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revision 1.918 by dimitri, Wed Dec 5 07:28:28 2007 UTC revision 1.1043 by jmc, Fri Nov 21 16:47:29 2008 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7  o pkg/seaice: removed SEAICE_FFIELDS.h and seaice_get_forcing.F  checkpoint61f
8    seaice forcing fields can now be read only through pkg/exf  o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
9      update results of global_ocean.cs32x15.icedyn test.
10    o move getcon.F from model/src to pkg/fizhi.
11    o pkg/exf: add parameter for extrapolation of temp up to the surface
12       and option to prevent negative evap (in bulk_largeyeager04 only).
13    o Prather Advection scheme: fix tracer conservation for divergent flow
14      (e.g., when using NonLin Free-Surface).
15    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
16    o gmredi (Visbeck-variable-K):
17     - add more parameters to Visbeck-variable-K.
18     - use a 5 points average for dSigmaR in Visbeck-K calculation
19       (more "homogenous": same stencil and same weights as in dSigmaH)
20     - update output of ideal_2D_oce experiment.
21    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
22      (#undef REAL4_IS_SLOW)
23     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
24       coordinate variable
25     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
26       (surface forcing fields), removes some of the functionality
27     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
28     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
29       probably not all: copy _RS surface flux fields to RL field before
30       calling DIAGNOSTICS_FILL
31     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
32       real*4 (CALL EXCH_*_RS) versions.
33     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
34       (generate new output).
35    
36    checkpoint61e
37    o gmredi (Visbeck-variable-K):
38      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
39      - change computation of Visbeck-K where Slope > Smax :        
40        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
41        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
42    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
43      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
44    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
45    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
46      does not become too large (to avoid precision problems in implicit-diffusion
47      solver); update ideal_2D_oce output.
48    o pkg ggl90:
49      - in ggl90_cal.F: compute only one set of visc/diff, used to
50        step forward TKE/T/S/momentum
51      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
52        have Prandlt =1)
53    o gmredi (fm07):
54      - add lower limit on Transition layer thickness + lower limit on 1/lambda
55      - allow to set few more params from data.gmredi
56    o pkg ggl90:
57          - add missing sqrt(2) factor in computation of mixing length
58            scale in ggl90_calc.F
59            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
60    
61    checkpoint61d
62    o adjoint modifs
63      - adapt to new field rhoInSitu
64      - allow to revert from StoreDynVars2D, StoreDynVars3D
65        to individual fields
66        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
67    o store 3-D (in-situ) density in commom block (DYNVARS.h)
68     - save 1 rho computation.
69     - no longer modify T & S inland when using down_slope pkg.
70    o gad_som : allow to switch to SOM advection for T & S without corresponding
71      pickup files (using new S/R: MDS_CHECK4FILE).
72    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
73      (for useSingleCpuIO to work in multi-threaded)
74    o pkg/shelfice:
75     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
76       with SHELFICEtopoFile in data.shelfice
77     - move code for reading ice shelf topography and modifying hFacC into separate
78       subroutines of the shelfice package
79     - separate initialisation of "fixed" and "variable" variables
80     - kTopC is not (yet) replaced by kSurfC, although this is possible
81    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
82    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
83      and rename:
84      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
85      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
86    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
87    
88    checkpoint61c
89    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
90      to add mass source/sink of fluid in the interior (3-D generalisation
91      of oceanic real-fresh water flux).
92    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
93    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
94    o new pkg: down_slope
95      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
96      - presently, modify T & S inland (dwnslp_calc_rho.F).
97        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
98      - implementation for ocean in P-coords not tested.
99      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
100    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
101      (to facilitate conversion of oceanic pkg to p-coordinate).
102    o change FIND_RHO to FIND_RHO_2D :
103      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
104    o new pkg: cheapaml
105    
106    checkpoint61b
107    o exch2:
108      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
109      - no longer depend on the order sequence (N,S,E,W).
110      - 3rd exchange no longer needed (tested with 24 tiles).
111      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
112      - exch_UV_A-grid readily available (but not yet tested).
113      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
114      (both are no longer needed) in exch_uv: no effect in forward run; but
115       get truncation error differences with adjoint exch.
116    o exch2:
117     - change index-bounds storage (moved from target to local tile,
118       more intuitive this way) ; rename/remove some variables.
119     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
120    
121    checkpoint61a
122    o exch2/matlab-topology-generator:
123      fix bug in index bounds for N-S internal exchange (hard to tell if this
124      had any effect on the solution).
125    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
126      is exceeded
127    o testreport: modify syntax of awk, so that it works also with
128      awk, and not only with nawk and gawk
129    
130    checkpoint61
131    o autodiff
132      Change default for TAF usage by removing argument '-nonew_arg'
133      This changes TAF subroutine argument list (ordering of active var.)
134      Omission of this flag leads to incompatibility w.r.t. TAMC
135      To restore TAMC-compatibility, need following modifs:
136      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
137      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
138      Tested TAF version is 1.9.22
139      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
140    
141    checkpoint60
142    --->>> This is the last checkpoint for which generating the adjoint
143    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
144    --->>> by default.
145    --->>> Future checkpoints will ommit this flag by default.
146    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
147    o pkg/grdchk: Add gradient check to etan0 perturbations.
148    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
149    o pkg/autodiff: more flexibility in zeroadj.
150      model/src: modifying do_oceanic_phys.F accordingly.
151    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
152    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
153      special setup of gmredi for which the adjoint is stable
154      enough for parameter optimization.
155    o bridging the gap between eddy stress and GM.
156      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
157          along with a change in CPP option (now ALLOW_EDDYPSI).
158      -> when using GM w/ GM_AdvForm:
159          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
160          is applied either in the tracer Eq. or in momentum Eq.
161          depending on data.gmredi (intro. GM_InMomAsStress).
162      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
163      The key modifications are in model/src/taueddy_external_forcing.F
164      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
165    
166    checkpoint59r
167    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
168      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
169      fix option to read coriolis(@ cell-corner) from files with CS-grid.
170    o pkg/mnc: add some attributes to standard 1D-coordinate variables
171    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
172      mass points, when using mnc for output
173      - add runtime parameter (missing_value, missing_value_int) to override
174        default (which is the value of getcon('UNDEF'))
175    o pkg/mnc: prepare mnc for the actual use of missing values with the
176      diagnostics package: small fix in mnc_cw_readwrite.template and more
177      initialisation of never used fields
178      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
179      versions
180    o pkg/thsice/thsice_ini_vars.F added default initial values so that
181      thermodynamics sea ice solver does not blow up when some initial fields
182      are missing.
183    o move from external_forcing_surf.F to ini_forcing.F
184      the p-coord. hack consisting in using pLoad to set phi0surf ;
185      update output of tutorial_global_oce_in_p (affected @ truncation level).
186    o Freshen up a bit hs94.1x64x5, notably:
187      remove rotationPeriod and tRef=5*0. (adjoint only), and add
188      exactConserv=.TRUE.
189    o pkg/generic_advdiff:
190      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
191      applies to files where Temperature & Salinity 2nd Order moments are used.
192    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
193      this uses a dynamically allocated internal state data structure
194      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
195      and requires a fortran 90 compiler
196    
197    checkpoint59q
198    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
199       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
200    o Refresh tutorial_global_oce_biogeo, notably:
201      - change bathymetry (put back seamounts in ACC, use hFacs)
202      - change EOS (POLY3 --> JMD95Z)
203      - use Bryan-Lewis vertical diffusivity
204      - use multidimensional advection
205      - remove old virtual virtual in dic pkg, now done through ptracer pkg
206      - change a couple of parameters in dic pkg
207    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
208    o pkg/obcs: change default to OBCSfixTopo = .true.,
209      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
210      - replace "debugMode" with "debugLevel .GE. debLevB"
211    o implementation of TAF directives for gchem,cfc,dic
212    o remove "exp5" (replaced by tutorial_deep_convection).
213    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
214      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
215      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
216      --> changes results in exp4, seaice_obcs
217    o tutorial_deep_convection :
218      update the set-up and increase resolution and domain size ; start
219      from pseudo initial conditions = output at t=120mn in order to see
220      something happening when running testreport.
221    o pkg/seaice: add os7mp as an advection scheme
222                  add check for advection schemes
223                  add a flag for restoring T and S underneath sea ice
224    o pkg/my82: add netcdf-support and diagnostics
225    o thsice pkg:
226      - Now hsMax limits snow height by turning it into ice following
227        flooding scheme (and now conserving energy)
228      - Slight rewriting of the formula in thsice_calc_thick.F
229      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
230      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
231    
232    checkpoint59p
233    o gchem / dic / cfc :
234      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
235      - add new parameter files: "data.dic" & "data.cfc" ;
236      - various re-arrangement in initialisation & header file ;
237      - fix tutorial_global_oce_biogeo for multi-threaded test.
238    o pkg/dic: test for "pickup_dic" file when restarting ;
239      if no pickup-file, can restart with a re-initialised pH (same as it did
240      before) providing pickupStrictlyMatch is set to False.
241    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
242      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
243    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
244      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
245    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
246     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
247       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
248    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
249       scheme to use for vorticty-term ;
250     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
251       (with default selectVortScheme, return to original discretisation)
252     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
253    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
254    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
255      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
256      also fix diagnostics VISCAHW & VISCA4W.
257    
258    checkpoint59o
259    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
260    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
261      move a few statemens out the main loop into separate loops
262    o pkg/shelfice:
263      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
264        (kg/m^2/s), does not break tests, because in verification/isomip,
265        rhoConstFresh=rhoConst (by accident)
266      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
267      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
268        new file model/src/seawater.F, so that they are available for all pkgs.
269      - convert potential temperature into in-situ temperature. This changes the
270        isomip tests => update tests
271    o add a flag writePickupAtEnd (default=true) to be able to suppress
272      writing a pickup at the last timestep
273    o tools/mpack-1.6 :
274      - disable automake (not working) and autoconf (not needed).
275      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
276        also cleaner with much less compilation warnings.
277    o pkg/profiles:
278      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
279      (for "less than 32 characters name" compiler requirement)
280    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
281      conditions that have a different sampling frequency than S/T/U/V obcs
282    o pkg/diagnostics (stats-diags):
283      - fix global Min/Max in case 1 processor get only empty tiles
284    o genmake2: replace (4 times)
285         make genmake_tc_1.o >> genmake_warnings 2>&1
286      with
287         COMM="$CC $CFLAGS -c genmake_tc_1.c"
288         echo $COMM >> genmake_warnings
289         $COMM >> genmake_warnings 2>&1
290      to make genmake2 always see the value of CC as specified in the optfile.
291    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
292      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
293      - modify verification advect_cs test to test SOM-advection on CS-grid.
294    o pkg/ctrl:
295      - Rewrite of ctrl_map_ini_ecco.F,
296        introducing a generic routine (ctrl_map_ini_gen.F).
297      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
298    
299    checkpoint59n
300    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
301      number in dedicate array "hdiag":
302      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
303        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
304      - many small changes (integer format) for large number of diagnostics
305      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
306        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
307    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
308      usingSphericalGrid, this allows to define the rotated grid coordinates
309      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
310      geographical coordinates according to the inverse of the rotation defined
311      by the Euler angles, so that Coriolis parameter and online-interpolation by
312      exf works with the geographical coordinates on XC/YC/XG/YG.
313      Naturally, this feature does not work with all packages, so some
314      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
315      profiles), because there the coordinates are assumed to be regular
316      spherical grid coordinates.
317    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
318      - introduce isopycnal diffusion coefficient control.
319    o tools/adjoint_options:
320      - additional control vector components.
321    o pkg/mnc: have mnc create marginally meaning full coordinate variables
322      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
323    o pkg/mypackage:
324      - add example of read/write pickup for state-var ;
325      - add entry points to the main code for state-vars diags & write-pickup.
326    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
327      transitions for useExfYearlyFields
328      - add new subroutine that determines the file to read from for
329        use*YearlyFields = .TRUE. and .FALSE.
330      - add a verification experiment to global_with_exf that tests
331        useExfYearlyFields with USE_EXF_INTERPOLATION defined
332    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
333      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
334      subroutines (which could be generated from a template, because they are
335      almost identical), for now they are included in obcs_prescribe_read.F for
336      simplicity
337    o pkg/exf:
338      - add a little more diagnostic to exf_interp_read (in analogy to
339        mds_read_field, can be turned off with debugLevel < debugLevA=1)
340      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
341        ugly but fast by unrolling short inner loops, inserting a unroll=8
342        directive in routine lagran, and splitting a loop and making do while the
343        outermost loop (the latter requires the intoduction of index arrays)
344    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
345    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
346      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
347    o verification/seaice_obcs: updated for restart test and latest options
348    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
349      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
350      for now this is only available for the C-grid code and also within
351      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
352    
353    checkpoint59m
354    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
355      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
356    o gad_som : fix flux output (& diagnostics) to have same units as other  
357      advection scheme fluxes (was previously multiplied by deltaT).  
358    o added verification/seaice_obcs both to test seaice open boundaries
359      and to provide an example matlab scrpt for generating them
360    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
361    o pkg/salt_plume: clean up salt_plume_frac.F to
362      remove redundancy in PlumeMethod 1 and 4
363    o pkg/kpp: added saltplume diagnostics
364    o pkg/obcs and pkg/seaice:
365      - do not set uice and vice to zero when OB*icefile are unspecified
366      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
367      - moved seaice tracer obcs after call to seaice_growth
368    o pkg/salt_plume: added various options for salt plume depth
369      criterion and for vertical distribution of the salt
370    
371    checkpoint59l
372    o pkg/ptracers: new version of ptracers pickup:
373      read meta file and write only fields which are needed to restart.
374      ( same logic as main pickup file ; also using pickupStrictlyMatch )
375    o pkg/seaice:
376      - add timescale for melting due to warm mixed layer as a means of
377        setting SEAICE_availHeatFrac more conveniently
378      - add a CPP-flag/runtime parameter check for flooding algorithm
379      - reformulated availHeat in seaice_growth.F to be independent of AREA
380    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
381      unit changes
382    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
383    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
384      SX vector computer.
385    o pkg/seaice:
386      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
387        seaice forcing fields can now be read only through pkg/exf
388      - removed some unused halos
389  o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP  o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
390  o pkg/exf: added CPP option EXF_SUBTRACT_UVVEL_FROM_UVWIND for subtracting  o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
391    UVEL and VVEL from UWIND and VWIND prior to applying bulk formulae.    or U/VICE from U/VWIND before computing U/VSTRESS
392    
393  checkpoint59k  checkpoint59k
394  o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between  o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
395    dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.    dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
396  o fix un-initialised variable problem (in mom_vecinv & shap_filt):  o fix un-initialised variable problem (in mom_vecinv & shap_filt):
397    all experiments pass when compile with un-initilised var. checking option.    all experiments pass when compile with un-initialised var. checking option.
398  o added pkg/salt_plume  o added pkg/salt_plume
399  o script to test restart (for now, in MITgcm_contrib/jmc_script)  o script to test restart (for now, in MITgcm_contrib/jmc_script)
400  o pkg/seaice: new read/write pickup version.  o pkg/seaice: new read/write pickup version.
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