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revision 1.729 by jmc, Fri Oct 6 19:44:51 2006 UTC revision 1.1020 by jmc, Sat Sep 6 17:55:27 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 add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
8      and rename:
9      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
10      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
11    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
12    
13    checkpoint61c
14    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
15      to add mass source/sink of fluid in the interior (3-D generalisation
16      of oceanic real-fresh water flux).
17    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
18    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
19    o new pkg: down_slope
20      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
21      - presently, modify T & S inland (dwnslp_calc_rho.F).
22        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
23      - implementation for ocean in P-coords not tested.
24      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
25    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
26      (to facilitate conversion of oceanic pkg to p-coordinate).
27    o change FIND_RHO to FIND_RHO_2D :
28      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
29    o new pkg: cheapaml
30    
31    checkpoint61b
32    o exch2:
33      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
34      - no longer depend on the order sequence (N,S,E,W).
35      - 3rd exchange no longer needed (tested with 24 tiles).
36      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
37      - exch_UV_A-grid readily available (but not yet tested).
38      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
39      (both are no longer needed) in exch_uv: no effect in forward run; but
40       get truncation error differences with adjoint exch.
41    o exch2:
42     - change index-bounds storage (moved from target to local tile,
43       more intuitive this way) ; rename/remove some variables.
44     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
45    
46    checkpoint61a
47    o exch2/matlab-topology-generator:
48      fix bug in index bounds for N-S internal exchange (hard to tell if this
49      had any effect on the solution).
50    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
51      is exceeded
52    o testreport: modify syntax of awk, so that it works also with
53      awk, and not only with nawk and gawk
54    
55    checkpoint61
56    o autodiff
57      Change default for TAF usage by removing argument '-nonew_arg'
58      This changes TAF subroutine argument list (ordering of active var.)
59      Omission of this flag leads to incompatibility w.r.t. TAMC
60      To restore TAMC-compatibility, need following modifs:
61      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
62      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
63      Tested TAF version is 1.9.22
64      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
65    
66    checkpoint60
67    --->>> This is the last checkpoint for which generating the adjoint
68    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
69    --->>> by default.
70    --->>> Future checkpoints will ommit this flag by default.
71    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
72    o pkg/grdchk: Add gradient check to etan0 perturbations.
73    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
74    o pkg/autodiff: more flexibility in zeroadj.
75      model/src: modifying do_oceanic_phys.F accordingly.
76    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
77    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
78      special setup of gmredi for which the adjoint is stable
79      enough for parameter optimization.
80    o bridging the gap between eddy stress and GM.
81      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
82          along with a change in CPP option (now ALLOW_EDDYPSI).
83      -> when using GM w/ GM_AdvForm:
84          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
85          is applied either in the tracer Eq. or in momentum Eq.
86          depending on data.gmredi (intro. GM_InMomAsStress).
87      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
88      The key modifications are in model/src/taueddy_external_forcing.F
89      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
90    
91    checkpoint59r
92    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
93      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
94      fix option to read coriolis(@ cell-corner) from files with CS-grid.
95    o pkg/mnc: add some attributes to standard 1D-coordinate variables
96    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
97      mass points, when using mnc for output
98      - add runtime parameter (missing_value, missing_value_int) to override
99        default (which is the value of getcon('UNDEF'))
100    o pkg/mnc: prepare mnc for the actual use of missing values with the
101      diagnostics package: small fix in mnc_cw_readwrite.template and more
102      initialisation of never used fields
103      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
104      versions
105    o pkg/thsice/thsice_ini_vars.F added default initial values so that
106      thermodynamics sea ice solver does not blow up when some initial fields
107      are missing.
108    o move from external_forcing_surf.F to ini_forcing.F
109      the p-coord. hack consisting in using pLoad to set phi0surf ;
110      update output of tutorial_global_oce_in_p (affected @ truncation level).
111    o Freshen up a bit hs94.1x64x5, notably:
112      remove rotationPeriod and tRef=5*0. (adjoint only), and add
113      exactConserv=.TRUE.
114    o pkg/generic_advdiff:
115      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
116      applies to files where Temperature & Salinity 2nd Order moments are used.
117    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
118      this uses a dynamically allocated internal state data structure
119      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
120      and requires a fortran 90 compiler
121    
122    checkpoint59q
123    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
124       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
125    o Refresh tutorial_global_oce_biogeo, notably:
126      - change bathymetry (put back seamounts in ACC, use hFacs)
127      - change EOS (POLY3 --> JMD95Z)
128      - use Bryan-Lewis vertical diffusivity
129      - use multidimensional advection
130      - remove old virtual virtual in dic pkg, now done through ptracer pkg
131      - change a couple of parameters in dic pkg
132    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
133    o pkg/obcs: change default to OBCSfixTopo = .true.,
134      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
135      - replace "debugMode" with "debugLevel .GE. debLevB"
136    o implementation of TAF directives for gchem,cfc,dic
137    o remove "exp5" (replaced by tutorial_deep_convection).
138    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
139      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
140      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
141      --> changes results in exp4, seaice_obcs
142    o tutorial_deep_convection :
143      update the set-up and increase resolution and domain size ; start
144      from pseudo initial conditions = output at t=120mn in order to see
145      something happening when running testreport.
146    o pkg/seaice: add os7mp as an advection scheme
147                  add check for advection schemes
148                  add a flag for restoring T and S underneath sea ice
149    o pkg/my82: add netcdf-support and diagnostics
150    o thsice pkg:
151      - Now hsMax limits snow height by turning it into ice following
152        flooding scheme (and now conserving energy)
153      - Slight rewriting of the formula in thsice_calc_thick.F
154      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
155      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
156    
157    checkpoint59p
158    o gchem / dic / cfc :
159      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
160      - add new parameter files: "data.dic" & "data.cfc" ;
161      - various re-arrangement in initialisation & header file ;
162      - fix tutorial_global_oce_biogeo for multi-threaded test.
163    o pkg/dic: test for "pickup_dic" file when restarting ;
164      if no pickup-file, can restart with a re-initialised pH (same as it did
165      before) providing pickupStrictlyMatch is set to False.
166    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
167      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
168    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
169      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
170    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
171     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
172       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
173    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
174       scheme to use for vorticty-term ;
175     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
176       (with default selectVortScheme, return to original discretisation)
177     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
178    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
179    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
180      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
181      also fix diagnostics VISCAHW & VISCA4W.
182    
183    checkpoint59o
184    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
185    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
186      move a few statemens out the main loop into separate loops
187    o pkg/shelfice:
188      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
189        (kg/m^2/s), does not break tests, because in verification/isomip,
190        rhoConstFresh=rhoConst (by accident)
191      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
192      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
193        new file model/src/seawater.F, so that they are available for all pkgs.
194      - convert potential temperature into in-situ temperature. This changes the
195        isomip tests => update tests
196    o add a flag writePickupAtEnd (default=true) to be able to suppress
197      writing a pickup at the last timestep
198    o tools/mpack-1.6 :
199      - disable automake (not working) and autoconf (not needed).
200      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
201        also cleaner with much less compilation warnings.
202    o pkg/profiles:
203      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
204      (for "less than 32 characters name" compiler requirement)
205    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
206      conditions that have a different sampling frequency than S/T/U/V obcs
207    o pkg/diagnostics (stats-diags):
208      - fix global Min/Max in case 1 processor get only empty tiles
209    o genmake2: replace (4 times)
210         make genmake_tc_1.o >> genmake_warnings 2>&1
211      with
212         COMM="$CC $CFLAGS -c genmake_tc_1.c"
213         echo $COMM >> genmake_warnings
214         $COMM >> genmake_warnings 2>&1
215      to make genmake2 always see the value of CC as specified in the optfile.
216    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
217      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
218      - modify verification advect_cs test to test SOM-advection on CS-grid.
219    o pkg/ctrl:
220      - Rewrite of ctrl_map_ini_ecco.F,
221        introducing a generic routine (ctrl_map_ini_gen.F).
222      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
223    
224    checkpoint59n
225    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
226      number in dedicate array "hdiag":
227      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
228        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
229      - many small changes (integer format) for large number of diagnostics
230      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
231        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
232    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
233      usingSphericalGrid, this allows to define the rotated grid coordinates
234      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
235      geographical coordinates according to the inverse of the rotation defined
236      by the Euler angles, so that Coriolis parameter and online-interpolation by
237      exf works with the geographical coordinates on XC/YC/XG/YG.
238      Naturally, this feature does not work with all packages, so some
239      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
240      profiles), because there the coordinates are assumed to be regular
241      spherical grid coordinates.
242    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
243      - introduce isopycnal diffusion coefficient control.
244    o tools/adjoint_options:
245      - additional control vector components.
246    o pkg/mnc: have mnc create marginally meaning full coordinate variables
247      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
248    o pkg/mypackage:
249      - add example of read/write pickup for state-var ;
250      - add entry points to the main code for state-vars diags & write-pickup.
251    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
252      transitions for useExfYearlyFields
253      - add new subroutine that determines the file to read from for
254        use*YearlyFields = .TRUE. and .FALSE.
255      - add a verification experiment to global_with_exf that tests
256        useExfYearlyFields with USE_EXF_INTERPOLATION defined
257    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
258      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
259      subroutines (which could be generated from a template, because they are
260      almost identical), for now they are included in obcs_prescribe_read.F for
261      simplicity
262    o pkg/exf:
263      - add a little more diagnostic to exf_interp_read (in analogy to
264        mds_read_field, can be turned off with debugLevel < debugLevA=1)
265      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
266        ugly but fast by unrolling short inner loops, inserting a unroll=8
267        directive in routine lagran, and splitting a loop and making do while the
268        outermost loop (the latter requires the intoduction of index arrays)
269    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
270    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
271      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
272    o verification/seaice_obcs: updated for restart test and latest options
273    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
274      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
275      for now this is only available for the C-grid code and also within
276      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
277    
278    checkpoint59m
279    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
280      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
281    o gad_som : fix flux output (& diagnostics) to have same units as other  
282      advection scheme fluxes (was previously multiplied by deltaT).  
283    o added verification/seaice_obcs both to test seaice open boundaries
284      and to provide an example matlab scrpt for generating them
285    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
286    o pkg/salt_plume: clean up salt_plume_frac.F to
287      remove redundancy in PlumeMethod 1 and 4
288    o pkg/kpp: added saltplume diagnostics
289    o pkg/obcs and pkg/seaice:
290      - do not set uice and vice to zero when OB*icefile are unspecified
291      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
292      - moved seaice tracer obcs after call to seaice_growth
293    o pkg/salt_plume: added various options for salt plume depth
294      criterion and for vertical distribution of the salt
295    
296    checkpoint59l
297    o pkg/ptracers: new version of ptracers pickup:
298      read meta file and write only fields which are needed to restart.
299      ( same logic as main pickup file ; also using pickupStrictlyMatch )
300    o pkg/seaice:
301      - add timescale for melting due to warm mixed layer as a means of
302        setting SEAICE_availHeatFrac more conveniently
303      - add a CPP-flag/runtime parameter check for flooding algorithm
304      - reformulated availHeat in seaice_growth.F to be independent of AREA
305    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
306      unit changes
307    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
308    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
309      SX vector computer.
310    o pkg/seaice:
311      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
312        seaice forcing fields can now be read only through pkg/exf
313      - removed some unused halos
314    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
315    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
316      or U/VICE from U/VWIND before computing U/VSTRESS
317    
318    checkpoint59k
319    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
320      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
321    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
322      all experiments pass when compile with un-initialised var. checking option.
323    o added pkg/salt_plume
324    o script to test restart (for now, in MITgcm_contrib/jmc_script)
325    o pkg/seaice: new read/write pickup version.
326      read meta file and write only fields which are needed to restart.
327      ( same logic as main pickup file ; also using pickupStrictlyMatch )
328    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
329    o lab_sea.hb87: modify the domain & update output.hb87.txt :
330      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
331      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
332      process. Fixed here by closing the domain at the Northern boundary.
333    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
334    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
335      a set of consecutive levels in/from a 3-D array.
336    o pkg/ptracers:
337      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
338      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
339    
340    checkpoint59j
341    o in pkgs: dic, obcs, offline, rbcs:
342      standard way to compute coeff. for time interpolation between 2 time reccords
343      which retains full precision (& make results less dependent on compiler).
344      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
345    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
346      packages instead of reading ice cover and wind speed separately
347    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
348     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
349      to allow to compile customized code before the update)
350    o cleaning-up:
351      - fix CPP instruction syntax in pkg/obcs
352      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
353        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
354      - fix some threads issue in IO parts.
355    o pkg/dic:
356      - add tons of "_d 0" (--> much better testreports !)
357       and then update outputs of tutorial_global_oce_biogeo
358    o pkg/mom_fluxform:
359      add a special version of momentum advection intended to conserve momentum
360      next to a bathymetry step or a coastline edge. (default = off = #undef)
361    o new read/write pickup version:
362      - for now, only implemented for main (mdsio) pickup file.
363      - write out only what is needed to restart; merge pickup_nh , pickup_ph
364        and main pickup together.
365      - read meta file; read only what is needed to restart; stop if a field
366        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
367        if it make sense (even if the restart is not perfect).
368      - if no meta file, assume that pickup to read corresponds exactly to
369        a pickup that would currently be written.
370      - read pickup written in the old format (until checkpoint59i) if it
371        recognizes an old meta file (no field-list).
372      - add a meta file in exp. which starts from a pickup: 2 cases:
373        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
374         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
375        b) a meta file describing the content of the associated pickup file
376         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
377    o pkg/mdsio & pkg/rw:
378      - new routine to read a meta file ; new set of routine to read
379        Multiple-fields file (with meta file).
380    o added open boundary conditions capability for seaice
381        HSNOW, HSALT, UICE, and VICE
382    
383    checkpoint59i
384    o adjoint:
385      * fix multiDimAdvection adjoint
386        (partial recomputation problem by TAF for fVerT(:,:,kDown)
387        and comlev1 size definition (maxpass vs. max. number of tracers)
388      * verification/global_ocean.90x45x15 adjoint now tests
389        NLFS and multiDimAdvection using DST3 (=30)
390      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
391    o pkg/kpp: add "_d 0" to real constant (if missing);
392      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
393      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
394    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
395      for internal parameters related to restart process (formerly from PARAMS.h)
396      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
397    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
398      as argument. (only atm2d & obcs write_pickup have not yet been updated)
399    o pkg/monitor:
400      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
401      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
402      - account for deep Atmosphere factor and density factor (anelastic)
403    o added open boundary conditions capability for seaice HEFF and AREA
404    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
405      thermodynamics
406      - requires a little reorganization, which affects the testreport results
407        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
408        so that now the conservative form is tested
409      - add a few comments
410    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
411    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
412    o add new diagnostics to seaice: advective, diffusive fluxes (only for
413      multidim-advection, for scheme 2 they are not filled) and transports,
414      thermodynamic growth rates
415    o change units of EmPmR (inside the code, + within coupling interface)
416      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
417      Affects results @ truncation level (cg2d match) and update output of
418       experiments: lab_sea(6), global_ocean.90x40x15(10),
419      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
420      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
421      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
422      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
423    
424    checkpoint59h
425    o pkg/exf:
426      - improve vectorization by moving if-statement out of loops in
427        exf_mapfields, exf_radiation
428      - exf_bulkformulae.F: introduce 2D fields and vectorize code
429    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
430    o testreport:
431      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
432        monitor & update offline_exf_seaice exp. output.
433      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
434    o pkg/seaice:
435      - bug fix in the evp solver: boundary conditions were affected be
436        masking of zMax/zMin (changes results)
437      - minor bug fix in boundary conditions in seaice_calc_strainrates
438        (changes results for no_slip)
439      - seaice_lsr.F: make interpolation of eta dependent on boundaries
440      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
441      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
442        stress formulation and no-slip boundary conditions
443    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
444      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
445    o pkg/seaice: a first HSALT time stepping equation has been checked in
446    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
447      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
448      without requiring DO-IF statements
449    o pkg/thsice:
450      use continuous power-law function for partition of energy between lateral
451      melting/freezing and thinning/thickening ; old code using step function
452      still available with #undef THSICE_FRACEN_POWERLAW
453      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
454    o testreport: change AD testing : check against results/output_adm.txt
455      using same scripts as for forward test.
456    
457    checkpoint59g
458    o adjoint testing: in preparation for changing testreport:
459      - output format: cost and grad written on separated lines
460      - ad output results in directory "results" (instead of "results_ad")
461    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
462    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
463    o pkg/ecco: allow user defined cost function contributions
464    o testreport:
465      Allow to choose (per experiment) the list of tested output variables
466       and the main variable (used to issue a pass/FAIL ) ;
467      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
468      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
469      Also modify printing of summary:
470       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
471       b) echo the list of tested variables in the individual summary.txt of
472          each experiment.
473    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
474      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
475      (but still depend on the tile decompostion of the domain).
476    o pkg/seaice: change a discretization detail to make the B-grid code
477      "more symmetric". This change is likely to remove all "ridges/leads" that
478      where quasi-aligned with the grid in B-grid solutions. It may also be
479      the solution to the stress coupling issues with the B-grid.
480    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
481      remove .cvsignore from input dir. (since testreport no longer run here).
482    o pkg/thsice:
483     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
484     - fix reshaping of sea-ice just after advection:
485       melt all the ice only if ice-volume is too small.
486     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
487       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
488     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
489    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
490      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
491    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
492      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
493      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
494      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
495      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
496      -> update output.txt
497    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
498     this affects truncation error: -> update output.txt of exp:
499      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
500      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
501    
502    checkpoint59f
503    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
504    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
505      a bounded range (in forward mode)
506    o pkg/ecco, ctrl, autodiff and mom_common:
507     internal parameter controls, completements of implementations
508    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
509    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
510      (not seem any difference in testing results).
511    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
512       at face corners.
513    o pkg/generic_advdiff:
514     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
515      loop range indices for computing vertical advection tendency
516      and do the calculation in the interior only (no overlap) ;
517      for now, only implemented for SOM advection (to save CPU time).
518     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
519    o exch2 adjoint
520      First set of changes:
521      - add exch2 hand-written adjoint templates
522      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
523        This will require cleanup in pkg/autodiff/*.F
524        (changed routines currently kept separate in verif. code/)
525      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
526        that used to hide exch2 or cubed-sphere specific code
527        (commented via 'cph-exch2')
528    o pkg/seaice
529      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
530    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
531       output of global_ocean.cs32x15.thsice .
532    
533    checkpoint59e
534    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
535      for B-grid vector (not yet tested) and C-grid vector (<- only used
536      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
537    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
538      (#ifdef ALLOW_SALT_PLUME)
539    o gather_2d/scatter_2d: removed halo regions
540    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
541      scheme and the corresponding test case (under front_relax dir). For now,
542      only available with Skew-flux form and not yet tested in realistic set-up.
543      adjoint: store directives updated, but gradient checks deteriorated,
544      so maybe GM/Redi adjoint is now broken.
545    o seaice adjoint
546      * add AREA, HEFF, HSNOW as control variable
547        (should not change lab_sea results)
548      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
549    o pkg/seaice:
550      * added computation of saltFlux in seaice_growth;
551        For time being, sea ice salinity is assumed constant
552        contribution of snow flooding to freshening of sea ice is neglected.
553        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
554        defaults to 0.0 in order to maintain backward compatibility.
555        Typical values for SEAICE_salinity are 4 to 10 g/kg.
556      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
557      * added SEAICE_availHeatFrac, which specifies fraction of surface level
558        heat content used to melt or grow ice
559      * commented out cap of HICE: it helps keep ice thinner
560      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
561      * applied OBCS T/S mask to HEFFM sea ice mask
562    
563    checkpoint59d
564    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
565     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
566     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
567    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
568     and change default value of parameter "GM_Small_Number";
569     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
570       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
571       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
572    o pkg/ecco: cost function when applying pkg/smooth to controls
573    o pkg/ctrl: add forcingPrecond run time parameter
574    o pkg/seaice:
575     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
576     - fix bug in metric terms of u-equation in LSR solver (implicit part),
577       changes verification/lab_sea
578     - rearrange implicit part of u-equation in LSR solver to make it easier to
579       read, understand, and debug. This causes changes at the truncation level.
580     - fix (serious) bug in the boundary conditions (sign error in the implicit
581       part) of the LSR solver. Changes all LSR results.
582     - fixed problem with HSNOW initialization to avoid thick snow when AREA
583       is initilized with small values - does not change lab_sea results.
584     - added HsnowFile initialization capability
585    o pkg/smooth: addition to model/src and pkg/ctrl so allow
586     initialization of pkg/smooth and application to control vector
587    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
588    o dependencies: pkg/profiles requires pkg/cal
589    o pkg/profiles:
590     - added option ALLOW_PROFILES_GENERICGRID
591         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
592         that interpolation information (grid points and coefficients) is provided
593         within the netcdf input files.
594         -> sample matlab scripts can be found in MITgcm_contrib/gael
595         that allow you to prepare netcdf input files.
596     - also modified: cleaner include statements, cleaner error print statements,
597       cleaner stops when error, and more tests of the netcdf input files consistency.
598    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
599    o pkg/seaice:
600     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
601       requires a new routine: seaice_diagnostics_fill.F
602     - make sure that seaice does not move if not forced (pressure replacement
603       method, Hibler and Ip, 1995), changes results
604     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
605     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
606       It is turned off by default (=-1.), because it changes the results.
607     - make it possible to read AREA from a file, too.
608    
609    checkpoint59c
610    o add S/R and diagnostics for oceanic mixed-layer depth
611    o move GMRedi call after all vertical mixing schemes (including KPP)
612    o pkg/thsice:
613     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
614      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
615    o pkg/obcs:
616     - bug fix for balance code
617    o pkg/seaice:
618      - allow values of SEAICE_elasticParm > 1
619      - add new parameter SEAICE_evpTauRelax as an alternative
620        to SEAICE_elasticParm
621      - make lsr boundary conditions free slip (by default), changes result
622      - add code for no slip boundary conditions for lsr
623      - set minimum of zeta to zero (and not 4e8) (changes results)
624      - add a cap on AREA after advecting AREA if seaice_growth is not called
625    o change calculation of Visbeck K:
626      - no longer depend on tapering scheme; instead, compute slope (limited
627        by GM_maxSlope). this is equivalent to what was comuted before with
628        clipping or linear tappering.
629      - fix vertical averaging (wrong by 1/2 level)
630      - leave the old version (but will not be maintained) within
631        #ifdef OLD_VISBECK_CALC / #endif
632      - update output of exp. ideal_2D_oce
633    o change error catch in calc_r_star to improve vectorization
634    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
635      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
636    o adjoint:
637      Re-organized adjoint checkpointing according to Matt Mazloff
638      (but with modifs/completions/cleanups)
639      Storing is now bundled into large arrays to optimized I/O
640      (and second step in cleanup of the_main_loop)
641    
642    checkpoint59b
643    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
644      - export/import (between ocean & coupler) fields needed for ocean DIC.
645    o pkg/seaice:
646      - get rid of three more exchanges seaice_calc_viscosities (required
647        different loop boundaries in seaice_lsr and seaice_ocean_stress)
648      - bug fix in seaice_ocean_stress (update of lab_sea required)
649      - reduce loop boundaries to necessary minimum also in seaice_evp
650      - go back to the old way of computing deltaC/Z as the adjoint likes that
651        better
652    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
653      passive tracer to an Age Tracer) + update output.txt
654    o pkg/exf:
655      - implement A-grid / C-grid selection for wind-stress input files.
656      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
657      for now, in exf_bulk_largeyeager04.F only :
658      - change implementation for case where windspeed + 2. components wind-stress
659        are read-in. AND use rhoConstFresh to convert evap.
660    o pkg/seaice:
661      - use correct EXCH_UV for wind-forcing (on A-grid).
662      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
663        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
664    o pkg/exf:
665      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
666      EXF_INTERPOLATION:
667      - merge global_with_exf/code version of exf_interp_read.F
668        to the main code ;
669      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
670        reading the file ; Important: This options needs to be defined to recover
671        previous code.
672        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
673      - no longer loose real*8 precision along the way when using exf_iprec=64.
674    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
675      - change discretisation of evp-solver in order to avoid another exchange
676        (changes lab_sea) and clean up a little
677      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
678        help the adjoint (this also changes the results slightly)
679      - add a few "_d 0" where they had been missing in seaice_evp.F
680      - cleaning up: remove unused seaice_calc_rhs.F
681    o pkg/exf: some cleaning-up:
682      - change various "constants" into runtime parameters
683      - cleaned-up Large&Yeager04 routine which should eventually
684        replace exf_bulkformulae.F (changed names of S/R and CPP)
685        and merged various ALLOW_ATM_WIND options
686     only used with thsice pkg (in thsice_get_exf.F):
687      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
688        which are used when useStabilityFct_overIce=TRUE (= the default)
689      - change default values of ice & snow emissivity and scale downward LW
690        by ice & snow emissivity.
691    o pkg/thsice:
692     fix few little problems, in thsice_calc_thickn.F:
693      - growth vertically (and not laterally) if iceFrac == iceMaskMax
694      - melt only laterally if hIce < hThinIce (as the comments say)
695      and in thsice_extend.F:
696      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
697      - start to form ice as soon as the minimum ice-volume is reachable.
698     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
699      and cpl_aim+ocn
700    o pkg/kpp
701     - move computation of surface related input fields to KPP into a new
702       subroutine kpp_forcing_surf.F
703     - remove wrong (within bi,bj loops) EXCH calls.
704     - little cleaning (add argument myThid in last position, cvs header ...)
705     - for now, fix conservation problem by exchanging KPPviscAz (may not
706       be the best fix)
707    o pkg/seaice
708     - check for inconsistent evp parameter/cpp-flag combination
709     - remove leftover errIO flat for obsolete name list error handling
710    o OpenAD
711     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
712    
713    checkpoint59a
714    o pkg/seaice: some parameter clarifications and a little bit of clean up
715    o pkg/thsice: rename run-time parameters:
716       himin       -> hIceMin
717       himin0      -> hThinIce
718       hihig       -> hThickIce
719       i0          -> i0swFrac
720       transCoef   -> bMeltCoef
721       frac_energy -> fracMelting
722      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
723       with default values (for now) that do not change the results.
724      remove old version of thsice vars advection in pkg/seaice.
725    o in FFIELDS.h:
726      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
727      - make pLoad & sIceLoad always available (but still only used if
728         ATMOSPHERIC_LOADING is #define).
729    o pkg/kpp: replaced _KPP_RL with _RL
730    o bug fixes for vertical diffusivity computations when both KPP and
731        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
732        are no longer updating the vertical diffusivity array
733        (passed as argument) but are (re-) setting those arrays.
734    o pkg/seaice: fix bug in evp solver, while doing that
735      - change (improve?) discretization of stress computations for both
736        cgrid-lsr and evp solver
737      - add a new routine to compute strain rates
738      - the above changes lab_sea results
739      - add no slip conditions for evp solver (off by default), lsr-version
740        may follow
741      - fix exchange for shear at Z-points (does not change lab_sea)
742      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
743        (to force the user to pick a time step since there is not "safe" way
744        of choosing it)
745      - add principal stress diagnostics
746      - rearrange fields for evp a little to avoid having to call a: too many
747        exchanges and b: exchanges for stress trensor components which we do
748        not have.
749      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
750        of evp, complete rewrite for lsr case (latter is does not yet work
751        in all cases)
752    o pkg/kpp: add code to have mixing in shelf ice caverns
753      - add myThid to all kpp routines (long overdue)
754    
755    checkpoint59
756    o pkg/exf:
757      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
758        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
759      - move exf header files from lower_case.h to UPPER_CASE.h ;
760        add missing cvs Header & Name
761      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
762      - add namelist param. selectStressGridPosition, exf_monFreq
763      - retire many _CLIM routines, and remove data.exf_clim
764        + params moved to data.exf
765        + climsst, climsss now handled by exf_set_gen, i.e.
766          climss?period=0 refers to constant field,
767          climss?period=-12 to monthly forcing
768      - split up namelists in data.exf
769    o pkg/seaice:
770      - remove seaice_exch and seaice_exch_uv
771      - remove superfluous exchange of theta
772      - add myThid to seaice_budget_ocean/ice
773      - add new interface for atmospheric wind forcing (C-grid only)
774        + new routine
775        + two new field (taux, tauy for stress over ice)
776        + removed one global field (DAIRN) for C-grid case only
777    o pkg/thsise
778      - 2nd set of modifs for thsice adjoint in conjunction with exf
779    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
780    
781    checkpoint58y_post
782    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
783      vertical diffusivity, similar to that in MOM4; turned on using
784      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
785      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
786    o Added capability for 3D specification of background vertical diffusion
787      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
788      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
789      "data" file that contains the 3D vertical diffusivity coefficients.
790    o ice dynamics (pkg/seaice) with thsice thermodynamics:
791      - add code within pkg thsice to advect & diffuse sea-ice fields
792      similar to (and will replace) what has been added in  seaice_advdiff.F,
793      but: - conserving Mass, Heat & Salt.
794           - better when using non-linear advection scheme (not yet fully tested)
795           - can also be used in atmospheric set-up (for now, only the diffusion).
796    
797    checkpoint58x_post
798    o IO option for global-file compact format:
799      - add options when generating topology (utils/exch2/matlab-topology-generator)
800      - add I/O capability (pkg/mdsio).
801      - adapt utils/matlab/rdmds.m to read this format.
802      for now long-line format not yet supported by pkg/mdsio (& exch2).
803    o shelfice: add a few diagnostics
804    
805    checkpoint58w_post
806    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
807      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
808      (and replace horiVertRatio in NH code).
809      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
810                         and tutorial_plume_on_slope (sensitive to truncation)
811    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
812      directly to drive seaice model (C-grid only)
813    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
814     - reintroduce computation of wind from stress,
815     - compute tau (in exf_bulkformulae.F) from windstress averaged to
816       mass points to avoid tau = 0
817     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
818    o rdmnc.m: make it work with "global" files created with gluemnc
819    o rdmnc.m : some improvements in dealing with singleton dimension
820      (tested on all testreport mnc output files).
821    o genmake2: disable pkg/profiles if netcdf test fails.
822    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
823    o move call to cal_readparms up to make calendar parameters/variable available
824      to all packages
825    
826    checkpoint58v_post
827    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
828      useDynP_inEos_Zc tested.
829    o pkg/exf: changes to properly interpolate/mask/scale initial fields
830    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
831      and portions thereof.  See read_cs.txt for description and examples.
832    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
833      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
834      following the great-circle arc between those 2 points.
835    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
836      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
837    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
838     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
839     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
840     - still needs work (not working with some options ; efficiency to improve)
841       and serious testing.
842     - use this scheme for temperature & salinity in 2 advection test exp.:
843       advect_xy & advect_xz, respectively.
844    
845    checkpoint58u_post
846    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
847    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
848    o testreport: add option "-skipdir" to skip some test.
849    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
850      momentum calculation.
851    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
852    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
853      remove checkpoint.F and the_correction_step.F (no longer used);
854      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
855    o add option (linFSConserveTr) to correct for tracer source/sink due to
856      Linear Free surface
857    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
858    o pkg/thsice: fix reading mnc-pickups
859    
860    checkpoint58t_post
861    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
862    o pkg/mdsio:
863     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
864       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
865       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
866     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
867     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
868       either MDS_READ_FIELD or MDS_WRITE_FIELD )
869     - new S/R (to replace MDSWRITEMETA), which allows to write more
870       informations (variable names, time ...) to meta files.
871     - modify rdmds.m to give back the meta file content.
872    o pkg/diagnostics: change vertical interpolation to be safer, and more
873       flexible (define p-levels to interpolate to in data.diagnostics);
874      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
875       diagnostic pointer.
876    o pkg/seaice: more cleaning up of seaice_growth, added many comments
877    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
878    o fix multi-category seaice:
879     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
880       SEAICE_MULTICATEGORY
881     - fix short wave heat flux
882    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
883       and allow to use EVP solver. Change forward lab_sea: test both EVP
884       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
885    o Initial check-in of lab_sea adjoint
886      (very similar to natl_box_adjoint/code_seaice)
887      * used C-grid and EVP solver
888      * used KPP, GM/Redi
889      * uses inAdExact=.TRUE.
890      * gradient checks fail for both ADM and TLM
891        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
892        f.d. gradients actually seem more problematic than ADM, TLM gradients;
893        issue is related to forward mismatch between g77 an ifort
894    o pkg/seaice: overhaul of thermodynamics
895     - growth.F and groatb.F are replaced by new routine seaice_growth.F
896     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
897     - move a few global fields out of SEAICE.h into seaice_growth.F and
898       make them 2D (FICE/QNETO/ ...)
899     - remove FO (it is the same as QNETO)
900     - introduce a few local fields to avoid modifying external fields such
901       as atemp, etc.
902    
903    checkpoint58s_post
904    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
905      changed exf_set_gen.F so that
906        genperiod=0 means input file is one time-constant field and
907        genperiod=-12 means input file contains 12 monthly means
908    o CG2D: use pre-computed solver main-diagonal (stored in common block);
909      this affects truncation error ; generate new output file for exp. which
910      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
911        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
912        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
913        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
914        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
915        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
916    o start implementation of deep-atmosphere and anelastic formulation
917    o verification: remove 2nd copy of input files and use script "prepare_run"
918      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
919    o mom_common/vecinv/fluxform: fix a few initialisation isssues
920    o profiles: fix for multithreaded case
921    
922    o diagnostics: rename few diags:
923      s/'PRESSURE'/'RCENTER '/g
924      s/'TICE    '/'oceFreez'/g
925      s/'TAUX    '/'oceTAUX '/g
926      s/'TAUY    '/'oceTAUY '/g
927      s/'SWFLUX  '/'oceQsw  '/g
928      s/DIFx/DFxE/g
929      s/DIFy/DFyE/g
930      and add few ocean-forcing diagnostics:
931      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
932    o modifications to pkg/seaice/growth.F and budget.F, which change results of
933      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
934      as actual snow thickness.  It now refers everywhere to effective snow
935      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
936    
937    checkpoint58r_post
938    o modifications to pkg/seaice/growth.F, which change results of
939      lab_sea experiment: fixes pertain to melting snow over open water, to
940      masking EVAP under sea ice, and to using the correct AREA variable for
941      computations of EVAP, PRECIP, HSNOW, and GHEFF
942    o add ability to read bathy, salt, and theta using MNC (off by def)
943    o add flooding algorithm and advection of HSNOW for pkg/seaice;
944      both are turned off by default and do no change any results
945    o seaice advection with pkg/thsice: a step toward the use of non-linear
946      advection scheme, but #ifdef or commented out for now (requires more EXCH).
947    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
948      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
949      in natl_box (affects results @ truncation level: update output.txt)
950    o multi-threading and IO:
951      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
952      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
953        (needed to work with SingleCpuIO): tested in all verif. exp.
954    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
955      affects the results (but none of the verification test uses this scheme).
956    o Adding some pkg/diagnostics capability to pkg/seaice
957      (will certainly be subject to changes)
958    o ctrl: adding new control variables:
959      lwflux, lwdown, evap, snowprecip, apressure, runoff
960    
961    checkpoint58q_post
962    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
963      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
964      high_res_cube configuration by 4% on Columbia.
965    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
966      add (in global_with_exf/code) a version of EXF_INTERP_READ without
967      dynamical allocation (seems to work in multi-threaded).
968    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
969      single CPU io) so that TAF does not have to see EESUPPORT.h
970  o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)  o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
971    
972  checkpoint58p_post  checkpoint58p_post
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