test to test SOM-advection on CS-grid.
213    o pkg/ctrl:
214      - Rewrite of ctrl_map_ini_ecco.F,
215        introducing a generic routine (ctrl_map_ini_gen.F).
216      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
217    
218    checkpoint59n
219    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
220      number in dedicate array "hdiag":
221      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
222        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
223      - many small changes (integer format) for large number of diagnostics
224      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
225        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
226    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
227      usingSphericalGrid, this allows to define the rotated grid coordinates
228      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
229      geographical coordinates according to the inverse of the rotation defined
230      by the Euler angles, so that Coriolis parameter and online-interpolation by
231      exf works with the geographical coordinates on XC/YC/XG/YG.
232      Naturally, this feature does not work with all packages, so some
233      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
234      profiles), because there the coordinates are assumed to be regular
235      spherical grid coordinates.
236    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
237      - introduce isopycnal diffusion coefficient control.
238    o tools/adjoint_options:
239      - additional control vector components.
240    o pkg/mnc: have mnc create marginally meaning full coordinate variables
241      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
242    o pkg/mypackage:
243      - add example of read/write pickup for state-var ;
244      - add entry points to the main code for state-vars diags & write-pickup.
245    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
246      transitions for useExfYearlyFields
247      - add new subroutine that determines the file to read from for
248        use*YearlyFields = .TRUE. and .FALSE.
249      - add a verification experiment to global_with_exf that tests
250        useExfYearlyFields with USE_EXF_INTERPOLATION defined
251    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
252      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
253      subroutines (which could be generated from a template, because they are
254      almost identical), for now they are included in obcs_prescribe_read.F for
255      simplicity
256    o pkg/exf:
257      - add a little more diagnostic to exf_interp_read (in analogy to
258        mds_read_field, can be turned off with debugLevel < debugLevA=1)
259      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
260        ugly but fast by unrolling short inner loops, inserting a unroll=8
261        directive in routine lagran, and splitting a loop and making do while the
262        outermost loop (the latter requires the intoduction of index arrays)
263    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
264    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
265      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
266    o verification/seaice_obcs: updated for restart test and latest options
267    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
268      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
269      for now this is only available for the C-grid code and also within
270      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
271    
272    checkpoint59m
273    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
274      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
275    o gad_som : fix flux output (& diagnostics) to have same units as other  
276      advection scheme fluxes (was previously multiplied by deltaT).  
277    o added verification/seaice_obcs both to test seaice open boundaries
278      and to provide an example matlab scrpt for generating them
279    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
280    o pkg/salt_plume: clean up salt_plume_frac.F to
281      remove redundancy in PlumeMethod 1 and 4
282    o pkg/kpp: added saltplume diagnostics
283    o pkg/obcs and pkg/seaice:
284      - do not set uice and vice to zero when OB*icefile are unspecified
285      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
286      - moved seaice tracer obcs after call to seaice_growth
287    o pkg/salt_plume: added various options for salt plume depth
288      criterion and for vertical distribution of the salt
289    
290    checkpoint59l
291    o pkg/ptracers: new version of ptracers pickup:
292      read meta file and write only fields which are needed to restart.
293      ( same logic as main pickup file ; also using pickupStrictlyMatch )
294    o pkg/seaice:
295      - add timescale for melting due to warm mixed layer as a means of
296        setting SEAICE_availHeatFrac more conveniently
297      - add a CPP-flag/runtime parameter check for flooding algorithm
298      - reformulated availHeat in seaice_growth.F to be independent of AREA
299    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
300      unit changes
301    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
302    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
303      SX vector computer.
304    o pkg/seaice:
305      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
306        seaice forcing fields can now be read only through pkg/exf
307      - removed some unused halos
308    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
309    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
310      or U/VICE from U/VWIND before computing U/VSTRESS
311    
312    checkpoint59k
313    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
314      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
315    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
316      all experiments pass when compile with un-initialised var. checking option.
317    o added pkg/salt_plume
318    o script to test restart (for now, in MITgcm_contrib/jmc_script)
319    o pkg/seaice: new read/write pickup version.
320      read meta file and write only fields which are needed to restart.
321      ( same logic as main pickup file ; also using pickupStrictlyMatch )
322    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
323    o lab_sea.hb87: modify the domain & update output.hb87.txt :
324      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
325      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
326      process. Fixed here by closing the domain at the Northern boundary.
327    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
328    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
329      a set of consecutive levels in/from a 3-D array.
330    o pkg/ptracers:
331      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
332      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
333    
334    checkpoint59j
335    o in pkgs: dic, obcs, offline, rbcs:
336      standard way to compute coeff. for time interpolation between 2 time reccords
337      which retains full precision (& make results less dependent on compiler).
338      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
339    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
340      packages instead of reading ice cover and wind speed separately
341    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
342     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
343      to allow to compile customized code before the update)
344    o cleaning-up:
345      - fix CPP instruction syntax in pkg/obcs
346      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
347        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
348      - fix some threads issue in IO parts.
349    o pkg/dic:
350      - add tons of "_d 0" (--> much better testreports !)
351       and then update outputs of tutorial_global_oce_biogeo
352    o pkg/mom_fluxform:
353      add a special version of momentum advection intended to conserve momentum
354      next to a bathymetry step or a coastline edge. (default = off = #undef)
355    o new read/write pickup version:
356      - for now, only implemented for main (mdsio) pickup file.
357      - write out only what is needed to restart; merge pickup_nh , pickup_ph
358        and main pickup together.
359      - read meta file; read only what is needed to restart; stop if a field
360        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
361        if it make sense (even if the restart is not perfect).
362      - if no meta file, assume that pickup to read corresponds exactly to
363        a pickup that would currently be written.
364      - read pickup written in the old format (until checkpoint59i) if it
365        recognizes an old meta file (no field-list).
366      - add a meta file in exp. which starts from a pickup: 2 cases:
367        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
368         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
369        b) a meta file describing the content of the associated pickup file
370         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
371    o pkg/mdsio & pkg/rw:
372      - new routine to read a meta file ; new set of routine to read
373        Multiple-fields file (with meta file).
374    o added open boundary conditions capability for seaice
375        HSNOW, HSALT, UICE, and VICE
376    
377    checkpoint59i
378    o adjoint:
379      * fix multiDimAdvection adjoint
380        (partial recomputation problem by TAF for fVerT(:,:,kDown)
381        and comlev1 size definition (maxpass vs. max. number of tracers)
382      * verification/global_ocean.90x45x15 adjoint now tests
383        NLFS and multiDimAdvection using DST3 (=30)
384      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
385    o pkg/kpp: add "_d 0" to real constant (if missing);
386      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
387      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
388    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
389      for internal parameters related to restart process (formerly from PARAMS.h)
390      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
391    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
392      as argument. (only atm2d & obcs write_pickup have not yet been updated)
393    o pkg/monitor:
394      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
395      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
396      - account for deep Atmosphere factor and density factor (anelastic)
397    o added open boundary conditions capability for seaice HEFF and AREA
398    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
399      thermodynamics
400      - requires a little reorganization, which affects the testreport results
401        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
402        so that now the conservative form is tested
403      - add a few comments
404    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
405    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
406    o add new diagnostics to seaice: advective, diffusive fluxes (only for
407      multidim-advection, for scheme 2 they are not filled) and transports,
408      thermodynamic growth rates
409    o change units of EmPmR (inside the code, + within coupling interface)
410      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
411      Affects results @ truncation level (cg2d match) and update output of
412       experiments: lab_sea(6), global_ocean.90x40x15(10),
413      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
414      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
415      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
416      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
417    
418    checkpoint59h
419    o pkg/exf:
420      - improve vectorization by moving if-statement out of loops in
421        exf_mapfields, exf_radiation
422      - exf_bulkformulae.F: introduce 2D fields and vectorize code
423    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
424    o testreport:
425      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
426        monitor & update offline_exf_seaice exp. output.
427      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
428    o pkg/seaice:
429      - bug fix in the evp solver: boundary conditions were affected be
430        masking of zMax/zMin (changes results)
431      - minor bug fix in boundary conditions in seaice_calc_strainrates
432        (changes results for no_slip)
433      - seaice_lsr.F: make interpolation of eta dependent on boundaries
434      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
435      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
436        stress formulation and no-slip boundary conditions
437    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
438      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
439    o pkg/seaice: a first HSALT time stepping equation has been checked in
440    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
441      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
442      without requiring DO-IF statements
443    o pkg/thsice:
444      use continuous power-law function for partition of energy between lateral
445      melting/freezing and thinning/thickening ; old code using step function
446      still available with #undef THSICE_FRACEN_POWERLAW
447      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
448    o testreport: change AD testing : check against results/output_adm.txt
449      using same scripts as for forward test.
450    
451    checkpoint59g
452    o adjoint testing: in preparation for changing testreport:
453      - output format: cost and grad written on separated lines
454      - ad output results in directory "results" (instead of "results_ad")
455    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
456    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
457    o pkg/ecco: allow user defined cost function contributions
458    o testreport:
459      Allow to choose (per experiment) the list of tested output variables
460       and the main variable (used to issue a pass/FAIL ) ;
461      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
462      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
463      Also modify printing of summary:
464       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
465       b) echo the list of tested variables in the individual summary.txt of
466          each experiment.
467    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
468      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
469      (but still depend on the tile decompostion of the domain).
470    o pkg/seaice: change a discretization detail to make the B-grid code
471      "more symmetric". This change is likely to remove all "ridges/leads" that
472      where quasi-aligned with the grid in B-grid solutions. It may also be
473      the solution to the stress coupling issues with the B-grid.
474    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
475      remove .cvsignore from input dir. (since testreport no longer run here).
476    o pkg/thsice:
477     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
478     - fix reshaping of sea-ice just after advection:
479       melt all the ice only if ice-volume is too small.
480     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
481       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
482     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
483    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
484      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
485    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
486      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
487      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
488      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
489      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
490      -> update output.txt
491    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
492     this affects truncation error: -> update output.txt of exp:
493      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
494      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
495    
496    checkpoint59f
497    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
498    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
499      a bounded range (in forward mode)
500    o pkg/ecco, ctrl, autodiff and mom_common:
501     internal parameter controls, completements of implementations
502    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
503    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
504      (not seem any difference in testing results).
505    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
506       at face corners.
507    o pkg/generic_advdiff:
508     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
509      loop range indices for computing vertical advection tendency
510      and do the calculation in the interior only (no overlap) ;
511      for now, only implemented for SOM advection (to save CPU time).
512     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
513    o exch2 adjoint
514      First set of changes:
515      - add exch2 hand-written adjoint templates
516      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
517        This will require cleanup in pkg/autodiff/*.F
518        (changed routines currently kept separate in verif. code/)
519      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
520        that used to hide exch2 or cubed-sphere specific code
521        (commented via 'cph-exch2')
522    o pkg/seaice
523      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
524    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
525       output of global_ocean.cs32x15.thsice .
526    
527    checkpoint59e
528    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
529      for B-grid vector (not yet tested) and C-grid vector (<- only used
530      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
531    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
532      (#ifdef ALLOW_SALT_PLUME)
533    o gather_2d/scatter_2d: removed halo regions
534    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
535      scheme and the corresponding test case (under front_relax dir). For now,
536      only available with Skew-flux form and not yet tested in realistic set-up.
537      adjoint: store directives updated, but gradient checks deteriorated,
538      so maybe GM/Redi adjoint is now broken.
539    o seaice adjoint
540      * add AREA, HEFF, HSNOW as control variable
541        (should not change lab_sea results)
542      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
543    o pkg/seaice:
544      * added computation of saltFlux in seaice_growth;
545        For time being, sea ice salinity is assumed constant
546        contribution of snow flooding to freshening of sea ice is neglected.
547        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
548        defaults to 0.0 in order to maintain backward compatibility.
549        Typical values for SEAICE_salinity are 4 to 10 g/kg.
550      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
551      * added SEAICE_availHeatFrac, which specifies fraction of surface level
552        heat content used to melt or grow ice
553      * commented out cap of HICE: it helps keep ice thinner
554      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
555      * applied OBCS T/S mask to HEFFM sea ice mask
556    
557    checkpoint59d
558    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
559     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
560     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
561    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
562     and change default value of parameter "GM_Small_Number";
563     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
564       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
565       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
566    o pkg/ecco: cost function when applying pkg/smooth to controls
567    o pkg/ctrl: add forcingPrecond run time parameter
568    o pkg/seaice:
569     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
570     - fix bug in metric terms of u-equation in LSR solver (implicit part),
571       changes verification/lab_sea
572     - rearrange implicit part of u-equation in LSR solver to make it easier to
573       read, understand, and debug. This causes changes at the truncation level.
574     - fix (serious) bug in the boundary conditions (sign error in the implicit
575       part) of the LSR solver. Changes all LSR results.
576     - fixed problem with HSNOW initialization to avoid thick snow when AREA
577       is initilized with small values - does not change lab_sea results.
578     - added HsnowFile initialization capability
579    o pkg/smooth: addition to model/src and pkg/ctrl so allow
580     initialization of pkg/smooth and application to control vector
581    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
582    o dependencies: pkg/profiles requires pkg/cal
583    o pkg/profiles:
584     - added option ALLOW_PROFILES_GENERICGRID
585         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
586         that interpolation information (grid points and coefficients) is provided
587         within the netcdf input files.
588         -> sample matlab scripts can be found in MITgcm_contrib/gael
589         that allow you to prepare netcdf input files.
590     - also modified: cleaner include statements, cleaner error print statements,
591       cleaner stops when error, and more tests of the netcdf input files consistency.
592    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
593    o pkg/seaice:
594     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
595       requires a new routine: seaice_diagnostics_fill.F
596     - make sure that seaice does not move if not forced (pressure replacement
597       method, Hibler and Ip, 1995), changes results
598     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
599     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
600       It is turned off by default (=-1.), because it changes the results.
601     - make it possible to read AREA from a file, too.
602    
603    checkpoint59c
604    o add S/R and diagnostics for oceanic mixed-layer depth
605    o move GMRedi call after all vertical mixing schemes (including KPP)
606    o pkg/thsice:
607     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
608      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
609    o pkg/obcs:
610     - bug fix for balance code
611    o pkg/seaice:
612      - allow values of SEAICE_elasticParm > 1
613      - add new parameter SEAICE_evpTauRelax as an alternative
614        to SEAICE_elasticParm
615      - make lsr boundary conditions free slip (by default), changes result
616      - add code for no slip boundary conditions for lsr
617      - set minimum of zeta to zero (and not 4e8) (changes results)
618      - add a cap on AREA after advecting AREA if seaice_growth is not called
619    o change calculation of Visbeck K:
620      - no longer depend on tapering scheme; instead, compute slope (limited
621        by GM_maxSlope). this is equivalent to what was comuted before with
622        clipping or linear tappering.
623      - fix vertical averaging (wrong by 1/2 level)
624      - leave the old version (but will not be maintained) within
625        #ifdef OLD_VISBECK_CALC / #endif
626      - update output of exp. ideal_2D_oce
627    o change error catch in calc_r_star to improve vectorization
628    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
629      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
630    o adjoint:
631      Re-organized adjoint checkpointing according to Matt Mazloff
632      (but with modifs/completions/cleanups)
633      Storing is now bundled into large arrays to optimized I/O
634      (and second step in cleanup of the_main_loop)
635    
636    checkpoint59b
637    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
638      - export/import (between ocean & coupler) fields needed for ocean DIC.
639    o pkg/seaice:
640      - get rid of three more exchanges seaice_calc_viscosities (required
641        different loop boundaries in seaice_lsr and seaice_ocean_stress)
642      - bug fix in seaice_ocean_stress (update of lab_sea required)
643      - reduce loop boundaries to necessary minimum also in seaice_evp
644      - go back to the old way of computing deltaC/Z as the adjoint likes that
645        better
646    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
647      passive tracer to an Age Tracer) + update output.txt
648    o pkg/exf:
649      - implement A-grid / C-grid selection for wind-stress input files.
650      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
651      for now, in exf_bulk_largeyeager04.F only :
652      - change implementation for case where windspeed + 2. components wind-stress
653        are read-in. AND use rhoConstFresh to convert evap.
654    o pkg/seaice:
655      - use correct EXCH_UV for wind-forcing (on A-grid).
656      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
657        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
658    o pkg/exf:
659      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
660      EXF_INTERPOLATION:
661      - merge global_with_exf/code version of exf_interp_read.F
662        to the main code ;
663      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
664        reading the file ; Important: This options needs to be defined to recover
665        previous code.
666        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
667      - no longer loose real*8 precision along the way when using exf_iprec=64.
668    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
669      - change discretisation of evp-solver in order to avoid another exchange
670        (changes lab_sea) and clean up a little
671      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
672        help the adjoint (this also changes the results slightly)
673      - add a few "_d 0" where they had been missing in seaice_evp.F
674      - cleaning up: remove unused seaice_calc_rhs.F
675    o pkg/exf: some cleaning-up:
676      - change various "constants" into runtime parameters
677      - cleaned-up Large&Yeager04 routine which should eventually
678        replace exf_bulkformulae.F (changed names of S/R and CPP)
679        and merged various ALLOW_ATM_WIND options
680     only used with thsice pkg (in thsice_get_exf.F):
681      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
682        which are used when useStabilityFct_overIce=TRUE (= the default)
683      - change default values of ice & snow emissivity and scale downward LW
684        by ice & snow emissivity.
685    o pkg/thsice:
686     fix few little problems, in thsice_calc_thickn.F:
687      - growth vertically (and not laterally) if iceFrac == iceMaskMax
688      - melt only laterally if hIce < hThinIce (as the comments say)
689      and in thsice_extend.F:
690      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
691      - start to form ice as soon as the minimum ice-volume is reachable.
692     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
693      and cpl_aim+ocn
694    o pkg/kpp
695     - move computation of surface related input fields to KPP into a new
696       subroutine kpp_forcing_surf.F
697     - remove wrong (within bi,bj loops) EXCH calls.
698     - little cleaning (add argument myThid in last position, cvs header ...)
699     - for now, fix conservation problem by exchanging KPPviscAz (may not
700       be the best fix)
701    o pkg/seaice
702     - check for inconsistent evp parameter/cpp-flag combination
703     - remove leftover errIO flat for obsolete name list error handling
704    o OpenAD
705     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
706    
707    checkpoint59a
708    o pkg/seaice: some parameter clarifications and a little bit of clean up
709    o pkg/thsice: rename run-time parameters:
710       himin       -> hIceMin
711       himin0      -> hThinIce
712       hihig       -> hThickIce
713       i0          -> i0swFrac
714       transCoef   -> bMeltCoef
715       frac_energy -> fracMelting
716      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
717       with default values (for now) that do not change the results.
718      remove old version of thsice vars advection in pkg/seaice.
719    o in FFIELDS.h:
720      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
721      - make pLoad & sIceLoad always available (but still only used if
722         ATMOSPHERIC_LOADING is #define).
723    o pkg/kpp: replaced _KPP_RL with _RL
724    o bug fixes for vertical diffusivity computations when both KPP and
725        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
726        are no longer updating the vertical diffusivity array
727        (passed as argument) but are (re-) setting those arrays.
728    o pkg/seaice: fix bug in evp solver, while doing that
729      - change (improve?) discretization of stress computations for both
730        cgrid-lsr and evp solver
731      - add a new routine to compute strain rates
732      - the above changes lab_sea results
733      - add no slip conditions for evp solver (off by default), lsr-version
734        may follow
735      - fix exchange for shear at Z-points (does not change lab_sea)
736      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
737        (to force the user to pick a time step since there is not "safe" way
738        of choosing it)
739      - add principal stress diagnostics
740      - rearrange fields for evp a little to avoid having to call a: too many
741        exchanges and b: exchanges for stress trensor components which we do
742        not have.
743      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
744        of evp, complete rewrite for lsr case (latter is does not yet work
745        in all cases)
746    o pkg/kpp: add code to have mixing in shelf ice caverns
747      - add myThid to all kpp routines (long overdue)
748    
749    checkpoint59
750    o pkg/exf:
751      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
752        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
753      - move exf header files from lower_case.h to UPPER_CASE.h ;
754        add missing cvs Header & Name
755      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
756      - add namelist param. selectStressGridPosition, exf_monFreq
757      - retire many _CLIM routines, and remove data.exf_clim
758        + params moved to data.exf
759        + climsst, climsss now handled by exf_set_gen, i.e.
760          climss?period=0 refers to constant field,
761          climss?period=-12 to monthly forcing
762      - split up namelists in data.exf
763    o pkg/seaice:
764      - remove seaice_exch and seaice_exch_uv
765      - remove superfluous exchange of theta
766      - add myThid to seaice_budget_ocean/ice
767      - add new interface for atmospheric wind forcing (C-grid only)
768        + new routine
769        + two new field (taux, tauy for stress over ice)
770        + removed one global field (DAIRN) for C-grid case only
771    o pkg/thsise
772      - 2nd set of modifs for thsice adjoint in conjunction with exf
773    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
774    
775    checkpoint58y_post
776    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
777      vertical diffusivity, similar to that in MOM4; turned on using
778      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
779      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
780    o Added capability for 3D specification of background vertical diffusion
781      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
782      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
783      "data" file that contains the 3D vertical diffusivity coefficients.
784    o ice dynamics (pkg/seaice) with thsice thermodynamics:
785      - add code within pkg thsice to advect & diffuse sea-ice fields
786      similar to (and will replace) what has been added in  seaice_advdiff.F,
787      but: - conserving Mass, Heat & Salt.
788           - better when using non-linear advection scheme (not yet fully tested)
789           - can also be used in atmospheric set-up (for now, only the diffusion).
790    
791    checkpoint58x_post
792    o IO option for global-file compact format:
793      - add options when generating topology (utils/exch2/matlab-topology-generator)
794      - add I/O capability (pkg/mdsio).
795      - adapt utils/matlab/rdmds.m to read this format.
796      for now long-line format not yet supported by pkg/mdsio (& exch2).
797    o shelfice: add a few diagnostics
798    
799    checkpoint58w_post
800    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
801      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
802      (and replace horiVertRatio in NH code).
803      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
804                         and tutorial_plume_on_slope (sensitive to truncation)
805    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
806      directly to drive seaice model (C-grid only)
807    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
808     - reintroduce computation of wind from stress,
809     - compute tau (in exf_bulkformulae.F) from windstress averaged to
810       mass points to avoid tau = 0
811     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
812    o rdmnc.m: make it work with "global" files created with gluemnc
813    o rdmnc.m : some improvements in dealing with singleton dimension
814      (tested on all testreport mnc output files).
815    o genmake2: disable pkg/profiles if netcdf test fails.
816    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
817    o move call to cal_readparms up to make calendar parameters/variable available
818      to all packages
819    
820    checkpoint58v_post
821    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
822      useDynP_inEos_Zc tested.
823    o pkg/exf: changes to properly interpolate/mask/scale initial fields
824    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
825      and portions thereof.  See read_cs.txt for description and examples.
826    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
827      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
828      following the great-circle arc between those 2 points.
829    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
830      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
831    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
832     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
833     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
834     - still needs work (not working with some options ; efficiency to improve)
835       and serious testing.
836     - use this scheme for temperature & salinity in 2 advection test exp.:
837       advect_xy & advect_xz, respectively.
838    
839    checkpoint58u_post
840    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
841    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
842    o testreport: add option "-skipdir" to skip some test.
843    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
844      momentum calculation.
845    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
846    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
847      remove checkpoint.F and the_correction_step.F (no longer used);
848      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
849    o add option (linFSConserveTr) to correct for tracer source/sink due to
850      Linear Free surface
851    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
852    o pkg/thsice: fix reading mnc-pickups
853    
854    checkpoint58t_post
855    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
856    o pkg/mdsio:
857     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
858       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
859       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
860     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
861     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
862       either MDS_READ_FIELD or MDS_WRITE_FIELD )
863     - new S/R (to replace MDSWRITEMETA), which allows to write more
864       informations (variable names, time ...) to meta files.
865     - modify rdmds.m to give back the meta file content.
866    o pkg/diagnostics: change vertical interpolation to be safer, and more
867       flexible (define p-levels to interpolate to in data.diagnostics);
868      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
869       diagnostic pointer.
870    o pkg/seaice: more cleaning up of seaice_growth, added many comments
871    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
872    o fix multi-category seaice:
873     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
874       SEAICE_MULTICATEGORY
875     - fix short wave heat flux
876    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
877       and allow to use EVP solver. Change forward lab_sea: test both EVP
878       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
879    o Initial check-in of lab_sea adjoint
880      (very similar to natl_box_adjoint/code_seaice)
881      * used C-grid and EVP solver
882      * used KPP, GM/Redi
883      * uses inAdExact=.TRUE.
884      * gradient checks fail for both ADM and TLM
885        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
886        f.d. gradients actually seem more problematic than ADM, TLM gradients;
887        issue is related to forward mismatch between g77 an ifort
888    o pkg/seaice: overhaul of thermodynamics
889     - growth.F and groatb.F are replaced by new routine seaice_growth.F
890     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
891     - move a few global fields out of SEAICE.h into seaice_growth.F and
892       make them 2D (FICE/QNETO/ ...)
893     - remove FO (it is the same as QNETO)
894     - introduce a few local fields to avoid modifying external fields such
895       as atemp, etc.
896    
897    checkpoint58s_post
898    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
899      changed exf_set_gen.F so that
900        genperiod=0 means input file is one time-constant field and
901        genperiod=-12 means input file contains 12 monthly means
902    o CG2D: use pre-computed solver main-diagonal (stored in common block);
903      this affects truncation error ; generate new output file for exp. which
904      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
905        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
906        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
907        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
908        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
909        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
910    o start implementation of deep-atmosphere and anelastic formulation
911    o verification: remove 2nd copy of input files and use script "prepare_run"
912      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
913    o mom_common/vecinv/fluxform: fix a few initialisation isssues
914    o profiles: fix for multithreaded case
915    
916    o diagnostics: rename few diags:
917      s/'PRESSURE'/'RCENTER '/g
918      s/'TICE    '/'oceFreez'/g
919      s/'TAUX    '/'oceTAUX '/g
920      s/'TAUY    '/'oceTAUY '/g
921      s/'SWFLUX  '/'oceQsw  '/g
922      s/DIFx/DFxE/g
923      s/DIFy/DFyE/g
924      and add few ocean-forcing diagnostics:
925      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
926    o modifications to pkg/seaice/growth.F and budget.F, which change results of
927      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
928      as actual snow thickness.  It now refers everywhere to effective snow
929      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
930    
931    checkpoint58r_post
932    o modifications to pkg/seaice/growth.F, which change results of
933      lab_sea experiment: fixes pertain to melting snow over open water, to
934      masking EVAP under sea ice, and to using the correct AREA variable for
935      computations of EVAP, PRECIP, HSNOW, and GHEFF
936    o add ability to read bathy, salt, and theta using MNC (off by def)
937    o add flooding algorithm and advection of HSNOW for pkg/seaice;
938      both are turned off by default and do no change any results
939    o seaice advection with pkg/thsice: a step toward the use of non-linear
940      advection scheme, but #ifdef or commented out for now (requires more EXCH).
941  o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens  o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
942    (identical results) and the standard version of EXTERNAL_FIELDS_LOAD    (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
943    in natl_box (affects results @ truncation level: update output.txt)    in natl_box (affects results @ truncation level: update output.txt)
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