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revision 1.730 by cnh, Wed Oct 11 19:30:01 2006 UTC revision 1.1044 by mlosch, Wed Nov 26 08:42:28 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 gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
8      a still unfixed compiler/optimization bug
9    
10    checkpoint61f
11    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
12      update results of global_ocean.cs32x15.icedyn test.
13    o move getcon.F from model/src to pkg/fizhi.
14    o pkg/exf: add parameter for extrapolation of temp up to the surface
15       and option to prevent negative evap (in bulk_largeyeager04 only).
16    o Prather Advection scheme: fix tracer conservation for divergent flow
17      (e.g., when using NonLin Free-Surface).
18    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
19    o gmredi (Visbeck-variable-K):
20     - add more parameters to Visbeck-variable-K.
21     - use a 5 points average for dSigmaR in Visbeck-K calculation
22       (more "homogenous": same stencil and same weights as in dSigmaH)
23     - update output of ideal_2D_oce experiment.
24    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
25      (#undef REAL4_IS_SLOW)
26     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
27       coordinate variable
28     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
29       (surface forcing fields), removes some of the functionality
30     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
31     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
32       probably not all: copy _RS surface flux fields to RL field before
33       calling DIAGNOSTICS_FILL
34     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
35       real*4 (CALL EXCH_*_RS) versions.
36     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
37       (generate new output).
38    
39    checkpoint61e
40    o gmredi (Visbeck-variable-K):
41      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
42      - change computation of Visbeck-K where Slope > Smax :        
43        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
44        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
45    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
46      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
47    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
48    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
49      does not become too large (to avoid precision problems in implicit-diffusion
50      solver); update ideal_2D_oce output.
51    o pkg ggl90:
52      - in ggl90_cal.F: compute only one set of visc/diff, used to
53        step forward TKE/T/S/momentum
54      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
55        have Prandlt =1)
56    o gmredi (fm07):
57      - add lower limit on Transition layer thickness + lower limit on 1/lambda
58      - allow to set few more params from data.gmredi
59    o pkg ggl90:
60          - add missing sqrt(2) factor in computation of mixing length
61            scale in ggl90_calc.F
62            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
63    
64    checkpoint61d
65    o adjoint modifs
66      - adapt to new field rhoInSitu
67      - allow to revert from StoreDynVars2D, StoreDynVars3D
68        to individual fields
69        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
70    o store 3-D (in-situ) density in commom block (DYNVARS.h)
71     - save 1 rho computation.
72     - no longer modify T & S inland when using down_slope pkg.
73    o gad_som : allow to switch to SOM advection for T & S without corresponding
74      pickup files (using new S/R: MDS_CHECK4FILE).
75    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
76      (for useSingleCpuIO to work in multi-threaded)
77    o pkg/shelfice:
78     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
79       with SHELFICEtopoFile in data.shelfice
80     - move code for reading ice shelf topography and modifying hFacC into separate
81       subroutines of the shelfice package
82     - separate initialisation of "fixed" and "variable" variables
83     - kTopC is not (yet) replaced by kSurfC, although this is possible
84    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
85    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
86      and rename:
87      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
88      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
89    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
90    
91    checkpoint61c
92    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
93      to add mass source/sink of fluid in the interior (3-D generalisation
94      of oceanic real-fresh water flux).
95    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
96    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
97    o new pkg: down_slope
98      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
99      - presently, modify T & S inland (dwnslp_calc_rho.F).
100        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
101      - implementation for ocean in P-coords not tested.
102      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
103    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
104      (to facilitate conversion of oceanic pkg to p-coordinate).
105    o change FIND_RHO to FIND_RHO_2D :
106      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
107    o new pkg: cheapaml
108    
109    checkpoint61b
110    o exch2:
111      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
112      - no longer depend on the order sequence (N,S,E,W).
113      - 3rd exchange no longer needed (tested with 24 tiles).
114      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
115      - exch_UV_A-grid readily available (but not yet tested).
116      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
117      (both are no longer needed) in exch_uv: no effect in forward run; but
118       get truncation error differences with adjoint exch.
119    o exch2:
120     - change index-bounds storage (moved from target to local tile,
121       more intuitive this way) ; rename/remove some variables.
122     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
123    
124    checkpoint61a
125    o exch2/matlab-topology-generator:
126      fix bug in index bounds for N-S internal exchange (hard to tell if this
127      had any effect on the solution).
128    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
129      is exceeded
130    o testreport: modify syntax of awk, so that it works also with
131      awk, and not only with nawk and gawk
132    
133    checkpoint61
134    o autodiff
135      Change default for TAF usage by removing argument '-nonew_arg'
136      This changes TAF subroutine argument list (ordering of active var.)
137      Omission of this flag leads to incompatibility w.r.t. TAMC
138      To restore TAMC-compatibility, need following modifs:
139      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
140      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
141      Tested TAF version is 1.9.22
142      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
143    
144    checkpoint60
145    --->>> This is the last checkpoint for which generating the adjoint
146    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
147    --->>> by default.
148    --->>> Future checkpoints will ommit this flag by default.
149    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
150    o pkg/grdchk: Add gradient check to etan0 perturbations.
151    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
152    o pkg/autodiff: more flexibility in zeroadj.
153      model/src: modifying do_oceanic_phys.F accordingly.
154    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
155    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
156      special setup of gmredi for which the adjoint is stable
157      enough for parameter optimization.
158    o bridging the gap between eddy stress and GM.
159      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
160          along with a change in CPP option (now ALLOW_EDDYPSI).
161      -> when using GM w/ GM_AdvForm:
162          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
163          is applied either in the tracer Eq. or in momentum Eq.
164          depending on data.gmredi (intro. GM_InMomAsStress).
165      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
166      The key modifications are in model/src/taueddy_external_forcing.F
167      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
168    
169    checkpoint59r
170    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
171      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
172      fix option to read coriolis(@ cell-corner) from files with CS-grid.
173    o pkg/mnc: add some attributes to standard 1D-coordinate variables
174    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
175      mass points, when using mnc for output
176      - add runtime parameter (missing_value, missing_value_int) to override
177        default (which is the value of getcon('UNDEF'))
178    o pkg/mnc: prepare mnc for the actual use of missing values with the
179      diagnostics package: small fix in mnc_cw_readwrite.template and more
180      initialisation of never used fields
181      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
182      versions
183    o pkg/thsice/thsice_ini_vars.F added default initial values so that
184      thermodynamics sea ice solver does not blow up when some initial fields
185      are missing.
186    o move from external_forcing_surf.F to ini_forcing.F
187      the p-coord. hack consisting in using pLoad to set phi0surf ;
188      update output of tutorial_global_oce_in_p (affected @ truncation level).
189    o Freshen up a bit hs94.1x64x5, notably:
190      remove rotationPeriod and tRef=5*0. (adjoint only), and add
191      exactConserv=.TRUE.
192    o pkg/generic_advdiff:
193      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
194      applies to files where Temperature & Salinity 2nd Order moments are used.
195    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
196      this uses a dynamically allocated internal state data structure
197      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
198      and requires a fortran 90 compiler
199    
200    checkpoint59q
201    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
202       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
203    o Refresh tutorial_global_oce_biogeo, notably:
204      - change bathymetry (put back seamounts in ACC, use hFacs)
205      - change EOS (POLY3 --> JMD95Z)
206      - use Bryan-Lewis vertical diffusivity
207      - use multidimensional advection
208      - remove old virtual virtual in dic pkg, now done through ptracer pkg
209      - change a couple of parameters in dic pkg
210    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
211    o pkg/obcs: change default to OBCSfixTopo = .true.,
212      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
213      - replace "debugMode" with "debugLevel .GE. debLevB"
214    o implementation of TAF directives for gchem,cfc,dic
215    o remove "exp5" (replaced by tutorial_deep_convection).
216    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
217      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
218      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
219      --> changes results in exp4, seaice_obcs
220    o tutorial_deep_convection :
221      update the set-up and increase resolution and domain size ; start
222      from pseudo initial conditions = output at t=120mn in order to see
223      something happening when running testreport.
224    o pkg/seaice: add os7mp as an advection scheme
225                  add check for advection schemes
226                  add a flag for restoring T and S underneath sea ice
227    o pkg/my82: add netcdf-support and diagnostics
228    o thsice pkg:
229      - Now hsMax limits snow height by turning it into ice following
230        flooding scheme (and now conserving energy)
231      - Slight rewriting of the formula in thsice_calc_thick.F
232      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
233      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
234    
235    checkpoint59p
236    o gchem / dic / cfc :
237      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
238      - add new parameter files: "data.dic" & "data.cfc" ;
239      - various re-arrangement in initialisation & header file ;
240      - fix tutorial_global_oce_biogeo for multi-threaded test.
241    o pkg/dic: test for "pickup_dic" file when restarting ;
242      if no pickup-file, can restart with a re-initialised pH (same as it did
243      before) providing pickupStrictlyMatch is set to False.
244    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
245      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
246    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
247      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
248    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
249     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
250       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
251    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
252       scheme to use for vorticty-term ;
253     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
254       (with default selectVortScheme, return to original discretisation)
255     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
256    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
257    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
258      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
259      also fix diagnostics VISCAHW & VISCA4W.
260    
261    checkpoint59o
262    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
263    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
264      move a few statemens out the main loop into separate loops
265    o pkg/shelfice:
266      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
267        (kg/m^2/s), does not break tests, because in verification/isomip,
268        rhoConstFresh=rhoConst (by accident)
269      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
270      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
271        new file model/src/seawater.F, so that they are available for all pkgs.
272      - convert potential temperature into in-situ temperature. This changes the
273        isomip tests => update tests
274    o add a flag writePickupAtEnd (default=true) to be able to suppress
275      writing a pickup at the last timestep
276    o tools/mpack-1.6 :
277      - disable automake (not working) and autoconf (not needed).
278      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
279        also cleaner with much less compilation warnings.
280    o pkg/profiles:
281      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
282      (for "less than 32 characters name" compiler requirement)
283    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
284      conditions that have a different sampling frequency than S/T/U/V obcs
285    o pkg/diagnostics (stats-diags):
286      - fix global Min/Max in case 1 processor get only empty tiles
287    o genmake2: replace (4 times)
288         make genmake_tc_1.o >> genmake_warnings 2>&1
289      with
290         COMM="$CC $CFLAGS -c genmake_tc_1.c"
291         echo $COMM >> genmake_warnings
292         $COMM >> genmake_warnings 2>&1
293      to make genmake2 always see the value of CC as specified in the optfile.
294    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
295      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
296      - modify verification advect_cs test to test SOM-advection on CS-grid.
297    o pkg/ctrl:
298      - Rewrite of ctrl_map_ini_ecco.F,
299        introducing a generic routine (ctrl_map_ini_gen.F).
300      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
301    
302    checkpoint59n
303    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
304      number in dedicate array "hdiag":
305      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
306        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
307      - many small changes (integer format) for large number of diagnostics
308      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
309        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
310    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
311      usingSphericalGrid, this allows to define the rotated grid coordinates
312      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
313      geographical coordinates according to the inverse of the rotation defined
314      by the Euler angles, so that Coriolis parameter and online-interpolation by
315      exf works with the geographical coordinates on XC/YC/XG/YG.
316      Naturally, this feature does not work with all packages, so some
317      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
318      profiles), because there the coordinates are assumed to be regular
319      spherical grid coordinates.
320    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
321      - introduce isopycnal diffusion coefficient control.
322    o tools/adjoint_options:
323      - additional control vector components.
324    o pkg/mnc: have mnc create marginally meaning full coordinate variables
325      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
326    o pkg/mypackage:
327      - add example of read/write pickup for state-var ;
328      - add entry points to the main code for state-vars diags & write-pickup.
329    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
330      transitions for useExfYearlyFields
331      - add new subroutine that determines the file to read from for
332        use*YearlyFields = .TRUE. and .FALSE.
333      - add a verification experiment to global_with_exf that tests
334        useExfYearlyFields with USE_EXF_INTERPOLATION defined
335    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
336      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
337      subroutines (which could be generated from a template, because they are
338      almost identical), for now they are included in obcs_prescribe_read.F for
339      simplicity
340    o pkg/exf:
341      - add a little more diagnostic to exf_interp_read (in analogy to
342        mds_read_field, can be turned off with debugLevel < debugLevA=1)
343      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
344        ugly but fast by unrolling short inner loops, inserting a unroll=8
345        directive in routine lagran, and splitting a loop and making do while the
346        outermost loop (the latter requires the intoduction of index arrays)
347    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
348    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
349      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
350    o verification/seaice_obcs: updated for restart test and latest options
351    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
352      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
353      for now this is only available for the C-grid code and also within
354      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
355    
356    checkpoint59m
357    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
358      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
359    o gad_som : fix flux output (& diagnostics) to have same units as other  
360      advection scheme fluxes (was previously multiplied by deltaT).  
361    o added verification/seaice_obcs both to test seaice open boundaries
362      and to provide an example matlab scrpt for generating them
363    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
364    o pkg/salt_plume: clean up salt_plume_frac.F to
365      remove redundancy in PlumeMethod 1 and 4
366    o pkg/kpp: added saltplume diagnostics
367    o pkg/obcs and pkg/seaice:
368      - do not set uice and vice to zero when OB*icefile are unspecified
369      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
370      - moved seaice tracer obcs after call to seaice_growth
371    o pkg/salt_plume: added various options for salt plume depth
372      criterion and for vertical distribution of the salt
373    
374    checkpoint59l
375    o pkg/ptracers: new version of ptracers pickup:
376      read meta file and write only fields which are needed to restart.
377      ( same logic as main pickup file ; also using pickupStrictlyMatch )
378    o pkg/seaice:
379      - add timescale for melting due to warm mixed layer as a means of
380        setting SEAICE_availHeatFrac more conveniently
381      - add a CPP-flag/runtime parameter check for flooding algorithm
382      - reformulated availHeat in seaice_growth.F to be independent of AREA
383    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
384      unit changes
385    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
386    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
387      SX vector computer.
388    o pkg/seaice:
389      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
390        seaice forcing fields can now be read only through pkg/exf
391      - removed some unused halos
392    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
393    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
394      or U/VICE from U/VWIND before computing U/VSTRESS
395    
396    checkpoint59k
397    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
398      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
399    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
400      all experiments pass when compile with un-initialised var. checking option.
401    o added pkg/salt_plume
402    o script to test restart (for now, in MITgcm_contrib/jmc_script)
403    o pkg/seaice: new read/write pickup version.
404      read meta file and write only fields which are needed to restart.
405      ( same logic as main pickup file ; also using pickupStrictlyMatch )
406    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
407    o lab_sea.hb87: modify the domain & update output.hb87.txt :
408      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
409      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
410      process. Fixed here by closing the domain at the Northern boundary.
411    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
412    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
413      a set of consecutive levels in/from a 3-D array.
414    o pkg/ptracers:
415      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
416      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
417    
418    checkpoint59j
419    o in pkgs: dic, obcs, offline, rbcs:
420      standard way to compute coeff. for time interpolation between 2 time reccords
421      which retains full precision (& make results less dependent on compiler).
422      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
423    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
424      packages instead of reading ice cover and wind speed separately
425    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
426     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
427      to allow to compile customized code before the update)
428    o cleaning-up:
429      - fix CPP instruction syntax in pkg/obcs
430      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
431        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
432      - fix some threads issue in IO parts.
433    o pkg/dic:
434      - add tons of "_d 0" (--> much better testreports !)
435       and then update outputs of tutorial_global_oce_biogeo
436    o pkg/mom_fluxform:
437      add a special version of momentum advection intended to conserve momentum
438      next to a bathymetry step or a coastline edge. (default = off = #undef)
439    o new read/write pickup version:
440      - for now, only implemented for main (mdsio) pickup file.
441      - write out only what is needed to restart; merge pickup_nh , pickup_ph
442        and main pickup together.
443      - read meta file; read only what is needed to restart; stop if a field
444        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
445        if it make sense (even if the restart is not perfect).
446      - if no meta file, assume that pickup to read corresponds exactly to
447        a pickup that would currently be written.
448      - read pickup written in the old format (until checkpoint59i) if it
449        recognizes an old meta file (no field-list).
450      - add a meta file in exp. which starts from a pickup: 2 cases:
451        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
452         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
453        b) a meta file describing the content of the associated pickup file
454         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
455    o pkg/mdsio & pkg/rw:
456      - new routine to read a meta file ; new set of routine to read
457        Multiple-fields file (with meta file).
458    o added open boundary conditions capability for seaice
459        HSNOW, HSALT, UICE, and VICE
460    
461    checkpoint59i
462    o adjoint:
463      * fix multiDimAdvection adjoint
464        (partial recomputation problem by TAF for fVerT(:,:,kDown)
465        and comlev1 size definition (maxpass vs. max. number of tracers)
466      * verification/global_ocean.90x45x15 adjoint now tests
467        NLFS and multiDimAdvection using DST3 (=30)
468      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
469    o pkg/kpp: add "_d 0" to real constant (if missing);
470      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
471      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
472    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
473      for internal parameters related to restart process (formerly from PARAMS.h)
474      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
475    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
476      as argument. (only atm2d & obcs write_pickup have not yet been updated)
477    o pkg/monitor:
478      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
479      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
480      - account for deep Atmosphere factor and density factor (anelastic)
481    o added open boundary conditions capability for seaice HEFF and AREA
482    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
483      thermodynamics
484      - requires a little reorganization, which affects the testreport results
485        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
486        so that now the conservative form is tested
487      - add a few comments
488    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
489    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
490    o add new diagnostics to seaice: advective, diffusive fluxes (only for
491      multidim-advection, for scheme 2 they are not filled) and transports,
492      thermodynamic growth rates
493    o change units of EmPmR (inside the code, + within coupling interface)
494      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
495      Affects results @ truncation level (cg2d match) and update output of
496       experiments: lab_sea(6), global_ocean.90x40x15(10),
497      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
498      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
499      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
500      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
501    
502    checkpoint59h
503    o pkg/exf:
504      - improve vectorization by moving if-statement out of loops in
505        exf_mapfields, exf_radiation
506      - exf_bulkformulae.F: introduce 2D fields and vectorize code
507    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
508    o testreport:
509      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
510        monitor & update offline_exf_seaice exp. output.
511      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
512    o pkg/seaice:
513      - bug fix in the evp solver: boundary conditions were affected be
514        masking of zMax/zMin (changes results)
515      - minor bug fix in boundary conditions in seaice_calc_strainrates
516        (changes results for no_slip)
517      - seaice_lsr.F: make interpolation of eta dependent on boundaries
518      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
519      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
520        stress formulation and no-slip boundary conditions
521    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
522      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
523    o pkg/seaice: a first HSALT time stepping equation has been checked in
524    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
525      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
526      without requiring DO-IF statements
527    o pkg/thsice:
528      use continuous power-law function for partition of energy between lateral
529      melting/freezing and thinning/thickening ; old code using step function
530      still available with #undef THSICE_FRACEN_POWERLAW
531      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
532    o testreport: change AD testing : check against results/output_adm.txt
533      using same scripts as for forward test.
534    
535    checkpoint59g
536    o adjoint testing: in preparation for changing testreport:
537      - output format: cost and grad written on separated lines
538      - ad output results in directory "results" (instead of "results_ad")
539    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
540    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
541    o pkg/ecco: allow user defined cost function contributions
542    o testreport:
543      Allow to choose (per experiment) the list of tested output variables
544       and the main variable (used to issue a pass/FAIL ) ;
545      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
546      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
547      Also modify printing of summary:
548       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
549       b) echo the list of tested variables in the individual summary.txt of
550          each experiment.
551    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
552      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
553      (but still depend on the tile decompostion of the domain).
554    o pkg/seaice: change a discretization detail to make the B-grid code
555      "more symmetric". This change is likely to remove all "ridges/leads" that
556      where quasi-aligned with the grid in B-grid solutions. It may also be
557      the solution to the stress coupling issues with the B-grid.
558    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
559      remove .cvsignore from input dir. (since testreport no longer run here).
560    o pkg/thsice:
561     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
562     - fix reshaping of sea-ice just after advection:
563       melt all the ice only if ice-volume is too small.
564     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
565       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
566     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
567    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
568      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
569    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
570      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
571      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
572      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
573      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
574      -> update output.txt
575    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
576     this affects truncation error: -> update output.txt of exp:
577      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
578      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
579    
580    checkpoint59f
581    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
582    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
583      a bounded range (in forward mode)
584    o pkg/ecco, ctrl, autodiff and mom_common:
585     internal parameter controls, completements of implementations
586    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
587    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
588      (not seem any difference in testing results).
589    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
590       at face corners.
591    o pkg/generic_advdiff:
592     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
593      loop range indices for computing vertical advection tendency
594      and do the calculation in the interior only (no overlap) ;
595      for now, only implemented for SOM advection (to save CPU time).
596     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
597    o exch2 adjoint
598      First set of changes:
599      - add exch2 hand-written adjoint templates
600      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
601        This will require cleanup in pkg/autodiff/*.F
602        (changed routines currently kept separate in verif. code/)
603      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
604        that used to hide exch2 or cubed-sphere specific code
605        (commented via 'cph-exch2')
606    o pkg/seaice
607      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
608    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
609       output of global_ocean.cs32x15.thsice .
610    
611    checkpoint59e
612    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
613      for B-grid vector (not yet tested) and C-grid vector (<- only used
614      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
615    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
616      (#ifdef ALLOW_SALT_PLUME)
617    o gather_2d/scatter_2d: removed halo regions
618    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
619      scheme and the corresponding test case (under front_relax dir). For now,
620      only available with Skew-flux form and not yet tested in realistic set-up.
621      adjoint: store directives updated, but gradient checks deteriorated,
622      so maybe GM/Redi adjoint is now broken.
623    o seaice adjoint
624      * add AREA, HEFF, HSNOW as control variable
625        (should not change lab_sea results)
626      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
627    o pkg/seaice:
628      * added computation of saltFlux in seaice_growth;
629        For time being, sea ice salinity is assumed constant
630        contribution of snow flooding to freshening of sea ice is neglected.
631        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
632        defaults to 0.0 in order to maintain backward compatibility.
633        Typical values for SEAICE_salinity are 4 to 10 g/kg.
634      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
635      * added SEAICE_availHeatFrac, which specifies fraction of surface level
636        heat content used to melt or grow ice
637      * commented out cap of HICE: it helps keep ice thinner
638      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
639      * applied OBCS T/S mask to HEFFM sea ice mask
640    
641    checkpoint59d
642    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
643     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
644     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
645    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
646     and change default value of parameter "GM_Small_Number";
647     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
648       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
649       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
650    o pkg/ecco: cost function when applying pkg/smooth to controls
651    o pkg/ctrl: add forcingPrecond run time parameter
652    o pkg/seaice:
653     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
654     - fix bug in metric terms of u-equation in LSR solver (implicit part),
655       changes verification/lab_sea
656     - rearrange implicit part of u-equation in LSR solver to make it easier to
657       read, understand, and debug. This causes changes at the truncation level.
658     - fix (serious) bug in the boundary conditions (sign error in the implicit
659       part) of the LSR solver. Changes all LSR results.
660     - fixed problem with HSNOW initialization to avoid thick snow when AREA
661       is initilized with small values - does not change lab_sea results.
662     - added HsnowFile initialization capability
663    o pkg/smooth: addition to model/src and pkg/ctrl so allow
664     initialization of pkg/smooth and application to control vector
665    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
666    o dependencies: pkg/profiles requires pkg/cal
667    o pkg/profiles:
668     - added option ALLOW_PROFILES_GENERICGRID
669         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
670         that interpolation information (grid points and coefficients) is provided
671         within the netcdf input files.
672         -> sample matlab scripts can be found in MITgcm_contrib/gael
673         that allow you to prepare netcdf input files.
674     - also modified: cleaner include statements, cleaner error print statements,
675       cleaner stops when error, and more tests of the netcdf input files consistency.
676    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
677    o pkg/seaice:
678     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
679       requires a new routine: seaice_diagnostics_fill.F
680     - make sure that seaice does not move if not forced (pressure replacement
681       method, Hibler and Ip, 1995), changes results
682     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
683     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
684       It is turned off by default (=-1.), because it changes the results.
685     - make it possible to read AREA from a file, too.
686    
687    checkpoint59c
688    o add S/R and diagnostics for oceanic mixed-layer depth
689    o move GMRedi call after all vertical mixing schemes (including KPP)
690    o pkg/thsice:
691     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
692      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
693    o pkg/obcs:
694     - bug fix for balance code
695    o pkg/seaice:
696      - allow values of SEAICE_elasticParm > 1
697      - add new parameter SEAICE_evpTauRelax as an alternative
698        to SEAICE_elasticParm
699      - make lsr boundary conditions free slip (by default), changes result
700      - add code for no slip boundary conditions for lsr
701      - set minimum of zeta to zero (and not 4e8) (changes results)
702      - add a cap on AREA after advecting AREA if seaice_growth is not called
703    o change calculation of Visbeck K:
704      - no longer depend on tapering scheme; instead, compute slope (limited
705        by GM_maxSlope). this is equivalent to what was comuted before with
706        clipping or linear tappering.
707      - fix vertical averaging (wrong by 1/2 level)
708      - leave the old version (but will not be maintained) within
709        #ifdef OLD_VISBECK_CALC / #endif
710      - update output of exp. ideal_2D_oce
711    o change error catch in calc_r_star to improve vectorization
712    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
713      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
714    o adjoint:
715      Re-organized adjoint checkpointing according to Matt Mazloff
716      (but with modifs/completions/cleanups)
717      Storing is now bundled into large arrays to optimized I/O
718      (and second step in cleanup of the_main_loop)
719    
720    checkpoint59b
721    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
722      - export/import (between ocean & coupler) fields needed for ocean DIC.
723    o pkg/seaice:
724      - get rid of three more exchanges seaice_calc_viscosities (required
725        different loop boundaries in seaice_lsr and seaice_ocean_stress)
726      - bug fix in seaice_ocean_stress (update of lab_sea required)
727      - reduce loop boundaries to necessary minimum also in seaice_evp
728      - go back to the old way of computing deltaC/Z as the adjoint likes that
729        better
730    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
731      passive tracer to an Age Tracer) + update output.txt
732    o pkg/exf:
733      - implement A-grid / C-grid selection for wind-stress input files.
734      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
735      for now, in exf_bulk_largeyeager04.F only :
736      - change implementation for case where windspeed + 2. components wind-stress
737        are read-in. AND use rhoConstFresh to convert evap.
738    o pkg/seaice:
739      - use correct EXCH_UV for wind-forcing (on A-grid).
740      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
741        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
742    o pkg/exf:
743      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
744      EXF_INTERPOLATION:
745      - merge global_with_exf/code version of exf_interp_read.F
746        to the main code ;
747      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
748        reading the file ; Important: This options needs to be defined to recover
749        previous code.
750        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
751      - no longer loose real*8 precision along the way when using exf_iprec=64.
752    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
753      - change discretisation of evp-solver in order to avoid another exchange
754        (changes lab_sea) and clean up a little
755      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
756        help the adjoint (this also changes the results slightly)
757      - add a few "_d 0" where they had been missing in seaice_evp.F
758      - cleaning up: remove unused seaice_calc_rhs.F
759    o pkg/exf: some cleaning-up:
760      - change various "constants" into runtime parameters
761      - cleaned-up Large&Yeager04 routine which should eventually
762        replace exf_bulkformulae.F (changed names of S/R and CPP)
763        and merged various ALLOW_ATM_WIND options
764     only used with thsice pkg (in thsice_get_exf.F):
765      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
766        which are used when useStabilityFct_overIce=TRUE (= the default)
767      - change default values of ice & snow emissivity and scale downward LW
768        by ice & snow emissivity.
769    o pkg/thsice:
770     fix few little problems, in thsice_calc_thickn.F:
771      - growth vertically (and not laterally) if iceFrac == iceMaskMax
772      - melt only laterally if hIce < hThinIce (as the comments say)
773      and in thsice_extend.F:
774      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
775      - start to form ice as soon as the minimum ice-volume is reachable.
776     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
777      and cpl_aim+ocn
778    o pkg/kpp
779     - move computation of surface related input fields to KPP into a new
780       subroutine kpp_forcing_surf.F
781     - remove wrong (within bi,bj loops) EXCH calls.
782     - little cleaning (add argument myThid in last position, cvs header ...)
783     - for now, fix conservation problem by exchanging KPPviscAz (may not
784       be the best fix)
785    o pkg/seaice
786     - check for inconsistent evp parameter/cpp-flag combination
787     - remove leftover errIO flat for obsolete name list error handling
788    o OpenAD
789     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
790    
791    checkpoint59a
792    o pkg/seaice: some parameter clarifications and a little bit of clean up
793    o pkg/thsice: rename run-time parameters:
794       himin       -> hIceMin
795       himin0      -> hThinIce
796       hihig       -> hThickIce
797       i0          -> i0swFrac
798       transCoef   -> bMeltCoef
799       frac_energy -> fracMelting
800      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
801       with default values (for now) that do not change the results.
802      remove old version of thsice vars advection in pkg/seaice.
803    o in FFIELDS.h:
804      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
805      - make pLoad & sIceLoad always available (but still only used if
806         ATMOSPHERIC_LOADING is #define).
807    o pkg/kpp: replaced _KPP_RL with _RL
808    o bug fixes for vertical diffusivity computations when both KPP and
809        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
810        are no longer updating the vertical diffusivity array
811        (passed as argument) but are (re-) setting those arrays.
812    o pkg/seaice: fix bug in evp solver, while doing that
813      - change (improve?) discretization of stress computations for both
814        cgrid-lsr and evp solver
815      - add a new routine to compute strain rates
816      - the above changes lab_sea results
817      - add no slip conditions for evp solver (off by default), lsr-version
818        may follow
819      - fix exchange for shear at Z-points (does not change lab_sea)
820      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
821        (to force the user to pick a time step since there is not "safe" way
822        of choosing it)
823      - add principal stress diagnostics
824      - rearrange fields for evp a little to avoid having to call a: too many
825        exchanges and b: exchanges for stress trensor components which we do
826        not have.
827      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
828        of evp, complete rewrite for lsr case (latter is does not yet work
829        in all cases)
830    o pkg/kpp: add code to have mixing in shelf ice caverns
831      - add myThid to all kpp routines (long overdue)
832    
833    checkpoint59
834    o pkg/exf:
835      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
836        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
837      - move exf header files from lower_case.h to UPPER_CASE.h ;
838        add missing cvs Header & Name
839      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
840      - add namelist param. selectStressGridPosition, exf_monFreq
841      - retire many _CLIM routines, and remove data.exf_clim
842        + params moved to data.exf
843        + climsst, climsss now handled by exf_set_gen, i.e.
844          climss?period=0 refers to constant field,
845          climss?period=-12 to monthly forcing
846      - split up namelists in data.exf
847    o pkg/seaice:
848      - remove seaice_exch and seaice_exch_uv
849      - remove superfluous exchange of theta
850      - add myThid to seaice_budget_ocean/ice
851      - add new interface for atmospheric wind forcing (C-grid only)
852        + new routine
853        + two new field (taux, tauy for stress over ice)
854        + removed one global field (DAIRN) for C-grid case only
855    o pkg/thsise
856      - 2nd set of modifs for thsice adjoint in conjunction with exf
857    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
858    
859    checkpoint58y_post
860    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
861      vertical diffusivity, similar to that in MOM4; turned on using
862      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
863      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
864    o Added capability for 3D specification of background vertical diffusion
865      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
866      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
867      "data" file that contains the 3D vertical diffusivity coefficients.
868    o ice dynamics (pkg/seaice) with thsice thermodynamics:
869      - add code within pkg thsice to advect & diffuse sea-ice fields
870      similar to (and will replace) what has been added in  seaice_advdiff.F,
871      but: - conserving Mass, Heat & Salt.
872           - better when using non-linear advection scheme (not yet fully tested)
873           - can also be used in atmospheric set-up (for now, only the diffusion).
874    
875    checkpoint58x_post
876    o IO option for global-file compact format:
877      - add options when generating topology (utils/exch2/matlab-topology-generator)
878      - add I/O capability (pkg/mdsio).
879      - adapt utils/matlab/rdmds.m to read this format.
880      for now long-line format not yet supported by pkg/mdsio (& exch2).
881    o shelfice: add a few diagnostics
882    
883    checkpoint58w_post
884    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
885      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
886      (and replace horiVertRatio in NH code).
887      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
888                         and tutorial_plume_on_slope (sensitive to truncation)
889    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
890      directly to drive seaice model (C-grid only)
891    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
892     - reintroduce computation of wind from stress,
893     - compute tau (in exf_bulkformulae.F) from windstress averaged to
894       mass points to avoid tau = 0
895     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
896    o rdmnc.m: make it work with "global" files created with gluemnc
897    o rdmnc.m : some improvements in dealing with singleton dimension
898      (tested on all testreport mnc output files).
899    o genmake2: disable pkg/profiles if netcdf test fails.
900    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
901    o move call to cal_readparms up to make calendar parameters/variable available
902      to all packages
903    
904    checkpoint58v_post
905    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
906      useDynP_inEos_Zc tested.
907    o pkg/exf: changes to properly interpolate/mask/scale initial fields
908    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
909      and portions thereof.  See read_cs.txt for description and examples.
910    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
911      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
912      following the great-circle arc between those 2 points.
913    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
914      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
915    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
916     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
917     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
918     - still needs work (not working with some options ; efficiency to improve)
919       and serious testing.
920     - use this scheme for temperature & salinity in 2 advection test exp.:
921       advect_xy & advect_xz, respectively.
922    
923    checkpoint58u_post
924    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
925    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
926    o testreport: add option "-skipdir" to skip some test.
927    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
928      momentum calculation.
929    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
930    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
931      remove checkpoint.F and the_correction_step.F (no longer used);
932      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
933    o add option (linFSConserveTr) to correct for tracer source/sink due to
934      Linear Free surface
935    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
936    o pkg/thsice: fix reading mnc-pickups
937    
938    checkpoint58t_post
939    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
940    o pkg/mdsio:
941     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
942       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
943       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
944     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
945     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
946       either MDS_READ_FIELD or MDS_WRITE_FIELD )
947     - new S/R (to replace MDSWRITEMETA), which allows to write more
948       informations (variable names, time ...) to meta files.
949     - modify rdmds.m to give back the meta file content.
950    o pkg/diagnostics: change vertical interpolation to be safer, and more
951       flexible (define p-levels to interpolate to in data.diagnostics);
952      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
953       diagnostic pointer.
954    o pkg/seaice: more cleaning up of seaice_growth, added many comments
955    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
956    o fix multi-category seaice:
957     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
958       SEAICE_MULTICATEGORY
959     - fix short wave heat flux
960    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
961       and allow to use EVP solver. Change forward lab_sea: test both EVP
962       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
963    o Initial check-in of lab_sea adjoint
964      (very similar to natl_box_adjoint/code_seaice)
965      * used C-grid and EVP solver
966      * used KPP, GM/Redi
967      * uses inAdExact=.TRUE.
968      * gradient checks fail for both ADM and TLM
969        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
970        f.d. gradients actually seem more problematic than ADM, TLM gradients;
971        issue is related to forward mismatch between g77 an ifort
972    o pkg/seaice: overhaul of thermodynamics
973     - growth.F and groatb.F are replaced by new routine seaice_growth.F
974     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
975     - move a few global fields out of SEAICE.h into seaice_growth.F and
976       make them 2D (FICE/QNETO/ ...)
977     - remove FO (it is the same as QNETO)
978     - introduce a few local fields to avoid modifying external fields such
979       as atemp, etc.
980    
981    checkpoint58s_post
982    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
983      changed exf_set_gen.F so that
984        genperiod=0 means input file is one time-constant field and
985        genperiod=-12 means input file contains 12 monthly means
986    o CG2D: use pre-computed solver main-diagonal (stored in common block);
987      this affects truncation error ; generate new output file for exp. which
988      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
989        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
990        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
991        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
992        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
993        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
994    o start implementation of deep-atmosphere and anelastic formulation
995    o verification: remove 2nd copy of input files and use script "prepare_run"
996      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
997    o mom_common/vecinv/fluxform: fix a few initialisation isssues
998    o profiles: fix for multithreaded case
999    
1000    o diagnostics: rename few diags:
1001      s/'PRESSURE'/'RCENTER '/g
1002      s/'TICE    '/'oceFreez'/g
1003      s/'TAUX    '/'oceTAUX '/g
1004      s/'TAUY    '/'oceTAUY '/g
1005      s/'SWFLUX  '/'oceQsw  '/g
1006      s/DIFx/DFxE/g
1007      s/DIFy/DFyE/g
1008      and add few ocean-forcing diagnostics:
1009      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
1010    o modifications to pkg/seaice/growth.F and budget.F, which change results of
1011      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
1012      as actual snow thickness.  It now refers everywhere to effective snow
1013      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
1014    
1015    checkpoint58r_post
1016    o modifications to pkg/seaice/growth.F, which change results of
1017      lab_sea experiment: fixes pertain to melting snow over open water, to
1018      masking EVAP under sea ice, and to using the correct AREA variable for
1019      computations of EVAP, PRECIP, HSNOW, and GHEFF
1020    o add ability to read bathy, salt, and theta using MNC (off by def)
1021    o add flooding algorithm and advection of HSNOW for pkg/seaice;
1022      both are turned off by default and do no change any results
1023    o seaice advection with pkg/thsice: a step toward the use of non-linear
1024      advection scheme, but #ifdef or commented out for now (requires more EXCH).
1025    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
1026      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
1027      in natl_box (affects results @ truncation level: update output.txt)
1028    o multi-threading and IO:
1029      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
1030      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
1031        (needed to work with SingleCpuIO): tested in all verif. exp.
1032    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
1033      affects the results (but none of the verification test uses this scheme).
1034    o Adding some pkg/diagnostics capability to pkg/seaice
1035      (will certainly be subject to changes)
1036    o ctrl: adding new control variables:
1037      lwflux, lwdown, evap, snowprecip, apressure, runoff
1038    
1039    checkpoint58q_post
1040    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
1041      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
1042      high_res_cube configuration by 4% on Columbia.
1043    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
1044      add (in global_with_exf/code) a version of EXF_INTERP_READ without
1045      dynamical allocation (seems to work in multi-threaded).
1046    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
1047      single CPU io) so that TAF does not have to see EESUPPORT.h
1048  o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)  o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
1049    
1050  checkpoint58p_post  checkpoint58p_post
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