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revision 1.733 by jmc, Tue Oct 17 19:08:57 2006 UTC revision 1.1061 by jmc, Thu Feb 5 01:39:48 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/mdsio & rw:
8     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
9     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
10    o pkg/flt:
11     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
12       init_fixed & ini_varia.
13     - clean-up & simplify linear interpolation S/R:
14       move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
15     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
16     - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
17     - add vert. coordinate & horiz. indices to output files.
18     - change vertical position in initial condition, from index to depth [m].
19    o pkg/ggl90: a few modifications:
20     - fix bottom boundary condition, and interpolation of KappaE
21       near top and bottom
22     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
23     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
24     - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
25    o rename thetaMin,phiMin -> xgOrigin,ygOrigin
26      (maintain temporary backward compatibility, until next checkpoint)
27    
28    checkpoint61h
29    o pkg/diagnostics with "periodic averaging diagnostics":
30      fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
31    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
32    o pkg/obcs: fix loop ranges for balancing code
33    o pkg/flt:
34     - improve criteria for finding which tile owns a float.
35     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
36    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
37      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
38      with ocean biogeo)
39    o pkg/flt:
40     - do some cleaning and fix the restart ;
41     - add output.txt in flt_example/results to get this pkg tested.
42    o genmake2: add an EXTENDED_SRC option and flag.
43       for now, cannot be turned on on command line (only through genmake_local)
44    o pkg/mdsio: read/write vector:
45     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
46     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
47       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
48     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
49      (drop to 4 digits matching for grad). But this test does not look very
50      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
51    
52    checkpoint61g
53    o pkg/flt:
54      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
55       + make OPTIONS file more standard.
56      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
57      - fix _BYTESWAPIO CPP-Flag
58      - standard reading of file-parameter "data.flt"
59      - fix argument list of S/R FLT_RESTART
60      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
61    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
62    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
63      a still unfixed compiler/optimization bug
64    
65    checkpoint61f
66    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
67      update results of global_ocean.cs32x15.icedyn test.
68    o move getcon.F from model/src to pkg/fizhi.
69    o pkg/exf: add parameter for extrapolation of temp up to the surface
70       and option to prevent negative evap (in bulk_largeyeager04 only).
71    o Prather Advection scheme: fix tracer conservation for divergent flow
72      (e.g., when using NonLin Free-Surface).
73    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
74    o gmredi (Visbeck-variable-K):
75     - add more parameters to Visbeck-variable-K.
76     - use a 5 points average for dSigmaR in Visbeck-K calculation
77       (more "homogenous": same stencil and same weights as in dSigmaH)
78     - update output of ideal_2D_oce experiment.
79    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
80      (#undef REAL4_IS_SLOW)
81     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
82       coordinate variable
83     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
84       (surface forcing fields), removes some of the functionality
85     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
86     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
87       probably not all: copy _RS surface flux fields to RL field before
88       calling DIAGNOSTICS_FILL
89     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
90       real*4 (CALL EXCH_*_RS) versions.
91     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
92       (generate new output).
93    
94    checkpoint61e
95    o gmredi (Visbeck-variable-K):
96      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
97      - change computation of Visbeck-K where Slope > Smax :        
98        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
99        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
100    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
101      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
102    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
103    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
104      does not become too large (to avoid precision problems in implicit-diffusion
105      solver); update ideal_2D_oce output.
106    o pkg ggl90:
107      - in ggl90_cal.F: compute only one set of visc/diff, used to
108        step forward TKE/T/S/momentum
109      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
110        have Prandlt =1)
111    o gmredi (fm07):
112      - add lower limit on Transition layer thickness + lower limit on 1/lambda
113      - allow to set few more params from data.gmredi
114    o pkg ggl90:
115          - add missing sqrt(2) factor in computation of mixing length
116            scale in ggl90_calc.F
117            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
118    
119    checkpoint61d
120    o adjoint modifs
121      - adapt to new field rhoInSitu
122      - allow to revert from StoreDynVars2D, StoreDynVars3D
123        to individual fields
124        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
125    o store 3-D (in-situ) density in commom block (DYNVARS.h)
126     - save 1 rho computation.
127     - no longer modify T & S inland when using down_slope pkg.
128    o gad_som : allow to switch to SOM advection for T & S without corresponding
129      pickup files (using new S/R: MDS_CHECK4FILE).
130    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
131      (for useSingleCpuIO to work in multi-threaded)
132    o pkg/shelfice:
133     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
134       with SHELFICEtopoFile in data.shelfice
135     - move code for reading ice shelf topography and modifying hFacC into separate
136       subroutines of the shelfice package
137     - separate initialisation of "fixed" and "variable" variables
138     - kTopC is not (yet) replaced by kSurfC, although this is possible
139    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
140    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
141      and rename:
142      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
143      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
144    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
145    
146    checkpoint61c
147    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
148      to add mass source/sink of fluid in the interior (3-D generalisation
149      of oceanic real-fresh water flux).
150    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
151    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
152    o new pkg: down_slope
153      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
154      - presently, modify T & S inland (dwnslp_calc_rho.F).
155        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
156      - implementation for ocean in P-coords not tested.
157      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
158    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
159      (to facilitate conversion of oceanic pkg to p-coordinate).
160    o change FIND_RHO to FIND_RHO_2D :
161      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
162    o new pkg: cheapaml
163    
164    checkpoint61b
165    o exch2:
166      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
167      - no longer depend on the order sequence (N,S,E,W).
168      - 3rd exchange no longer needed (tested with 24 tiles).
169      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
170      - exch_UV_A-grid readily available (but not yet tested).
171      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
172      (both are no longer needed) in exch_uv: no effect in forward run; but
173       get truncation error differences with adjoint exch.
174    o exch2:
175     - change index-bounds storage (moved from target to local tile,
176       more intuitive this way) ; rename/remove some variables.
177     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
178    
179    checkpoint61a
180    o exch2/matlab-topology-generator:
181      fix bug in index bounds for N-S internal exchange (hard to tell if this
182      had any effect on the solution).
183    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
184      is exceeded
185    o testreport: modify syntax of awk, so that it works also with
186      awk, and not only with nawk and gawk
187    
188    checkpoint61
189    o autodiff
190      Change default for TAF usage by removing argument '-nonew_arg'
191      This changes TAF subroutine argument list (ordering of active var.)
192      Omission of this flag leads to incompatibility w.r.t. TAMC
193      To restore TAMC-compatibility, need following modifs:
194      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
195      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
196      Tested TAF version is 1.9.22
197      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
198    
199    checkpoint60
200    --->>> This is the last checkpoint for which generating the adjoint
201    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
202    --->>> by default.
203    --->>> Future checkpoints will ommit this flag by default.
204    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
205    o pkg/grdchk: Add gradient check to etan0 perturbations.
206    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
207    o pkg/autodiff: more flexibility in zeroadj.
208      model/src: modifying do_oceanic_phys.F accordingly.
209    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
210    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
211      special setup of gmredi for which the adjoint is stable
212      enough for parameter optimization.
213    o bridging the gap between eddy stress and GM.
214      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
215          along with a change in CPP option (now ALLOW_EDDYPSI).
216      -> when using GM w/ GM_AdvForm:
217          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
218          is applied either in the tracer Eq. or in momentum Eq.
219          depending on data.gmredi (intro. GM_InMomAsStress).
220      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
221      The key modifications are in model/src/taueddy_external_forcing.F
222      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
223    
224    checkpoint59r
225    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
226      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
227      fix option to read coriolis(@ cell-corner) from files with CS-grid.
228    o pkg/mnc: add some attributes to standard 1D-coordinate variables
229    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
230      mass points, when using mnc for output
231      - add runtime parameter (missing_value, missing_value_int) to override
232        default (which is the value of getcon('UNDEF'))
233    o pkg/mnc: prepare mnc for the actual use of missing values with the
234      diagnostics package: small fix in mnc_cw_readwrite.template and more
235      initialisation of never used fields
236      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
237      versions
238    o pkg/thsice/thsice_ini_vars.F added default initial values so that
239      thermodynamics sea ice solver does not blow up when some initial fields
240      are missing.
241    o move from external_forcing_surf.F to ini_forcing.F
242      the p-coord. hack consisting in using pLoad to set phi0surf ;
243      update output of tutorial_global_oce_in_p (affected @ truncation level).
244    o Freshen up a bit hs94.1x64x5, notably:
245      remove rotationPeriod and tRef=5*0. (adjoint only), and add
246      exactConserv=.TRUE.
247    o pkg/generic_advdiff:
248      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
249      applies to files where Temperature & Salinity 2nd Order moments are used.
250    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
251      this uses a dynamically allocated internal state data structure
252      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
253      and requires a fortran 90 compiler
254    
255    checkpoint59q
256    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
257       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
258    o Refresh tutorial_global_oce_biogeo, notably:
259      - change bathymetry (put back seamounts in ACC, use hFacs)
260      - change EOS (POLY3 --> JMD95Z)
261      - use Bryan-Lewis vertical diffusivity
262      - use multidimensional advection
263      - remove old virtual virtual in dic pkg, now done through ptracer pkg
264      - change a couple of parameters in dic pkg
265    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
266    o pkg/obcs: change default to OBCSfixTopo = .true.,
267      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
268      - replace "debugMode" with "debugLevel .GE. debLevB"
269    o implementation of TAF directives for gchem,cfc,dic
270    o remove "exp5" (replaced by tutorial_deep_convection).
271    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
272      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
273      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
274      --> changes results in exp4, seaice_obcs
275    o tutorial_deep_convection :
276      update the set-up and increase resolution and domain size ; start
277      from pseudo initial conditions = output at t=120mn in order to see
278      something happening when running testreport.
279    o pkg/seaice: add os7mp as an advection scheme
280                  add check for advection schemes
281                  add a flag for restoring T and S underneath sea ice
282    o pkg/my82: add netcdf-support and diagnostics
283    o thsice pkg:
284      - Now hsMax limits snow height by turning it into ice following
285        flooding scheme (and now conserving energy)
286      - Slight rewriting of the formula in thsice_calc_thick.F
287      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
288      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
289    
290    checkpoint59p
291    o gchem / dic / cfc :
292      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
293      - add new parameter files: "data.dic" & "data.cfc" ;
294      - various re-arrangement in initialisation & header file ;
295      - fix tutorial_global_oce_biogeo for multi-threaded test.
296    o pkg/dic: test for "pickup_dic" file when restarting ;
297      if no pickup-file, can restart with a re-initialised pH (same as it did
298      before) providing pickupStrictlyMatch is set to False.
299    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
300      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
301    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
302      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
303    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
304     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
305       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
306    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
307       scheme to use for vorticty-term ;
308     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
309       (with default selectVortScheme, return to original discretisation)
310     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
311    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
312    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
313      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
314      also fix diagnostics VISCAHW & VISCA4W.
315    
316    checkpoint59o
317    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
318    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
319      move a few statemens out the main loop into separate loops
320    o pkg/shelfice:
321      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
322        (kg/m^2/s), does not break tests, because in verification/isomip,
323        rhoConstFresh=rhoConst (by accident)
324      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
325      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
326        new file model/src/seawater.F, so that they are available for all pkgs.
327      - convert potential temperature into in-situ temperature. This changes the
328        isomip tests => update tests
329    o add a flag writePickupAtEnd (default=true) to be able to suppress
330      writing a pickup at the last timestep
331    o tools/mpack-1.6 :
332      - disable automake (not working) and autoconf (not needed).
333      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
334        also cleaner with much less compilation warnings.
335    o pkg/profiles:
336      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
337      (for "less than 32 characters name" compiler requirement)
338    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
339      conditions that have a different sampling frequency than S/T/U/V obcs
340    o pkg/diagnostics (stats-diags):
341      - fix global Min/Max in case 1 processor get only empty tiles
342    o genmake2: replace (4 times)
343         make genmake_tc_1.o >> genmake_warnings 2>&1
344      with
345         COMM="$CC $CFLAGS -c genmake_tc_1.c"
346         echo $COMM >> genmake_warnings
347         $COMM >> genmake_warnings 2>&1
348      to make genmake2 always see the value of CC as specified in the optfile.
349    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
350      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
351      - modify verification advect_cs test to test SOM-advection on CS-grid.
352    o pkg/ctrl:
353      - Rewrite of ctrl_map_ini_ecco.F,
354        introducing a generic routine (ctrl_map_ini_gen.F).
355      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
356    
357    checkpoint59n
358    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
359      number in dedicate array "hdiag":
360      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
361        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
362      - many small changes (integer format) for large number of diagnostics
363      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
364        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
365    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
366      usingSphericalGrid, this allows to define the rotated grid coordinates
367      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
368      geographical coordinates according to the inverse of the rotation defined
369      by the Euler angles, so that Coriolis parameter and online-interpolation by
370      exf works with the geographical coordinates on XC/YC/XG/YG.
371      Naturally, this feature does not work with all packages, so some
372      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
373      profiles), because there the coordinates are assumed to be regular
374      spherical grid coordinates.
375    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
376      - introduce isopycnal diffusion coefficient control.
377    o tools/adjoint_options:
378      - additional control vector components.
379    o pkg/mnc: have mnc create marginally meaning full coordinate variables
380      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
381    o pkg/mypackage:
382      - add example of read/write pickup for state-var ;
383      - add entry points to the main code for state-vars diags & write-pickup.
384    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
385      transitions for useExfYearlyFields
386      - add new subroutine that determines the file to read from for
387        use*YearlyFields = .TRUE. and .FALSE.
388      - add a verification experiment to global_with_exf that tests
389        useExfYearlyFields with USE_EXF_INTERPOLATION defined
390    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
391      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
392      subroutines (which could be generated from a template, because they are
393      almost identical), for now they are included in obcs_prescribe_read.F for
394      simplicity
395    o pkg/exf:
396      - add a little more diagnostic to exf_interp_read (in analogy to
397        mds_read_field, can be turned off with debugLevel < debugLevA=1)
398      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
399        ugly but fast by unrolling short inner loops, inserting a unroll=8
400        directive in routine lagran, and splitting a loop and making do while the
401        outermost loop (the latter requires the intoduction of index arrays)
402    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
403    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
404      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
405    o verification/seaice_obcs: updated for restart test and latest options
406    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
407      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
408      for now this is only available for the C-grid code and also within
409      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
410    
411    checkpoint59m
412    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
413      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
414    o gad_som : fix flux output (& diagnostics) to have same units as other  
415      advection scheme fluxes (was previously multiplied by deltaT).  
416    o added verification/seaice_obcs both to test seaice open boundaries
417      and to provide an example matlab scrpt for generating them
418    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
419    o pkg/salt_plume: clean up salt_plume_frac.F to
420      remove redundancy in PlumeMethod 1 and 4
421    o pkg/kpp: added saltplume diagnostics
422    o pkg/obcs and pkg/seaice:
423      - do not set uice and vice to zero when OB*icefile are unspecified
424      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
425      - moved seaice tracer obcs after call to seaice_growth
426    o pkg/salt_plume: added various options for salt plume depth
427      criterion and for vertical distribution of the salt
428    
429    checkpoint59l
430    o pkg/ptracers: new version of ptracers pickup:
431      read meta file and write only fields which are needed to restart.
432      ( same logic as main pickup file ; also using pickupStrictlyMatch )
433    o pkg/seaice:
434      - add timescale for melting due to warm mixed layer as a means of
435        setting SEAICE_availHeatFrac more conveniently
436      - add a CPP-flag/runtime parameter check for flooding algorithm
437      - reformulated availHeat in seaice_growth.F to be independent of AREA
438    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
439      unit changes
440    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
441    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
442      SX vector computer.
443    o pkg/seaice:
444      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
445        seaice forcing fields can now be read only through pkg/exf
446      - removed some unused halos
447    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
448    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
449      or U/VICE from U/VWIND before computing U/VSTRESS
450    
451    checkpoint59k
452    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
453      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
454    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
455      all experiments pass when compile with un-initialised var. checking option.
456    o added pkg/salt_plume
457    o script to test restart (for now, in MITgcm_contrib/jmc_script)
458    o pkg/seaice: new read/write pickup version.
459      read meta file and write only fields which are needed to restart.
460      ( same logic as main pickup file ; also using pickupStrictlyMatch )
461    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
462    o lab_sea.hb87: modify the domain & update output.hb87.txt :
463      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
464      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
465      process. Fixed here by closing the domain at the Northern boundary.
466    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
467    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
468      a set of consecutive levels in/from a 3-D array.
469    o pkg/ptracers:
470      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
471      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
472    
473    checkpoint59j
474    o in pkgs: dic, obcs, offline, rbcs:
475      standard way to compute coeff. for time interpolation between 2 time reccords
476      which retains full precision (& make results less dependent on compiler).
477      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
478    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
479      packages instead of reading ice cover and wind speed separately
480    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
481     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
482      to allow to compile customized code before the update)
483    o cleaning-up:
484      - fix CPP instruction syntax in pkg/obcs
485      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
486        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
487      - fix some threads issue in IO parts.
488    o pkg/dic:
489      - add tons of "_d 0" (--> much better testreports !)
490       and then update outputs of tutorial_global_oce_biogeo
491    o pkg/mom_fluxform:
492      add a special version of momentum advection intended to conserve momentum
493      next to a bathymetry step or a coastline edge. (default = off = #undef)
494    o new read/write pickup version:
495      - for now, only implemented for main (mdsio) pickup file.
496      - write out only what is needed to restart; merge pickup_nh , pickup_ph
497        and main pickup together.
498      - read meta file; read only what is needed to restart; stop if a field
499        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
500        if it make sense (even if the restart is not perfect).
501      - if no meta file, assume that pickup to read corresponds exactly to
502        a pickup that would currently be written.
503      - read pickup written in the old format (until checkpoint59i) if it
504        recognizes an old meta file (no field-list).
505      - add a meta file in exp. which starts from a pickup: 2 cases:
506        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
507         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
508        b) a meta file describing the content of the associated pickup file
509         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
510    o pkg/mdsio & pkg/rw:
511      - new routine to read a meta file ; new set of routine to read
512        Multiple-fields file (with meta file).
513    o added open boundary conditions capability for seaice
514        HSNOW, HSALT, UICE, and VICE
515    
516    checkpoint59i
517    o adjoint:
518      * fix multiDimAdvection adjoint
519        (partial recomputation problem by TAF for fVerT(:,:,kDown)
520        and comlev1 size definition (maxpass vs. max. number of tracers)
521      * verification/global_ocean.90x45x15 adjoint now tests
522        NLFS and multiDimAdvection using DST3 (=30)
523      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
524    o pkg/kpp: add "_d 0" to real constant (if missing);
525      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
526      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
527    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
528      for internal parameters related to restart process (formerly from PARAMS.h)
529      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
530    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
531      as argument. (only atm2d & obcs write_pickup have not yet been updated)
532    o pkg/monitor:
533      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
534      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
535      - account for deep Atmosphere factor and density factor (anelastic)
536    o added open boundary conditions capability for seaice HEFF and AREA
537    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
538      thermodynamics
539      - requires a little reorganization, which affects the testreport results
540        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
541        so that now the conservative form is tested
542      - add a few comments
543    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
544    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
545    o add new diagnostics to seaice: advective, diffusive fluxes (only for
546      multidim-advection, for scheme 2 they are not filled) and transports,
547      thermodynamic growth rates
548    o change units of EmPmR (inside the code, + within coupling interface)
549      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
550      Affects results @ truncation level (cg2d match) and update output of
551       experiments: lab_sea(6), global_ocean.90x40x15(10),
552      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
553      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
554      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
555      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
556    
557    checkpoint59h
558    o pkg/exf:
559      - improve vectorization by moving if-statement out of loops in
560        exf_mapfields, exf_radiation
561      - exf_bulkformulae.F: introduce 2D fields and vectorize code
562    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
563    o testreport:
564      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
565        monitor & update offline_exf_seaice exp. output.
566      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
567    o pkg/seaice:
568      - bug fix in the evp solver: boundary conditions were affected be
569        masking of zMax/zMin (changes results)
570      - minor bug fix in boundary conditions in seaice_calc_strainrates
571        (changes results for no_slip)
572      - seaice_lsr.F: make interpolation of eta dependent on boundaries
573      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
574      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
575        stress formulation and no-slip boundary conditions
576    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
577      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
578    o pkg/seaice: a first HSALT time stepping equation has been checked in
579    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
580      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
581      without requiring DO-IF statements
582    o pkg/thsice:
583      use continuous power-law function for partition of energy between lateral
584      melting/freezing and thinning/thickening ; old code using step function
585      still available with #undef THSICE_FRACEN_POWERLAW
586      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
587    o testreport: change AD testing : check against results/output_adm.txt
588      using same scripts as for forward test.
589    
590    checkpoint59g
591    o adjoint testing: in preparation for changing testreport:
592      - output format: cost and grad written on separated lines
593      - ad output results in directory "results" (instead of "results_ad")
594    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
595    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
596    o pkg/ecco: allow user defined cost function contributions
597    o testreport:
598      Allow to choose (per experiment) the list of tested output variables
599       and the main variable (used to issue a pass/FAIL ) ;
600      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
601      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
602      Also modify printing of summary:
603       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
604       b) echo the list of tested variables in the individual summary.txt of
605          each experiment.
606    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
607      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
608      (but still depend on the tile decompostion of the domain).
609    o pkg/seaice: change a discretization detail to make the B-grid code
610      "more symmetric". This change is likely to remove all "ridges/leads" that
611      where quasi-aligned with the grid in B-grid solutions. It may also be
612      the solution to the stress coupling issues with the B-grid.
613    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
614      remove .cvsignore from input dir. (since testreport no longer run here).
615    o pkg/thsice:
616     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
617     - fix reshaping of sea-ice just after advection:
618       melt all the ice only if ice-volume is too small.
619     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
620       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
621     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
622    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
623      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
624    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
625      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
626      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
627      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
628      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
629      -> update output.txt
630    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
631     this affects truncation error: -> update output.txt of exp:
632      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
633      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
634    
635    checkpoint59f
636    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
637    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
638      a bounded range (in forward mode)
639    o pkg/ecco, ctrl, autodiff and mom_common:
640     internal parameter controls, completements of implementations
641    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
642    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
643      (not seem any difference in testing results).
644    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
645       at face corners.
646    o pkg/generic_advdiff:
647     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
648      loop range indices for computing vertical advection tendency
649      and do the calculation in the interior only (no overlap) ;
650      for now, only implemented for SOM advection (to save CPU time).
651     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
652    o exch2 adjoint
653      First set of changes:
654      - add exch2 hand-written adjoint templates
655      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
656        This will require cleanup in pkg/autodiff/*.F
657        (changed routines currently kept separate in verif. code/)
658      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
659        that used to hide exch2 or cubed-sphere specific code
660        (commented via 'cph-exch2')
661    o pkg/seaice
662      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
663    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
664       output of global_ocean.cs32x15.thsice .
665    
666    checkpoint59e
667    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
668      for B-grid vector (not yet tested) and C-grid vector (<- only used
669      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
670    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
671      (#ifdef ALLOW_SALT_PLUME)
672    o gather_2d/scatter_2d: removed halo regions
673    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
674      scheme and the corresponding test case (under front_relax dir). For now,
675      only available with Skew-flux form and not yet tested in realistic set-up.
676      adjoint: store directives updated, but gradient checks deteriorated,
677      so maybe GM/Redi adjoint is now broken.
678    o seaice adjoint
679      * add AREA, HEFF, HSNOW as control variable
680        (should not change lab_sea results)
681      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
682    o pkg/seaice:
683      * added computation of saltFlux in seaice_growth;
684        For time being, sea ice salinity is assumed constant
685        contribution of snow flooding to freshening of sea ice is neglected.
686        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
687        defaults to 0.0 in order to maintain backward compatibility.
688        Typical values for SEAICE_salinity are 4 to 10 g/kg.
689      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
690      * added SEAICE_availHeatFrac, which specifies fraction of surface level
691        heat content used to melt or grow ice
692      * commented out cap of HICE: it helps keep ice thinner
693      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
694      * applied OBCS T/S mask to HEFFM sea ice mask
695    
696    checkpoint59d
697    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
698     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
699     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
700    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
701     and change default value of parameter "GM_Small_Number";
702     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
703       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
704       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
705    o pkg/ecco: cost function when applying pkg/smooth to controls
706    o pkg/ctrl: add forcingPrecond run time parameter
707    o pkg/seaice:
708     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
709     - fix bug in metric terms of u-equation in LSR solver (implicit part),
710       changes verification/lab_sea
711     - rearrange implicit part of u-equation in LSR solver to make it easier to
712       read, understand, and debug. This causes changes at the truncation level.
713     - fix (serious) bug in the boundary conditions (sign error in the implicit
714       part) of the LSR solver. Changes all LSR results.
715     - fixed problem with HSNOW initialization to avoid thick snow when AREA
716       is initilized with small values - does not change lab_sea results.
717     - added HsnowFile initialization capability
718    o pkg/smooth: addition to model/src and pkg/ctrl so allow
719     initialization of pkg/smooth and application to control vector
720    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
721    o dependencies: pkg/profiles requires pkg/cal
722    o pkg/profiles:
723     - added option ALLOW_PROFILES_GENERICGRID
724         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
725         that interpolation information (grid points and coefficients) is provided
726         within the netcdf input files.
727         -> sample matlab scripts can be found in MITgcm_contrib/gael
728         that allow you to prepare netcdf input files.
729     - also modified: cleaner include statements, cleaner error print statements,
730       cleaner stops when error, and more tests of the netcdf input files consistency.
731    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
732    o pkg/seaice:
733     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
734       requires a new routine: seaice_diagnostics_fill.F
735     - make sure that seaice does not move if not forced (pressure replacement
736       method, Hibler and Ip, 1995), changes results
737     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
738     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
739       It is turned off by default (=-1.), because it changes the results.
740     - make it possible to read AREA from a file, too.
741    
742    checkpoint59c
743    o add S/R and diagnostics for oceanic mixed-layer depth
744    o move GMRedi call after all vertical mixing schemes (including KPP)
745    o pkg/thsice:
746     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
747      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
748    o pkg/obcs:
749     - bug fix for balance code
750    o pkg/seaice:
751      - allow values of SEAICE_elasticParm > 1
752      - add new parameter SEAICE_evpTauRelax as an alternative
753        to SEAICE_elasticParm
754      - make lsr boundary conditions free slip (by default), changes result
755      - add code for no slip boundary conditions for lsr
756      - set minimum of zeta to zero (and not 4e8) (changes results)
757      - add a cap on AREA after advecting AREA if seaice_growth is not called
758    o change calculation of Visbeck K:
759      - no longer depend on tapering scheme; instead, compute slope (limited
760        by GM_maxSlope). this is equivalent to what was comuted before with
761        clipping or linear tappering.
762      - fix vertical averaging (wrong by 1/2 level)
763      - leave the old version (but will not be maintained) within
764        #ifdef OLD_VISBECK_CALC / #endif
765      - update output of exp. ideal_2D_oce
766    o change error catch in calc_r_star to improve vectorization
767    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
768      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
769    o adjoint:
770      Re-organized adjoint checkpointing according to Matt Mazloff
771      (but with modifs/completions/cleanups)
772      Storing is now bundled into large arrays to optimized I/O
773      (and second step in cleanup of the_main_loop)
774    
775    checkpoint59b
776    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
777      - export/import (between ocean & coupler) fields needed for ocean DIC.
778    o pkg/seaice:
779      - get rid of three more exchanges seaice_calc_viscosities (required
780        different loop boundaries in seaice_lsr and seaice_ocean_stress)
781      - bug fix in seaice_ocean_stress (update of lab_sea required)
782      - reduce loop boundaries to necessary minimum also in seaice_evp
783      - go back to the old way of computing deltaC/Z as the adjoint likes that
784        better
785    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
786      passive tracer to an Age Tracer) + update output.txt
787    o pkg/exf:
788      - implement A-grid / C-grid selection for wind-stress input files.
789      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
790      for now, in exf_bulk_largeyeager04.F only :
791      - change implementation for case where windspeed + 2. components wind-stress
792        are read-in. AND use rhoConstFresh to convert evap.
793    o pkg/seaice:
794      - use correct EXCH_UV for wind-forcing (on A-grid).
795      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
796        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
797    o pkg/exf:
798      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
799      EXF_INTERPOLATION:
800      - merge global_with_exf/code version of exf_interp_read.F
801        to the main code ;
802      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
803        reading the file ; Important: This options needs to be defined to recover
804        previous code.
805        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
806      - no longer loose real*8 precision along the way when using exf_iprec=64.
807    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
808      - change discretisation of evp-solver in order to avoid another exchange
809        (changes lab_sea) and clean up a little
810      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
811        help the adjoint (this also changes the results slightly)
812      - add a few "_d 0" where they had been missing in seaice_evp.F
813      - cleaning up: remove unused seaice_calc_rhs.F
814    o pkg/exf: some cleaning-up:
815      - change various "constants" into runtime parameters
816      - cleaned-up Large&Yeager04 routine which should eventually
817        replace exf_bulkformulae.F (changed names of S/R and CPP)
818        and merged various ALLOW_ATM_WIND options
819     only used with thsice pkg (in thsice_get_exf.F):
820      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
821        which are used when useStabilityFct_overIce=TRUE (= the default)
822      - change default values of ice & snow emissivity and scale downward LW
823        by ice & snow emissivity.
824    o pkg/thsice:
825     fix few little problems, in thsice_calc_thickn.F:
826      - growth vertically (and not laterally) if iceFrac == iceMaskMax
827      - melt only laterally if hIce < hThinIce (as the comments say)
828      and in thsice_extend.F:
829      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
830      - start to form ice as soon as the minimum ice-volume is reachable.
831     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
832      and cpl_aim+ocn
833    o pkg/kpp
834     - move computation of surface related input fields to KPP into a new
835       subroutine kpp_forcing_surf.F
836     - remove wrong (within bi,bj loops) EXCH calls.
837     - little cleaning (add argument myThid in last position, cvs header ...)
838     - for now, fix conservation problem by exchanging KPPviscAz (may not
839       be the best fix)
840    o pkg/seaice
841     - check for inconsistent evp parameter/cpp-flag combination
842     - remove leftover errIO flat for obsolete name list error handling
843    o OpenAD
844     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
845    
846    checkpoint59a
847    o pkg/seaice: some parameter clarifications and a little bit of clean up
848    o pkg/thsice: rename run-time parameters:
849       himin       -> hIceMin
850       himin0      -> hThinIce
851       hihig       -> hThickIce
852       i0          -> i0swFrac
853       transCoef   -> bMeltCoef
854       frac_energy -> fracMelting
855      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
856       with default values (for now) that do not change the results.
857      remove old version of thsice vars advection in pkg/seaice.
858    o in FFIELDS.h:
859      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
860      - make pLoad & sIceLoad always available (but still only used if
861         ATMOSPHERIC_LOADING is #define).
862    o pkg/kpp: replaced _KPP_RL with _RL
863    o bug fixes for vertical diffusivity computations when both KPP and
864        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
865        are no longer updating the vertical diffusivity array
866        (passed as argument) but are (re-) setting those arrays.
867    o pkg/seaice: fix bug in evp solver, while doing that
868      - change (improve?) discretization of stress computations for both
869        cgrid-lsr and evp solver
870      - add a new routine to compute strain rates
871      - the above changes lab_sea results
872      - add no slip conditions for evp solver (off by default), lsr-version
873        may follow
874      - fix exchange for shear at Z-points (does not change lab_sea)
875      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
876        (to force the user to pick a time step since there is not "safe" way
877        of choosing it)
878      - add principal stress diagnostics
879      - rearrange fields for evp a little to avoid having to call a: too many
880        exchanges and b: exchanges for stress trensor components which we do
881        not have.
882      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
883        of evp, complete rewrite for lsr case (latter is does not yet work
884        in all cases)
885    o pkg/kpp: add code to have mixing in shelf ice caverns
886      - add myThid to all kpp routines (long overdue)
887    
888    checkpoint59
889    o pkg/exf:
890      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
891        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
892      - move exf header files from lower_case.h to UPPER_CASE.h ;
893        add missing cvs Header & Name
894      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
895      - add namelist param. selectStressGridPosition, exf_monFreq
896      - retire many _CLIM routines, and remove data.exf_clim
897        + params moved to data.exf
898        + climsst, climsss now handled by exf_set_gen, i.e.
899          climss?period=0 refers to constant field,
900          climss?period=-12 to monthly forcing
901      - split up namelists in data.exf
902    o pkg/seaice:
903      - remove seaice_exch and seaice_exch_uv
904      - remove superfluous exchange of theta
905      - add myThid to seaice_budget_ocean/ice
906      - add new interface for atmospheric wind forcing (C-grid only)
907        + new routine
908        + two new field (taux, tauy for stress over ice)
909        + removed one global field (DAIRN) for C-grid case only
910    o pkg/thsise
911      - 2nd set of modifs for thsice adjoint in conjunction with exf
912    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
913    
914    checkpoint58y_post
915    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
916      vertical diffusivity, similar to that in MOM4; turned on using
917      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
918      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
919    o Added capability for 3D specification of background vertical diffusion
920      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
921      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
922      "data" file that contains the 3D vertical diffusivity coefficients.
923    o ice dynamics (pkg/seaice) with thsice thermodynamics:
924      - add code within pkg thsice to advect & diffuse sea-ice fields
925      similar to (and will replace) what has been added in  seaice_advdiff.F,
926      but: - conserving Mass, Heat & Salt.
927           - better when using non-linear advection scheme (not yet fully tested)
928           - can also be used in atmospheric set-up (for now, only the diffusion).
929    
930    checkpoint58x_post
931    o IO option for global-file compact format:
932      - add options when generating topology (utils/exch2/matlab-topology-generator)
933      - add I/O capability (pkg/mdsio).
934      - adapt utils/matlab/rdmds.m to read this format.
935      for now long-line format not yet supported by pkg/mdsio (& exch2).
936    o shelfice: add a few diagnostics
937    
938    checkpoint58w_post
939    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
940      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
941      (and replace horiVertRatio in NH code).
942      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
943                         and tutorial_plume_on_slope (sensitive to truncation)
944    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
945      directly to drive seaice model (C-grid only)
946    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
947     - reintroduce computation of wind from stress,
948     - compute tau (in exf_bulkformulae.F) from windstress averaged to
949       mass points to avoid tau = 0
950     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
951    o rdmnc.m: make it work with "global" files created with gluemnc
952    o rdmnc.m : some improvements in dealing with singleton dimension
953      (tested on all testreport mnc output files).
954    o genmake2: disable pkg/profiles if netcdf test fails.
955    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
956    o move call to cal_readparms up to make calendar parameters/variable available
957      to all packages
958    
959    checkpoint58v_post
960    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
961      useDynP_inEos_Zc tested.
962    o pkg/exf: changes to properly interpolate/mask/scale initial fields
963    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
964      and portions thereof.  See read_cs.txt for description and examples.
965    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
966      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
967      following the great-circle arc between those 2 points.
968    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
969      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
970    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
971     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
972     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
973     - still needs work (not working with some options ; efficiency to improve)
974       and serious testing.
975     - use this scheme for temperature & salinity in 2 advection test exp.:
976       advect_xy & advect_xz, respectively.
977    
978    checkpoint58u_post
979    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
980    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
981    o testreport: add option "-skipdir" to skip some test.
982    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
983      momentum calculation.
984    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
985    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
986      remove checkpoint.F and the_correction_step.F (no longer used);
987      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
988    o add option (linFSConserveTr) to correct for tracer source/sink due to
989      Linear Free surface
990    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
991    o pkg/thsice: fix reading mnc-pickups
992    
993    checkpoint58t_post
994    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
995    o pkg/mdsio:
996     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
997       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
998       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
999     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
1000     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
1001       either MDS_READ_FIELD or MDS_WRITE_FIELD )
1002     - new S/R (to replace MDSWRITEMETA), which allows to write more
1003       informations (variable names, time ...) to meta files.
1004     - modify rdmds.m to give back the meta file content.
1005    o pkg/diagnostics: change vertical interpolation to be safer, and more
1006       flexible (define p-levels to interpolate to in data.diagnostics);
1007      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
1008       diagnostic pointer.
1009    o pkg/seaice: more cleaning up of seaice_growth, added many comments
1010    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
1011    o fix multi-category seaice:
1012     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
1013       SEAICE_MULTICATEGORY
1014     - fix short wave heat flux
1015    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
1016       and allow to use EVP solver. Change forward lab_sea: test both EVP
1017       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
1018    o Initial check-in of lab_sea adjoint
1019      (very similar to natl_box_adjoint/code_seaice)
1020      * used C-grid and EVP solver
1021      * used KPP, GM/Redi
1022      * uses inAdExact=.TRUE.
1023      * gradient checks fail for both ADM and TLM
1024        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
1025        f.d. gradients actually seem more problematic than ADM, TLM gradients;
1026        issue is related to forward mismatch between g77 an ifort
1027    o pkg/seaice: overhaul of thermodynamics
1028     - growth.F and groatb.F are replaced by new routine seaice_growth.F
1029     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
1030     - move a few global fields out of SEAICE.h into seaice_growth.F and
1031       make them 2D (FICE/QNETO/ ...)
1032     - remove FO (it is the same as QNETO)
1033     - introduce a few local fields to avoid modifying external fields such
1034       as atemp, etc.
1035    
1036    checkpoint58s_post
1037    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
1038      changed exf_set_gen.F so that
1039        genperiod=0 means input file is one time-constant field and
1040        genperiod=-12 means input file contains 12 monthly means
1041    o CG2D: use pre-computed solver main-diagonal (stored in common block);
1042      this affects truncation error ; generate new output file for exp. which
1043      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
1044        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
1045        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
1046        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
1047        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
1048        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
1049    o start implementation of deep-atmosphere and anelastic formulation
1050    o verification: remove 2nd copy of input files and use script "prepare_run"
1051      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
1052    o mom_common/vecinv/fluxform: fix a few initialisation isssues
1053    o profiles: fix for multithreaded case
1054    
1055    o diagnostics: rename few diags:
1056      s/'PRESSURE'/'RCENTER '/g
1057      s/'TICE    '/'oceFreez'/g
1058      s/'TAUX    '/'oceTAUX '/g
1059      s/'TAUY    '/'oceTAUY '/g
1060      s/'SWFLUX  '/'oceQsw  '/g
1061      s/DIFx/DFxE/g
1062      s/DIFy/DFyE/g
1063      and add few ocean-forcing diagnostics:
1064      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
1065    o modifications to pkg/seaice/growth.F and budget.F, which change results of
1066      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
1067      as actual snow thickness.  It now refers everywhere to effective snow
1068      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
1069    
1070    checkpoint58r_post
1071    o modifications to pkg/seaice/growth.F, which change results of
1072      lab_sea experiment: fixes pertain to melting snow over open water, to
1073      masking EVAP under sea ice, and to using the correct AREA variable for
1074      computations of EVAP, PRECIP, HSNOW, and GHEFF
1075    o add ability to read bathy, salt, and theta using MNC (off by def)
1076    o add flooding algorithm and advection of HSNOW for pkg/seaice;
1077      both are turned off by default and do no change any results
1078    o seaice advection with pkg/thsice: a step toward the use of non-linear
1079      advection scheme, but #ifdef or commented out for now (requires more EXCH).
1080    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
1081      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
1082      in natl_box (affects results @ truncation level: update output.txt)
1083    o multi-threading and IO:
1084      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
1085      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
1086        (needed to work with SingleCpuIO): tested in all verif. exp.
1087    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
1088      affects the results (but none of the verification test uses this scheme).
1089    o Adding some pkg/diagnostics capability to pkg/seaice
1090      (will certainly be subject to changes)
1091    o ctrl: adding new control variables:
1092      lwflux, lwdown, evap, snowprecip, apressure, runoff
1093    
1094    checkpoint58q_post
1095    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
1096      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
1097      high_res_cube configuration by 4% on Columbia.
1098  o clean-up multi-threaded problems (reported by debugger tcheck on ACES);  o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
1099    add (in global_with_exf/code) a version of EXF_INTERP_READ without    add (in global_with_exf/code) a version of EXF_INTERP_READ without
1100    dynamical allocation (seems to work in multi-threaded).    dynamical allocation (seems to work in multi-threaded).
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