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revision 1.729 by jmc, Fri Oct 6 19:44:51 2006 UTC revision 1.1059 by jmc, Sun Feb 1 22:37:40 2009 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/flt:
8     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
9       init_fixed & ini_varia.
10     - clean-up & simplify linear interpolation S/R:
11       move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
12     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
13    o pkg/ggl90: a few modifications:
14     - fix bottom boundary condition, and interpolation of KappaE
15       near top and bottom
16     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
17     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
18     - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
19    o rename thetaMin,phiMin -> xgOrigin,ygOrigin
20      (maintain temporary backward compatibility, until next checkpoint)
21    
22    checkpoint61h
23    o pkg/diagnostics with "periodic averaging diagnostics":
24      fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
25    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
26    o pkg/obcs: fix loop ranges for balancing code
27    o pkg/flt:
28     - improve criteria for finding which tile owns a float.
29     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
30    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
31      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
32      with ocean biogeo)
33    o pkg/flt:
34     - do some cleaning and fix the restart ;
35     - add output.txt in flt_example/results to get this pkg tested.
36    o genmake2: add an EXTENDED_SRC option and flag.
37       for now, cannot be turned on on command line (only through genmake_local)
38    o pkg/mdsio: read/write vector:
39     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
40     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
41       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
42     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
43      (drop to 4 digits matching for grad). But this test does not look very
44      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
45    
46    checkpoint61g
47    o pkg/flt:
48      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
49       + make OPTIONS file more standard.
50      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
51      - fix _BYTESWAPIO CPP-Flag
52      - standard reading of file-parameter "data.flt"
53      - fix argument list of S/R FLT_RESTART
54      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
55    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
56    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
57      a still unfixed compiler/optimization bug
58    
59    checkpoint61f
60    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
61      update results of global_ocean.cs32x15.icedyn test.
62    o move getcon.F from model/src to pkg/fizhi.
63    o pkg/exf: add parameter for extrapolation of temp up to the surface
64       and option to prevent negative evap (in bulk_largeyeager04 only).
65    o Prather Advection scheme: fix tracer conservation for divergent flow
66      (e.g., when using NonLin Free-Surface).
67    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
68    o gmredi (Visbeck-variable-K):
69     - add more parameters to Visbeck-variable-K.
70     - use a 5 points average for dSigmaR in Visbeck-K calculation
71       (more "homogenous": same stencil and same weights as in dSigmaH)
72     - update output of ideal_2D_oce experiment.
73    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
74      (#undef REAL4_IS_SLOW)
75     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
76       coordinate variable
77     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
78       (surface forcing fields), removes some of the functionality
79     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
80     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
81       probably not all: copy _RS surface flux fields to RL field before
82       calling DIAGNOSTICS_FILL
83     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
84       real*4 (CALL EXCH_*_RS) versions.
85     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
86       (generate new output).
87    
88    checkpoint61e
89    o gmredi (Visbeck-variable-K):
90      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
91      - change computation of Visbeck-K where Slope > Smax :        
92        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
93        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
94    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
95      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
96    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
97    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
98      does not become too large (to avoid precision problems in implicit-diffusion
99      solver); update ideal_2D_oce output.
100    o pkg ggl90:
101      - in ggl90_cal.F: compute only one set of visc/diff, used to
102        step forward TKE/T/S/momentum
103      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
104        have Prandlt =1)
105    o gmredi (fm07):
106      - add lower limit on Transition layer thickness + lower limit on 1/lambda
107      - allow to set few more params from data.gmredi
108    o pkg ggl90:
109          - add missing sqrt(2) factor in computation of mixing length
110            scale in ggl90_calc.F
111            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
112    
113    checkpoint61d
114    o adjoint modifs
115      - adapt to new field rhoInSitu
116      - allow to revert from StoreDynVars2D, StoreDynVars3D
117        to individual fields
118        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
119    o store 3-D (in-situ) density in commom block (DYNVARS.h)
120     - save 1 rho computation.
121     - no longer modify T & S inland when using down_slope pkg.
122    o gad_som : allow to switch to SOM advection for T & S without corresponding
123      pickup files (using new S/R: MDS_CHECK4FILE).
124    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
125      (for useSingleCpuIO to work in multi-threaded)
126    o pkg/shelfice:
127     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
128       with SHELFICEtopoFile in data.shelfice
129     - move code for reading ice shelf topography and modifying hFacC into separate
130       subroutines of the shelfice package
131     - separate initialisation of "fixed" and "variable" variables
132     - kTopC is not (yet) replaced by kSurfC, although this is possible
133    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
134    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
135      and rename:
136      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
137      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
138    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
139    
140    checkpoint61c
141    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
142      to add mass source/sink of fluid in the interior (3-D generalisation
143      of oceanic real-fresh water flux).
144    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
145    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
146    o new pkg: down_slope
147      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
148      - presently, modify T & S inland (dwnslp_calc_rho.F).
149        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
150      - implementation for ocean in P-coords not tested.
151      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
152    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
153      (to facilitate conversion of oceanic pkg to p-coordinate).
154    o change FIND_RHO to FIND_RHO_2D :
155      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
156    o new pkg: cheapaml
157    
158    checkpoint61b
159    o exch2:
160      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
161      - no longer depend on the order sequence (N,S,E,W).
162      - 3rd exchange no longer needed (tested with 24 tiles).
163      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
164      - exch_UV_A-grid readily available (but not yet tested).
165      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
166      (both are no longer needed) in exch_uv: no effect in forward run; but
167       get truncation error differences with adjoint exch.
168    o exch2:
169     - change index-bounds storage (moved from target to local tile,
170       more intuitive this way) ; rename/remove some variables.
171     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
172    
173    checkpoint61a
174    o exch2/matlab-topology-generator:
175      fix bug in index bounds for N-S internal exchange (hard to tell if this
176      had any effect on the solution).
177    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
178      is exceeded
179    o testreport: modify syntax of awk, so that it works also with
180      awk, and not only with nawk and gawk
181    
182    checkpoint61
183    o autodiff
184      Change default for TAF usage by removing argument '-nonew_arg'
185      This changes TAF subroutine argument list (ordering of active var.)
186      Omission of this flag leads to incompatibility w.r.t. TAMC
187      To restore TAMC-compatibility, need following modifs:
188      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
189      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
190      Tested TAF version is 1.9.22
191      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
192    
193    checkpoint60
194    --->>> This is the last checkpoint for which generating the adjoint
195    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
196    --->>> by default.
197    --->>> Future checkpoints will ommit this flag by default.
198    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
199    o pkg/grdchk: Add gradient check to etan0 perturbations.
200    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
201    o pkg/autodiff: more flexibility in zeroadj.
202      model/src: modifying do_oceanic_phys.F accordingly.
203    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
204    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
205      special setup of gmredi for which the adjoint is stable
206      enough for parameter optimization.
207    o bridging the gap between eddy stress and GM.
208      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
209          along with a change in CPP option (now ALLOW_EDDYPSI).
210      -> when using GM w/ GM_AdvForm:
211          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
212          is applied either in the tracer Eq. or in momentum Eq.
213          depending on data.gmredi (intro. GM_InMomAsStress).
214      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
215      The key modifications are in model/src/taueddy_external_forcing.F
216      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
217    
218    checkpoint59r
219    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
220      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
221      fix option to read coriolis(@ cell-corner) from files with CS-grid.
222    o pkg/mnc: add some attributes to standard 1D-coordinate variables
223    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
224      mass points, when using mnc for output
225      - add runtime parameter (missing_value, missing_value_int) to override
226        default (which is the value of getcon('UNDEF'))
227    o pkg/mnc: prepare mnc for the actual use of missing values with the
228      diagnostics package: small fix in mnc_cw_readwrite.template and more
229      initialisation of never used fields
230      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
231      versions
232    o pkg/thsice/thsice_ini_vars.F added default initial values so that
233      thermodynamics sea ice solver does not blow up when some initial fields
234      are missing.
235    o move from external_forcing_surf.F to ini_forcing.F
236      the p-coord. hack consisting in using pLoad to set phi0surf ;
237      update output of tutorial_global_oce_in_p (affected @ truncation level).
238    o Freshen up a bit hs94.1x64x5, notably:
239      remove rotationPeriod and tRef=5*0. (adjoint only), and add
240      exactConserv=.TRUE.
241    o pkg/generic_advdiff:
242      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
243      applies to files where Temperature & Salinity 2nd Order moments are used.
244    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
245      this uses a dynamically allocated internal state data structure
246      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
247      and requires a fortran 90 compiler
248    
249    checkpoint59q
250    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
251       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
252    o Refresh tutorial_global_oce_biogeo, notably:
253      - change bathymetry (put back seamounts in ACC, use hFacs)
254      - change EOS (POLY3 --> JMD95Z)
255      - use Bryan-Lewis vertical diffusivity
256      - use multidimensional advection
257      - remove old virtual virtual in dic pkg, now done through ptracer pkg
258      - change a couple of parameters in dic pkg
259    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
260    o pkg/obcs: change default to OBCSfixTopo = .true.,
261      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
262      - replace "debugMode" with "debugLevel .GE. debLevB"
263    o implementation of TAF directives for gchem,cfc,dic
264    o remove "exp5" (replaced by tutorial_deep_convection).
265    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
266      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
267      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
268      --> changes results in exp4, seaice_obcs
269    o tutorial_deep_convection :
270      update the set-up and increase resolution and domain size ; start
271      from pseudo initial conditions = output at t=120mn in order to see
272      something happening when running testreport.
273    o pkg/seaice: add os7mp as an advection scheme
274                  add check for advection schemes
275                  add a flag for restoring T and S underneath sea ice
276    o pkg/my82: add netcdf-support and diagnostics
277    o thsice pkg:
278      - Now hsMax limits snow height by turning it into ice following
279        flooding scheme (and now conserving energy)
280      - Slight rewriting of the formula in thsice_calc_thick.F
281      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
282      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
283    
284    checkpoint59p
285    o gchem / dic / cfc :
286      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
287      - add new parameter files: "data.dic" & "data.cfc" ;
288      - various re-arrangement in initialisation & header file ;
289      - fix tutorial_global_oce_biogeo for multi-threaded test.
290    o pkg/dic: test for "pickup_dic" file when restarting ;
291      if no pickup-file, can restart with a re-initialised pH (same as it did
292      before) providing pickupStrictlyMatch is set to False.
293    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
294      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
295    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
296      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
297    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
298     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
299       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
300    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
301       scheme to use for vorticty-term ;
302     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
303       (with default selectVortScheme, return to original discretisation)
304     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
305    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
306    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
307      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
308      also fix diagnostics VISCAHW & VISCA4W.
309    
310    checkpoint59o
311    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
312    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
313      move a few statemens out the main loop into separate loops
314    o pkg/shelfice:
315      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
316        (kg/m^2/s), does not break tests, because in verification/isomip,
317        rhoConstFresh=rhoConst (by accident)
318      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
319      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
320        new file model/src/seawater.F, so that they are available for all pkgs.
321      - convert potential temperature into in-situ temperature. This changes the
322        isomip tests => update tests
323    o add a flag writePickupAtEnd (default=true) to be able to suppress
324      writing a pickup at the last timestep
325    o tools/mpack-1.6 :
326      - disable automake (not working) and autoconf (not needed).
327      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
328        also cleaner with much less compilation warnings.
329    o pkg/profiles:
330      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
331      (for "less than 32 characters name" compiler requirement)
332    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
333      conditions that have a different sampling frequency than S/T/U/V obcs
334    o pkg/diagnostics (stats-diags):
335      - fix global Min/Max in case 1 processor get only empty tiles
336    o genmake2: replace (4 times)
337         make genmake_tc_1.o >> genmake_warnings 2>&1
338      with
339         COMM="$CC $CFLAGS -c genmake_tc_1.c"
340         echo $COMM >> genmake_warnings
341         $COMM >> genmake_warnings 2>&1
342      to make genmake2 always see the value of CC as specified in the optfile.
343    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
344      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
345      - modify verification advect_cs test to test SOM-advection on CS-grid.
346    o pkg/ctrl:
347      - Rewrite of ctrl_map_ini_ecco.F,
348        introducing a generic routine (ctrl_map_ini_gen.F).
349      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
350    
351    checkpoint59n
352    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
353      number in dedicate array "hdiag":
354      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
355        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
356      - many small changes (integer format) for large number of diagnostics
357      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
358        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
359    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
360      usingSphericalGrid, this allows to define the rotated grid coordinates
361      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
362      geographical coordinates according to the inverse of the rotation defined
363      by the Euler angles, so that Coriolis parameter and online-interpolation by
364      exf works with the geographical coordinates on XC/YC/XG/YG.
365      Naturally, this feature does not work with all packages, so some
366      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
367      profiles), because there the coordinates are assumed to be regular
368      spherical grid coordinates.
369    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
370      - introduce isopycnal diffusion coefficient control.
371    o tools/adjoint_options:
372      - additional control vector components.
373    o pkg/mnc: have mnc create marginally meaning full coordinate variables
374      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
375    o pkg/mypackage:
376      - add example of read/write pickup for state-var ;
377      - add entry points to the main code for state-vars diags & write-pickup.
378    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
379      transitions for useExfYearlyFields
380      - add new subroutine that determines the file to read from for
381        use*YearlyFields = .TRUE. and .FALSE.
382      - add a verification experiment to global_with_exf that tests
383        useExfYearlyFields with USE_EXF_INTERPOLATION defined
384    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
385      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
386      subroutines (which could be generated from a template, because they are
387      almost identical), for now they are included in obcs_prescribe_read.F for
388      simplicity
389    o pkg/exf:
390      - add a little more diagnostic to exf_interp_read (in analogy to
391        mds_read_field, can be turned off with debugLevel < debugLevA=1)
392      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
393        ugly but fast by unrolling short inner loops, inserting a unroll=8
394        directive in routine lagran, and splitting a loop and making do while the
395        outermost loop (the latter requires the intoduction of index arrays)
396    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
397    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
398      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
399    o verification/seaice_obcs: updated for restart test and latest options
400    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
401      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
402      for now this is only available for the C-grid code and also within
403      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
404    
405    checkpoint59m
406    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
407      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
408    o gad_som : fix flux output (& diagnostics) to have same units as other  
409      advection scheme fluxes (was previously multiplied by deltaT).  
410    o added verification/seaice_obcs both to test seaice open boundaries
411      and to provide an example matlab scrpt for generating them
412    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
413    o pkg/salt_plume: clean up salt_plume_frac.F to
414      remove redundancy in PlumeMethod 1 and 4
415    o pkg/kpp: added saltplume diagnostics
416    o pkg/obcs and pkg/seaice:
417      - do not set uice and vice to zero when OB*icefile are unspecified
418      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
419      - moved seaice tracer obcs after call to seaice_growth
420    o pkg/salt_plume: added various options for salt plume depth
421      criterion and for vertical distribution of the salt
422    
423    checkpoint59l
424    o pkg/ptracers: new version of ptracers pickup:
425      read meta file and write only fields which are needed to restart.
426      ( same logic as main pickup file ; also using pickupStrictlyMatch )
427    o pkg/seaice:
428      - add timescale for melting due to warm mixed layer as a means of
429        setting SEAICE_availHeatFrac more conveniently
430      - add a CPP-flag/runtime parameter check for flooding algorithm
431      - reformulated availHeat in seaice_growth.F to be independent of AREA
432    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
433      unit changes
434    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
435    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
436      SX vector computer.
437    o pkg/seaice:
438      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
439        seaice forcing fields can now be read only through pkg/exf
440      - removed some unused halos
441    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
442    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
443      or U/VICE from U/VWIND before computing U/VSTRESS
444    
445    checkpoint59k
446    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
447      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
448    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
449      all experiments pass when compile with un-initialised var. checking option.
450    o added pkg/salt_plume
451    o script to test restart (for now, in MITgcm_contrib/jmc_script)
452    o pkg/seaice: new read/write pickup version.
453      read meta file and write only fields which are needed to restart.
454      ( same logic as main pickup file ; also using pickupStrictlyMatch )
455    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
456    o lab_sea.hb87: modify the domain & update output.hb87.txt :
457      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
458      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
459      process. Fixed here by closing the domain at the Northern boundary.
460    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
461    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
462      a set of consecutive levels in/from a 3-D array.
463    o pkg/ptracers:
464      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
465      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
466    
467    checkpoint59j
468    o in pkgs: dic, obcs, offline, rbcs:
469      standard way to compute coeff. for time interpolation between 2 time reccords
470      which retains full precision (& make results less dependent on compiler).
471      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
472    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
473      packages instead of reading ice cover and wind speed separately
474    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
475     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
476      to allow to compile customized code before the update)
477    o cleaning-up:
478      - fix CPP instruction syntax in pkg/obcs
479      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
480        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
481      - fix some threads issue in IO parts.
482    o pkg/dic:
483      - add tons of "_d 0" (--> much better testreports !)
484       and then update outputs of tutorial_global_oce_biogeo
485    o pkg/mom_fluxform:
486      add a special version of momentum advection intended to conserve momentum
487      next to a bathymetry step or a coastline edge. (default = off = #undef)
488    o new read/write pickup version:
489      - for now, only implemented for main (mdsio) pickup file.
490      - write out only what is needed to restart; merge pickup_nh , pickup_ph
491        and main pickup together.
492      - read meta file; read only what is needed to restart; stop if a field
493        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
494        if it make sense (even if the restart is not perfect).
495      - if no meta file, assume that pickup to read corresponds exactly to
496        a pickup that would currently be written.
497      - read pickup written in the old format (until checkpoint59i) if it
498        recognizes an old meta file (no field-list).
499      - add a meta file in exp. which starts from a pickup: 2 cases:
500        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
501         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
502        b) a meta file describing the content of the associated pickup file
503         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
504    o pkg/mdsio & pkg/rw:
505      - new routine to read a meta file ; new set of routine to read
506        Multiple-fields file (with meta file).
507    o added open boundary conditions capability for seaice
508        HSNOW, HSALT, UICE, and VICE
509    
510    checkpoint59i
511    o adjoint:
512      * fix multiDimAdvection adjoint
513        (partial recomputation problem by TAF for fVerT(:,:,kDown)
514        and comlev1 size definition (maxpass vs. max. number of tracers)
515      * verification/global_ocean.90x45x15 adjoint now tests
516        NLFS and multiDimAdvection using DST3 (=30)
517      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
518    o pkg/kpp: add "_d 0" to real constant (if missing);
519      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
520      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
521    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
522      for internal parameters related to restart process (formerly from PARAMS.h)
523      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
524    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
525      as argument. (only atm2d & obcs write_pickup have not yet been updated)
526    o pkg/monitor:
527      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
528      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
529      - account for deep Atmosphere factor and density factor (anelastic)
530    o added open boundary conditions capability for seaice HEFF and AREA
531    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
532      thermodynamics
533      - requires a little reorganization, which affects the testreport results
534        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
535        so that now the conservative form is tested
536      - add a few comments
537    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
538    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
539    o add new diagnostics to seaice: advective, diffusive fluxes (only for
540      multidim-advection, for scheme 2 they are not filled) and transports,
541      thermodynamic growth rates
542    o change units of EmPmR (inside the code, + within coupling interface)
543      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
544      Affects results @ truncation level (cg2d match) and update output of
545       experiments: lab_sea(6), global_ocean.90x40x15(10),
546      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
547      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
548      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
549      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
550    
551    checkpoint59h
552    o pkg/exf:
553      - improve vectorization by moving if-statement out of loops in
554        exf_mapfields, exf_radiation
555      - exf_bulkformulae.F: introduce 2D fields and vectorize code
556    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
557    o testreport:
558      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
559        monitor & update offline_exf_seaice exp. output.
560      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
561    o pkg/seaice:
562      - bug fix in the evp solver: boundary conditions were affected be
563        masking of zMax/zMin (changes results)
564      - minor bug fix in boundary conditions in seaice_calc_strainrates
565        (changes results for no_slip)
566      - seaice_lsr.F: make interpolation of eta dependent on boundaries
567      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
568      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
569        stress formulation and no-slip boundary conditions
570    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
571      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
572    o pkg/seaice: a first HSALT time stepping equation has been checked in
573    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
574      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
575      without requiring DO-IF statements
576    o pkg/thsice:
577      use continuous power-law function for partition of energy between lateral
578      melting/freezing and thinning/thickening ; old code using step function
579      still available with #undef THSICE_FRACEN_POWERLAW
580      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
581    o testreport: change AD testing : check against results/output_adm.txt
582      using same scripts as for forward test.
583    
584    checkpoint59g
585    o adjoint testing: in preparation for changing testreport:
586      - output format: cost and grad written on separated lines
587      - ad output results in directory "results" (instead of "results_ad")
588    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
589    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
590    o pkg/ecco: allow user defined cost function contributions
591    o testreport:
592      Allow to choose (per experiment) the list of tested output variables
593       and the main variable (used to issue a pass/FAIL ) ;
594      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
595      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
596      Also modify printing of summary:
597       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
598       b) echo the list of tested variables in the individual summary.txt of
599          each experiment.
600    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
601      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
602      (but still depend on the tile decompostion of the domain).
603    o pkg/seaice: change a discretization detail to make the B-grid code
604      "more symmetric". This change is likely to remove all "ridges/leads" that
605      where quasi-aligned with the grid in B-grid solutions. It may also be
606      the solution to the stress coupling issues with the B-grid.
607    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
608      remove .cvsignore from input dir. (since testreport no longer run here).
609    o pkg/thsice:
610     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
611     - fix reshaping of sea-ice just after advection:
612       melt all the ice only if ice-volume is too small.
613     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
614       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
615     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
616    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
617      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
618    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
619      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
620      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
621      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
622      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
623      -> update output.txt
624    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
625     this affects truncation error: -> update output.txt of exp:
626      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
627      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
628    
629    checkpoint59f
630    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
631    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
632      a bounded range (in forward mode)
633    o pkg/ecco, ctrl, autodiff and mom_common:
634     internal parameter controls, completements of implementations
635    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
636    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
637      (not seem any difference in testing results).
638    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
639       at face corners.
640    o pkg/generic_advdiff:
641     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
642      loop range indices for computing vertical advection tendency
643      and do the calculation in the interior only (no overlap) ;
644      for now, only implemented for SOM advection (to save CPU time).
645     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
646    o exch2 adjoint
647      First set of changes:
648      - add exch2 hand-written adjoint templates
649      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
650        This will require cleanup in pkg/autodiff/*.F
651        (changed routines currently kept separate in verif. code/)
652      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
653        that used to hide exch2 or cubed-sphere specific code
654        (commented via 'cph-exch2')
655    o pkg/seaice
656      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
657    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
658       output of global_ocean.cs32x15.thsice .
659    
660    checkpoint59e
661    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
662      for B-grid vector (not yet tested) and C-grid vector (<- only used
663      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
664    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
665      (#ifdef ALLOW_SALT_PLUME)
666    o gather_2d/scatter_2d: removed halo regions
667    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
668      scheme and the corresponding test case (under front_relax dir). For now,
669      only available with Skew-flux form and not yet tested in realistic set-up.
670      adjoint: store directives updated, but gradient checks deteriorated,
671      so maybe GM/Redi adjoint is now broken.
672    o seaice adjoint
673      * add AREA, HEFF, HSNOW as control variable
674        (should not change lab_sea results)
675      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
676    o pkg/seaice:
677      * added computation of saltFlux in seaice_growth;
678        For time being, sea ice salinity is assumed constant
679        contribution of snow flooding to freshening of sea ice is neglected.
680        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
681        defaults to 0.0 in order to maintain backward compatibility.
682        Typical values for SEAICE_salinity are 4 to 10 g/kg.
683      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
684      * added SEAICE_availHeatFrac, which specifies fraction of surface level
685        heat content used to melt or grow ice
686      * commented out cap of HICE: it helps keep ice thinner
687      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
688      * applied OBCS T/S mask to HEFFM sea ice mask
689    
690    checkpoint59d
691    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
692     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
693     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
694    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
695     and change default value of parameter "GM_Small_Number";
696     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
697       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
698       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
699    o pkg/ecco: cost function when applying pkg/smooth to controls
700    o pkg/ctrl: add forcingPrecond run time parameter
701    o pkg/seaice:
702     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
703     - fix bug in metric terms of u-equation in LSR solver (implicit part),
704       changes verification/lab_sea
705     - rearrange implicit part of u-equation in LSR solver to make it easier to
706       read, understand, and debug. This causes changes at the truncation level.
707     - fix (serious) bug in the boundary conditions (sign error in the implicit
708       part) of the LSR solver. Changes all LSR results.
709     - fixed problem with HSNOW initialization to avoid thick snow when AREA
710       is initilized with small values - does not change lab_sea results.
711     - added HsnowFile initialization capability
712    o pkg/smooth: addition to model/src and pkg/ctrl so allow
713     initialization of pkg/smooth and application to control vector
714    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
715    o dependencies: pkg/profiles requires pkg/cal
716    o pkg/profiles:
717     - added option ALLOW_PROFILES_GENERICGRID
718         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
719         that interpolation information (grid points and coefficients) is provided
720         within the netcdf input files.
721         -> sample matlab scripts can be found in MITgcm_contrib/gael
722         that allow you to prepare netcdf input files.
723     - also modified: cleaner include statements, cleaner error print statements,
724       cleaner stops when error, and more tests of the netcdf input files consistency.
725    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
726    o pkg/seaice:
727     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
728       requires a new routine: seaice_diagnostics_fill.F
729     - make sure that seaice does not move if not forced (pressure replacement
730       method, Hibler and Ip, 1995), changes results
731     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
732     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
733       It is turned off by default (=-1.), because it changes the results.
734     - make it possible to read AREA from a file, too.
735    
736    checkpoint59c
737    o add S/R and diagnostics for oceanic mixed-layer depth
738    o move GMRedi call after all vertical mixing schemes (including KPP)
739    o pkg/thsice:
740     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
741      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
742    o pkg/obcs:
743     - bug fix for balance code
744    o pkg/seaice:
745      - allow values of SEAICE_elasticParm > 1
746      - add new parameter SEAICE_evpTauRelax as an alternative
747        to SEAICE_elasticParm
748      - make lsr boundary conditions free slip (by default), changes result
749      - add code for no slip boundary conditions for lsr
750      - set minimum of zeta to zero (and not 4e8) (changes results)
751      - add a cap on AREA after advecting AREA if seaice_growth is not called
752    o change calculation of Visbeck K:
753      - no longer depend on tapering scheme; instead, compute slope (limited
754        by GM_maxSlope). this is equivalent to what was comuted before with
755        clipping or linear tappering.
756      - fix vertical averaging (wrong by 1/2 level)
757      - leave the old version (but will not be maintained) within
758        #ifdef OLD_VISBECK_CALC / #endif
759      - update output of exp. ideal_2D_oce
760    o change error catch in calc_r_star to improve vectorization
761    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
762      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
763    o adjoint:
764      Re-organized adjoint checkpointing according to Matt Mazloff
765      (but with modifs/completions/cleanups)
766      Storing is now bundled into large arrays to optimized I/O
767      (and second step in cleanup of the_main_loop)
768    
769    checkpoint59b
770    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
771      - export/import (between ocean & coupler) fields needed for ocean DIC.
772    o pkg/seaice:
773      - get rid of three more exchanges seaice_calc_viscosities (required
774        different loop boundaries in seaice_lsr and seaice_ocean_stress)
775      - bug fix in seaice_ocean_stress (update of lab_sea required)
776      - reduce loop boundaries to necessary minimum also in seaice_evp
777      - go back to the old way of computing deltaC/Z as the adjoint likes that
778        better
779    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
780      passive tracer to an Age Tracer) + update output.txt
781    o pkg/exf:
782      - implement A-grid / C-grid selection for wind-stress input files.
783      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
784      for now, in exf_bulk_largeyeager04.F only :
785      - change implementation for case where windspeed + 2. components wind-stress
786        are read-in. AND use rhoConstFresh to convert evap.
787    o pkg/seaice:
788      - use correct EXCH_UV for wind-forcing (on A-grid).
789      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
790        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
791    o pkg/exf:
792      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
793      EXF_INTERPOLATION:
794      - merge global_with_exf/code version of exf_interp_read.F
795        to the main code ;
796      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
797        reading the file ; Important: This options needs to be defined to recover
798        previous code.
799        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
800      - no longer loose real*8 precision along the way when using exf_iprec=64.
801    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
802      - change discretisation of evp-solver in order to avoid another exchange
803        (changes lab_sea) and clean up a little
804      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
805        help the adjoint (this also changes the results slightly)
806      - add a few "_d 0" where they had been missing in seaice_evp.F
807      - cleaning up: remove unused seaice_calc_rhs.F
808    o pkg/exf: some cleaning-up:
809      - change various "constants" into runtime parameters
810      - cleaned-up Large&Yeager04 routine which should eventually
811        replace exf_bulkformulae.F (changed names of S/R and CPP)
812        and merged various ALLOW_ATM_WIND options
813     only used with thsice pkg (in thsice_get_exf.F):
814      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
815        which are used when useStabilityFct_overIce=TRUE (= the default)
816      - change default values of ice & snow emissivity and scale downward LW
817        by ice & snow emissivity.
818    o pkg/thsice:
819     fix few little problems, in thsice_calc_thickn.F:
820      - growth vertically (and not laterally) if iceFrac == iceMaskMax
821      - melt only laterally if hIce < hThinIce (as the comments say)
822      and in thsice_extend.F:
823      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
824      - start to form ice as soon as the minimum ice-volume is reachable.
825     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
826      and cpl_aim+ocn
827    o pkg/kpp
828     - move computation of surface related input fields to KPP into a new
829       subroutine kpp_forcing_surf.F
830     - remove wrong (within bi,bj loops) EXCH calls.
831     - little cleaning (add argument myThid in last position, cvs header ...)
832     - for now, fix conservation problem by exchanging KPPviscAz (may not
833       be the best fix)
834    o pkg/seaice
835     - check for inconsistent evp parameter/cpp-flag combination
836     - remove leftover errIO flat for obsolete name list error handling
837    o OpenAD
838     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
839    
840    checkpoint59a
841    o pkg/seaice: some parameter clarifications and a little bit of clean up
842    o pkg/thsice: rename run-time parameters:
843       himin       -> hIceMin
844       himin0      -> hThinIce
845       hihig       -> hThickIce
846       i0          -> i0swFrac
847       transCoef   -> bMeltCoef
848       frac_energy -> fracMelting
849      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
850       with default values (for now) that do not change the results.
851      remove old version of thsice vars advection in pkg/seaice.
852    o in FFIELDS.h:
853      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
854      - make pLoad & sIceLoad always available (but still only used if
855         ATMOSPHERIC_LOADING is #define).
856    o pkg/kpp: replaced _KPP_RL with _RL
857    o bug fixes for vertical diffusivity computations when both KPP and
858        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
859        are no longer updating the vertical diffusivity array
860        (passed as argument) but are (re-) setting those arrays.
861    o pkg/seaice: fix bug in evp solver, while doing that
862      - change (improve?) discretization of stress computations for both
863        cgrid-lsr and evp solver
864      - add a new routine to compute strain rates
865      - the above changes lab_sea results
866      - add no slip conditions for evp solver (off by default), lsr-version
867        may follow
868      - fix exchange for shear at Z-points (does not change lab_sea)
869      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
870        (to force the user to pick a time step since there is not "safe" way
871        of choosing it)
872      - add principal stress diagnostics
873      - rearrange fields for evp a little to avoid having to call a: too many
874        exchanges and b: exchanges for stress trensor components which we do
875        not have.
876      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
877        of evp, complete rewrite for lsr case (latter is does not yet work
878        in all cases)
879    o pkg/kpp: add code to have mixing in shelf ice caverns
880      - add myThid to all kpp routines (long overdue)
881    
882    checkpoint59
883    o pkg/exf:
884      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
885        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
886      - move exf header files from lower_case.h to UPPER_CASE.h ;
887        add missing cvs Header & Name
888      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
889      - add namelist param. selectStressGridPosition, exf_monFreq
890      - retire many _CLIM routines, and remove data.exf_clim
891        + params moved to data.exf
892        + climsst, climsss now handled by exf_set_gen, i.e.
893          climss?period=0 refers to constant field,
894          climss?period=-12 to monthly forcing
895      - split up namelists in data.exf
896    o pkg/seaice:
897      - remove seaice_exch and seaice_exch_uv
898      - remove superfluous exchange of theta
899      - add myThid to seaice_budget_ocean/ice
900      - add new interface for atmospheric wind forcing (C-grid only)
901        + new routine
902        + two new field (taux, tauy for stress over ice)
903        + removed one global field (DAIRN) for C-grid case only
904    o pkg/thsise
905      - 2nd set of modifs for thsice adjoint in conjunction with exf
906    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
907    
908    checkpoint58y_post
909    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
910      vertical diffusivity, similar to that in MOM4; turned on using
911      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
912      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
913    o Added capability for 3D specification of background vertical diffusion
914      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
915      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
916      "data" file that contains the 3D vertical diffusivity coefficients.
917    o ice dynamics (pkg/seaice) with thsice thermodynamics:
918      - add code within pkg thsice to advect & diffuse sea-ice fields
919      similar to (and will replace) what has been added in  seaice_advdiff.F,
920      but: - conserving Mass, Heat & Salt.
921           - better when using non-linear advection scheme (not yet fully tested)
922           - can also be used in atmospheric set-up (for now, only the diffusion).
923    
924    checkpoint58x_post
925    o IO option for global-file compact format:
926      - add options when generating topology (utils/exch2/matlab-topology-generator)
927      - add I/O capability (pkg/mdsio).
928      - adapt utils/matlab/rdmds.m to read this format.
929      for now long-line format not yet supported by pkg/mdsio (& exch2).
930    o shelfice: add a few diagnostics
931    
932    checkpoint58w_post
933    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
934      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
935      (and replace horiVertRatio in NH code).
936      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
937                         and tutorial_plume_on_slope (sensitive to truncation)
938    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
939      directly to drive seaice model (C-grid only)
940    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
941     - reintroduce computation of wind from stress,
942     - compute tau (in exf_bulkformulae.F) from windstress averaged to
943       mass points to avoid tau = 0
944     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
945    o rdmnc.m: make it work with "global" files created with gluemnc
946    o rdmnc.m : some improvements in dealing with singleton dimension
947      (tested on all testreport mnc output files).
948    o genmake2: disable pkg/profiles if netcdf test fails.
949    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
950    o move call to cal_readparms up to make calendar parameters/variable available
951      to all packages
952    
953    checkpoint58v_post
954    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
955      useDynP_inEos_Zc tested.
956    o pkg/exf: changes to properly interpolate/mask/scale initial fields
957    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
958      and portions thereof.  See read_cs.txt for description and examples.
959    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
960      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
961      following the great-circle arc between those 2 points.
962    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
963      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
964    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
965     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
966     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
967     - still needs work (not working with some options ; efficiency to improve)
968       and serious testing.
969     - use this scheme for temperature & salinity in 2 advection test exp.:
970       advect_xy & advect_xz, respectively.
971    
972    checkpoint58u_post
973    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
974    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
975    o testreport: add option "-skipdir" to skip some test.
976    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
977      momentum calculation.
978    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
979    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
980      remove checkpoint.F and the_correction_step.F (no longer used);
981      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
982    o add option (linFSConserveTr) to correct for tracer source/sink due to
983      Linear Free surface
984    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
985    o pkg/thsice: fix reading mnc-pickups
986    
987    checkpoint58t_post
988    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
989    o pkg/mdsio:
990     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
991       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
992       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
993     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
994     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
995       either MDS_READ_FIELD or MDS_WRITE_FIELD )
996     - new S/R (to replace MDSWRITEMETA), which allows to write more
997       informations (variable names, time ...) to meta files.
998     - modify rdmds.m to give back the meta file content.
999    o pkg/diagnostics: change vertical interpolation to be safer, and more
1000       flexible (define p-levels to interpolate to in data.diagnostics);
1001      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
1002       diagnostic pointer.
1003    o pkg/seaice: more cleaning up of seaice_growth, added many comments
1004    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
1005    o fix multi-category seaice:
1006     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
1007       SEAICE_MULTICATEGORY
1008     - fix short wave heat flux
1009    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
1010       and allow to use EVP solver. Change forward lab_sea: test both EVP
1011       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
1012    o Initial check-in of lab_sea adjoint
1013      (very similar to natl_box_adjoint/code_seaice)
1014      * used C-grid and EVP solver
1015      * used KPP, GM/Redi
1016      * uses inAdExact=.TRUE.
1017      * gradient checks fail for both ADM and TLM
1018        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
1019        f.d. gradients actually seem more problematic than ADM, TLM gradients;
1020        issue is related to forward mismatch between g77 an ifort
1021    o pkg/seaice: overhaul of thermodynamics
1022     - growth.F and groatb.F are replaced by new routine seaice_growth.F
1023     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
1024     - move a few global fields out of SEAICE.h into seaice_growth.F and
1025       make them 2D (FICE/QNETO/ ...)
1026     - remove FO (it is the same as QNETO)
1027     - introduce a few local fields to avoid modifying external fields such
1028       as atemp, etc.
1029    
1030    checkpoint58s_post
1031    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
1032      changed exf_set_gen.F so that
1033        genperiod=0 means input file is one time-constant field and
1034        genperiod=-12 means input file contains 12 monthly means
1035    o CG2D: use pre-computed solver main-diagonal (stored in common block);
1036      this affects truncation error ; generate new output file for exp. which
1037      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
1038        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
1039        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
1040        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
1041        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
1042        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
1043    o start implementation of deep-atmosphere and anelastic formulation
1044    o verification: remove 2nd copy of input files and use script "prepare_run"
1045      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
1046    o mom_common/vecinv/fluxform: fix a few initialisation isssues
1047    o profiles: fix for multithreaded case
1048    
1049    o diagnostics: rename few diags:
1050      s/'PRESSURE'/'RCENTER '/g
1051      s/'TICE    '/'oceFreez'/g
1052      s/'TAUX    '/'oceTAUX '/g
1053      s/'TAUY    '/'oceTAUY '/g
1054      s/'SWFLUX  '/'oceQsw  '/g
1055      s/DIFx/DFxE/g
1056      s/DIFy/DFyE/g
1057      and add few ocean-forcing diagnostics:
1058      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
1059    o modifications to pkg/seaice/growth.F and budget.F, which change results of
1060      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
1061      as actual snow thickness.  It now refers everywhere to effective snow
1062      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
1063    
1064    checkpoint58r_post
1065    o modifications to pkg/seaice/growth.F, which change results of
1066      lab_sea experiment: fixes pertain to melting snow over open water, to
1067      masking EVAP under sea ice, and to using the correct AREA variable for
1068      computations of EVAP, PRECIP, HSNOW, and GHEFF
1069    o add ability to read bathy, salt, and theta using MNC (off by def)
1070    o add flooding algorithm and advection of HSNOW for pkg/seaice;
1071      both are turned off by default and do no change any results
1072    o seaice advection with pkg/thsice: a step toward the use of non-linear
1073      advection scheme, but #ifdef or commented out for now (requires more EXCH).
1074    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
1075      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
1076      in natl_box (affects results @ truncation level: update output.txt)
1077    o multi-threading and IO:
1078      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
1079      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
1080        (needed to work with SingleCpuIO): tested in all verif. exp.
1081    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
1082      affects the results (but none of the verification test uses this scheme).
1083    o Adding some pkg/diagnostics capability to pkg/seaice
1084      (will certainly be subject to changes)
1085    o ctrl: adding new control variables:
1086      lwflux, lwdown, evap, snowprecip, apressure, runoff
1087    
1088    checkpoint58q_post
1089    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
1090      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
1091      high_res_cube configuration by 4% on Columbia.
1092    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
1093      add (in global_with_exf/code) a version of EXF_INTERP_READ without
1094      dynamical allocation (seems to work in multi-threaded).
1095    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
1096      single CPU io) so that TAF does not have to see EESUPPORT.h
1097  o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)  o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
1098    
1099  checkpoint58p_post  checkpoint58p_post
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