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revision 1.766 by jmc, Tue Jan 16 19:45:13 2007 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  o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
832   - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)   - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
833   - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)   - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
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