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revision 1.715 by mlosch, Mon Aug 14 16:53:08 2006 UTC revision 1.1030 by jmc, Thu Oct 16 18:38:55 2008 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7  o shelfice: add a simple boundary layer scheme to reduce noise  o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
8      does not become too large (to avoid precision problems in implicit-diffusion
9      solver); update ideal_2D_oce output.
10    o pkg ggl90:
11      - in ggl90_cal.F: compute only one set of visc/diff, used to
12        step forward TKE/T/S/momentum
13      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
14        have Prandlt =1)
15    o gmredi(fm07):
16      - add lower limit on Transition layer thickness + lower limit on 1/lambda
17      - allow to set few more params from data.gmredi
18    o pkg ggl90:
19          - add missing sqrt(2) factor in computation of mixing length
20            scale in ggl90_calc.F
21            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
22    
23    checkpoint61d
24    o adjoint modifs
25      - adapt to new field rhoInSitu
26      - allow to revert from StoreDynVars2D, StoreDynVars3D
27        to individual fields
28        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
29    o store 3-D (in-situ) density in commom block (DYNVARS.h)
30     - save 1 rho computation.
31     - no longer modify T & S inland when using down_slope pkg.
32    o gad_som : allow to switch to SOM advection for T & S without corresponding
33      pickup files (using new S/R: MDS_CHECK4FILE).
34    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
35      (for useSingleCpuIO to work in multi-threaded)
36    o pkg/shelfice:
37     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
38       with SHELFICEtopoFile in data.shelfice
39     - move code for reading ice shelf topography and modifying hFacC into separate
40       subroutines of the shelfice package
41     - separate initialisation of "fixed" and "variable" variables
42     - kTopC is not (yet) replaced by kSurfC, although this is possible
43    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
44    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
45      and rename:
46      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
47      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
48    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
49    
50    checkpoint61c
51    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
52      to add mass source/sink of fluid in the interior (3-D generalisation
53      of oceanic real-fresh water flux).
54    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
55    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
56    o new pkg: down_slope
57      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
58      - presently, modify T & S inland (dwnslp_calc_rho.F).
59        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
60      - implementation for ocean in P-coords not tested.
61      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
62    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
63      (to facilitate conversion of oceanic pkg to p-coordinate).
64    o change FIND_RHO to FIND_RHO_2D :
65      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
66    o new pkg: cheapaml
67    
68    checkpoint61b
69    o exch2:
70      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
71      - no longer depend on the order sequence (N,S,E,W).
72      - 3rd exchange no longer needed (tested with 24 tiles).
73      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
74      - exch_UV_A-grid readily available (but not yet tested).
75      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
76      (both are no longer needed) in exch_uv: no effect in forward run; but
77       get truncation error differences with adjoint exch.
78    o exch2:
79     - change index-bounds storage (moved from target to local tile,
80       more intuitive this way) ; rename/remove some variables.
81     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
82    
83    checkpoint61a
84    o exch2/matlab-topology-generator:
85      fix bug in index bounds for N-S internal exchange (hard to tell if this
86      had any effect on the solution).
87    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
88      is exceeded
89    o testreport: modify syntax of awk, so that it works also with
90      awk, and not only with nawk and gawk
91    
92    checkpoint61
93    o autodiff
94      Change default for TAF usage by removing argument '-nonew_arg'
95      This changes TAF subroutine argument list (ordering of active var.)
96      Omission of this flag leads to incompatibility w.r.t. TAMC
97      To restore TAMC-compatibility, need following modifs:
98      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
99      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
100      Tested TAF version is 1.9.22
101      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
102    
103    checkpoint60
104    --->>> This is the last checkpoint for which generating the adjoint
105    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
106    --->>> by default.
107    --->>> Future checkpoints will ommit this flag by default.
108    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
109    o pkg/grdchk: Add gradient check to etan0 perturbations.
110    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
111    o pkg/autodiff: more flexibility in zeroadj.
112      model/src: modifying do_oceanic_phys.F accordingly.
113    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
114    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
115      special setup of gmredi for which the adjoint is stable
116      enough for parameter optimization.
117    o bridging the gap between eddy stress and GM.
118      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
119          along with a change in CPP option (now ALLOW_EDDYPSI).
120      -> when using GM w/ GM_AdvForm:
121          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
122          is applied either in the tracer Eq. or in momentum Eq.
123          depending on data.gmredi (intro. GM_InMomAsStress).
124      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
125      The key modifications are in model/src/taueddy_external_forcing.F
126      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
127    
128    checkpoint59r
129    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
130      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
131      fix option to read coriolis(@ cell-corner) from files with CS-grid.
132    o pkg/mnc: add some attributes to standard 1D-coordinate variables
133    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
134      mass points, when using mnc for output
135      - add runtime parameter (missing_value, missing_value_int) to override
136        default (which is the value of getcon('UNDEF'))
137    o pkg/mnc: prepare mnc for the actual use of missing values with the
138      diagnostics package: small fix in mnc_cw_readwrite.template and more
139      initialisation of never used fields
140      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
141      versions
142    o pkg/thsice/thsice_ini_vars.F added default initial values so that
143      thermodynamics sea ice solver does not blow up when some initial fields
144      are missing.
145    o move from external_forcing_surf.F to ini_forcing.F
146      the p-coord. hack consisting in using pLoad to set phi0surf ;
147      update output of tutorial_global_oce_in_p (affected @ truncation level).
148    o Freshen up a bit hs94.1x64x5, notably:
149      remove rotationPeriod and tRef=5*0. (adjoint only), and add
150      exactConserv=.TRUE.
151    o pkg/generic_advdiff:
152      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
153      applies to files where Temperature & Salinity 2nd Order moments are used.
154    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
155      this uses a dynamically allocated internal state data structure
156      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
157      and requires a fortran 90 compiler
158    
159    checkpoint59q
160    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
161       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
162    o Refresh tutorial_global_oce_biogeo, notably:
163      - change bathymetry (put back seamounts in ACC, use hFacs)
164      - change EOS (POLY3 --> JMD95Z)
165      - use Bryan-Lewis vertical diffusivity
166      - use multidimensional advection
167      - remove old virtual virtual in dic pkg, now done through ptracer pkg
168      - change a couple of parameters in dic pkg
169    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
170    o pkg/obcs: change default to OBCSfixTopo = .true.,
171      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
172      - replace "debugMode" with "debugLevel .GE. debLevB"
173    o implementation of TAF directives for gchem,cfc,dic
174    o remove "exp5" (replaced by tutorial_deep_convection).
175    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
176      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
177      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
178      --> changes results in exp4, seaice_obcs
179    o tutorial_deep_convection :
180      update the set-up and increase resolution and domain size ; start
181      from pseudo initial conditions = output at t=120mn in order to see
182      something happening when running testreport.
183    o pkg/seaice: add os7mp as an advection scheme
184                  add check for advection schemes
185                  add a flag for restoring T and S underneath sea ice
186    o pkg/my82: add netcdf-support and diagnostics
187    o thsice pkg:
188      - Now hsMax limits snow height by turning it into ice following
189        flooding scheme (and now conserving energy)
190      - Slight rewriting of the formula in thsice_calc_thick.F
191      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
192      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
193    
194    checkpoint59p
195    o gchem / dic / cfc :
196      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
197      - add new parameter files: "data.dic" & "data.cfc" ;
198      - various re-arrangement in initialisation & header file ;
199      - fix tutorial_global_oce_biogeo for multi-threaded test.
200    o pkg/dic: test for "pickup_dic" file when restarting ;
201      if no pickup-file, can restart with a re-initialised pH (same as it did
202      before) providing pickupStrictlyMatch is set to False.
203    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
204      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
205    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
206      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
207    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
208     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
209       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
210    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
211       scheme to use for vorticty-term ;
212     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
213       (with default selectVortScheme, return to original discretisation)
214     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
215    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
216    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
217      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
218      also fix diagnostics VISCAHW & VISCA4W.
219    
220    checkpoint59o
221    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
222    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
223      move a few statemens out the main loop into separate loops
224    o pkg/shelfice:
225      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
226        (kg/m^2/s), does not break tests, because in verification/isomip,
227        rhoConstFresh=rhoConst (by accident)
228      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
229      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
230        new file model/src/seawater.F, so that they are available for all pkgs.
231      - convert potential temperature into in-situ temperature. This changes the
232        isomip tests => update tests
233    o add a flag writePickupAtEnd (default=true) to be able to suppress
234      writing a pickup at the last timestep
235    o tools/mpack-1.6 :
236      - disable automake (not working) and autoconf (not needed).
237      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
238        also cleaner with much less compilation warnings.
239    o pkg/profiles:
240      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
241      (for "less than 32 characters name" compiler requirement)
242    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
243      conditions that have a different sampling frequency than S/T/U/V obcs
244    o pkg/diagnostics (stats-diags):
245      - fix global Min/Max in case 1 processor get only empty tiles
246    o genmake2: replace (4 times)
247         make genmake_tc_1.o >> genmake_warnings 2>&1
248      with
249         COMM="$CC $CFLAGS -c genmake_tc_1.c"
250         echo $COMM >> genmake_warnings
251         $COMM >> genmake_warnings 2>&1
252      to make genmake2 always see the value of CC as specified in the optfile.
253    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
254      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
255      - modify verification advect_cs test to test SOM-advection on CS-grid.
256    o pkg/ctrl:
257      - Rewrite of ctrl_map_ini_ecco.F,
258        introducing a generic routine (ctrl_map_ini_gen.F).
259      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
260    
261    checkpoint59n
262    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
263      number in dedicate array "hdiag":
264      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
265        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
266      - many small changes (integer format) for large number of diagnostics
267      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
268        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
269    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
270      usingSphericalGrid, this allows to define the rotated grid coordinates
271      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
272      geographical coordinates according to the inverse of the rotation defined
273      by the Euler angles, so that Coriolis parameter and online-interpolation by
274      exf works with the geographical coordinates on XC/YC/XG/YG.
275      Naturally, this feature does not work with all packages, so some
276      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
277      profiles), because there the coordinates are assumed to be regular
278      spherical grid coordinates.
279    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
280      - introduce isopycnal diffusion coefficient control.
281    o tools/adjoint_options:
282      - additional control vector components.
283    o pkg/mnc: have mnc create marginally meaning full coordinate variables
284      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
285    o pkg/mypackage:
286      - add example of read/write pickup for state-var ;
287      - add entry points to the main code for state-vars diags & write-pickup.
288    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
289      transitions for useExfYearlyFields
290      - add new subroutine that determines the file to read from for
291        use*YearlyFields = .TRUE. and .FALSE.
292      - add a verification experiment to global_with_exf that tests
293        useExfYearlyFields with USE_EXF_INTERPOLATION defined
294    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
295      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
296      subroutines (which could be generated from a template, because they are
297      almost identical), for now they are included in obcs_prescribe_read.F for
298      simplicity
299    o pkg/exf:
300      - add a little more diagnostic to exf_interp_read (in analogy to
301        mds_read_field, can be turned off with debugLevel < debugLevA=1)
302      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
303        ugly but fast by unrolling short inner loops, inserting a unroll=8
304        directive in routine lagran, and splitting a loop and making do while the
305        outermost loop (the latter requires the intoduction of index arrays)
306    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
307    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
308      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
309    o verification/seaice_obcs: updated for restart test and latest options
310    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
311      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
312      for now this is only available for the C-grid code and also within
313      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
314    
315    checkpoint59m
316    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
317      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
318    o gad_som : fix flux output (& diagnostics) to have same units as other  
319      advection scheme fluxes (was previously multiplied by deltaT).  
320    o added verification/seaice_obcs both to test seaice open boundaries
321      and to provide an example matlab scrpt for generating them
322    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
323    o pkg/salt_plume: clean up salt_plume_frac.F to
324      remove redundancy in PlumeMethod 1 and 4
325    o pkg/kpp: added saltplume diagnostics
326    o pkg/obcs and pkg/seaice:
327      - do not set uice and vice to zero when OB*icefile are unspecified
328      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
329      - moved seaice tracer obcs after call to seaice_growth
330    o pkg/salt_plume: added various options for salt plume depth
331      criterion and for vertical distribution of the salt
332    
333    checkpoint59l
334    o pkg/ptracers: new version of ptracers pickup:
335      read meta file and write only fields which are needed to restart.
336      ( same logic as main pickup file ; also using pickupStrictlyMatch )
337    o pkg/seaice:
338      - add timescale for melting due to warm mixed layer as a means of
339        setting SEAICE_availHeatFrac more conveniently
340      - add a CPP-flag/runtime parameter check for flooding algorithm
341      - reformulated availHeat in seaice_growth.F to be independent of AREA
342    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
343      unit changes
344    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
345    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
346      SX vector computer.
347    o pkg/seaice:
348      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
349        seaice forcing fields can now be read only through pkg/exf
350      - removed some unused halos
351    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
352    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
353      or U/VICE from U/VWIND before computing U/VSTRESS
354    
355    checkpoint59k
356    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
357      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
358    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
359      all experiments pass when compile with un-initialised var. checking option.
360    o added pkg/salt_plume
361    o script to test restart (for now, in MITgcm_contrib/jmc_script)
362    o pkg/seaice: new read/write pickup version.
363      read meta file and write only fields which are needed to restart.
364      ( same logic as main pickup file ; also using pickupStrictlyMatch )
365    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
366    o lab_sea.hb87: modify the domain & update output.hb87.txt :
367      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
368      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
369      process. Fixed here by closing the domain at the Northern boundary.
370    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
371    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
372      a set of consecutive levels in/from a 3-D array.
373    o pkg/ptracers:
374      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
375      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
376    
377    checkpoint59j
378    o in pkgs: dic, obcs, offline, rbcs:
379      standard way to compute coeff. for time interpolation between 2 time reccords
380      which retains full precision (& make results less dependent on compiler).
381      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
382    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
383      packages instead of reading ice cover and wind speed separately
384    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
385     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
386      to allow to compile customized code before the update)
387    o cleaning-up:
388      - fix CPP instruction syntax in pkg/obcs
389      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
390        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
391      - fix some threads issue in IO parts.
392    o pkg/dic:
393      - add tons of "_d 0" (--> much better testreports !)
394       and then update outputs of tutorial_global_oce_biogeo
395    o pkg/mom_fluxform:
396      add a special version of momentum advection intended to conserve momentum
397      next to a bathymetry step or a coastline edge. (default = off = #undef)
398    o new read/write pickup version:
399      - for now, only implemented for main (mdsio) pickup file.
400      - write out only what is needed to restart; merge pickup_nh , pickup_ph
401        and main pickup together.
402      - read meta file; read only what is needed to restart; stop if a field
403        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
404        if it make sense (even if the restart is not perfect).
405      - if no meta file, assume that pickup to read corresponds exactly to
406        a pickup that would currently be written.
407      - read pickup written in the old format (until checkpoint59i) if it
408        recognizes an old meta file (no field-list).
409      - add a meta file in exp. which starts from a pickup: 2 cases:
410        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
411         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
412        b) a meta file describing the content of the associated pickup file
413         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
414    o pkg/mdsio & pkg/rw:
415      - new routine to read a meta file ; new set of routine to read
416        Multiple-fields file (with meta file).
417    o added open boundary conditions capability for seaice
418        HSNOW, HSALT, UICE, and VICE
419    
420    checkpoint59i
421    o adjoint:
422      * fix multiDimAdvection adjoint
423        (partial recomputation problem by TAF for fVerT(:,:,kDown)
424        and comlev1 size definition (maxpass vs. max. number of tracers)
425      * verification/global_ocean.90x45x15 adjoint now tests
426        NLFS and multiDimAdvection using DST3 (=30)
427      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
428    o pkg/kpp: add "_d 0" to real constant (if missing);
429      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
430      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
431    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
432      for internal parameters related to restart process (formerly from PARAMS.h)
433      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
434    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
435      as argument. (only atm2d & obcs write_pickup have not yet been updated)
436    o pkg/monitor:
437      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
438      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
439      - account for deep Atmosphere factor and density factor (anelastic)
440    o added open boundary conditions capability for seaice HEFF and AREA
441    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
442      thermodynamics
443      - requires a little reorganization, which affects the testreport results
444        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
445        so that now the conservative form is tested
446      - add a few comments
447    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
448    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
449    o add new diagnostics to seaice: advective, diffusive fluxes (only for
450      multidim-advection, for scheme 2 they are not filled) and transports,
451      thermodynamic growth rates
452    o change units of EmPmR (inside the code, + within coupling interface)
453      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
454      Affects results @ truncation level (cg2d match) and update output of
455       experiments: lab_sea(6), global_ocean.90x40x15(10),
456      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
457      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
458      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
459      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
460    
461    checkpoint59h
462    o pkg/exf:
463      - improve vectorization by moving if-statement out of loops in
464        exf_mapfields, exf_radiation
465      - exf_bulkformulae.F: introduce 2D fields and vectorize code
466    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
467    o testreport:
468      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
469        monitor & update offline_exf_seaice exp. output.
470      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
471    o pkg/seaice:
472      - bug fix in the evp solver: boundary conditions were affected be
473        masking of zMax/zMin (changes results)
474      - minor bug fix in boundary conditions in seaice_calc_strainrates
475        (changes results for no_slip)
476      - seaice_lsr.F: make interpolation of eta dependent on boundaries
477      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
478      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
479        stress formulation and no-slip boundary conditions
480    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
481      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
482    o pkg/seaice: a first HSALT time stepping equation has been checked in
483    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
484      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
485      without requiring DO-IF statements
486    o pkg/thsice:
487      use continuous power-law function for partition of energy between lateral
488      melting/freezing and thinning/thickening ; old code using step function
489      still available with #undef THSICE_FRACEN_POWERLAW
490      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
491    o testreport: change AD testing : check against results/output_adm.txt
492      using same scripts as for forward test.
493    
494    checkpoint59g
495    o adjoint testing: in preparation for changing testreport:
496      - output format: cost and grad written on separated lines
497      - ad output results in directory "results" (instead of "results_ad")
498    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
499    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
500    o pkg/ecco: allow user defined cost function contributions
501    o testreport:
502      Allow to choose (per experiment) the list of tested output variables
503       and the main variable (used to issue a pass/FAIL ) ;
504      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
505      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
506      Also modify printing of summary:
507       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
508       b) echo the list of tested variables in the individual summary.txt of
509          each experiment.
510    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
511      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
512      (but still depend on the tile decompostion of the domain).
513    o pkg/seaice: change a discretization detail to make the B-grid code
514      "more symmetric". This change is likely to remove all "ridges/leads" that
515      where quasi-aligned with the grid in B-grid solutions. It may also be
516      the solution to the stress coupling issues with the B-grid.
517    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
518      remove .cvsignore from input dir. (since testreport no longer run here).
519    o pkg/thsice:
520     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
521     - fix reshaping of sea-ice just after advection:
522       melt all the ice only if ice-volume is too small.
523     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
524       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
525     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
526    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
527      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
528    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
529      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
530      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
531      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
532      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
533      -> update output.txt
534    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
535     this affects truncation error: -> update output.txt of exp:
536      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
537      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
538    
539    checkpoint59f
540    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
541    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
542      a bounded range (in forward mode)
543    o pkg/ecco, ctrl, autodiff and mom_common:
544     internal parameter controls, completements of implementations
545    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
546    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
547      (not seem any difference in testing results).
548    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
549       at face corners.
550    o pkg/generic_advdiff:
551     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
552      loop range indices for computing vertical advection tendency
553      and do the calculation in the interior only (no overlap) ;
554      for now, only implemented for SOM advection (to save CPU time).
555     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
556    o exch2 adjoint
557      First set of changes:
558      - add exch2 hand-written adjoint templates
559      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
560        This will require cleanup in pkg/autodiff/*.F
561        (changed routines currently kept separate in verif. code/)
562      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
563        that used to hide exch2 or cubed-sphere specific code
564        (commented via 'cph-exch2')
565    o pkg/seaice
566      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
567    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
568       output of global_ocean.cs32x15.thsice .
569    
570    checkpoint59e
571    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
572      for B-grid vector (not yet tested) and C-grid vector (<- only used
573      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
574    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
575      (#ifdef ALLOW_SALT_PLUME)
576    o gather_2d/scatter_2d: removed halo regions
577    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
578      scheme and the corresponding test case (under front_relax dir). For now,
579      only available with Skew-flux form and not yet tested in realistic set-up.
580      adjoint: store directives updated, but gradient checks deteriorated,
581      so maybe GM/Redi adjoint is now broken.
582    o seaice adjoint
583      * add AREA, HEFF, HSNOW as control variable
584        (should not change lab_sea results)
585      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
586    o pkg/seaice:
587      * added computation of saltFlux in seaice_growth;
588        For time being, sea ice salinity is assumed constant
589        contribution of snow flooding to freshening of sea ice is neglected.
590        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
591        defaults to 0.0 in order to maintain backward compatibility.
592        Typical values for SEAICE_salinity are 4 to 10 g/kg.
593      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
594      * added SEAICE_availHeatFrac, which specifies fraction of surface level
595        heat content used to melt or grow ice
596      * commented out cap of HICE: it helps keep ice thinner
597      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
598      * applied OBCS T/S mask to HEFFM sea ice mask
599    
600    checkpoint59d
601    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
602     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
603     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
604    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
605     and change default value of parameter "GM_Small_Number";
606     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
607       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
608       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
609    o pkg/ecco: cost function when applying pkg/smooth to controls
610    o pkg/ctrl: add forcingPrecond run time parameter
611    o pkg/seaice:
612     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
613     - fix bug in metric terms of u-equation in LSR solver (implicit part),
614       changes verification/lab_sea
615     - rearrange implicit part of u-equation in LSR solver to make it easier to
616       read, understand, and debug. This causes changes at the truncation level.
617     - fix (serious) bug in the boundary conditions (sign error in the implicit
618       part) of the LSR solver. Changes all LSR results.
619     - fixed problem with HSNOW initialization to avoid thick snow when AREA
620       is initilized with small values - does not change lab_sea results.
621     - added HsnowFile initialization capability
622    o pkg/smooth: addition to model/src and pkg/ctrl so allow
623     initialization of pkg/smooth and application to control vector
624    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
625    o dependencies: pkg/profiles requires pkg/cal
626    o pkg/profiles:
627     - added option ALLOW_PROFILES_GENERICGRID
628         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
629         that interpolation information (grid points and coefficients) is provided
630         within the netcdf input files.
631         -> sample matlab scripts can be found in MITgcm_contrib/gael
632         that allow you to prepare netcdf input files.
633     - also modified: cleaner include statements, cleaner error print statements,
634       cleaner stops when error, and more tests of the netcdf input files consistency.
635    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
636    o pkg/seaice:
637     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
638       requires a new routine: seaice_diagnostics_fill.F
639     - make sure that seaice does not move if not forced (pressure replacement
640       method, Hibler and Ip, 1995), changes results
641     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
642     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
643       It is turned off by default (=-1.), because it changes the results.
644     - make it possible to read AREA from a file, too.
645    
646    checkpoint59c
647    o add S/R and diagnostics for oceanic mixed-layer depth
648    o move GMRedi call after all vertical mixing schemes (including KPP)
649    o pkg/thsice:
650     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
651      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
652    o pkg/obcs:
653     - bug fix for balance code
654    o pkg/seaice:
655      - allow values of SEAICE_elasticParm > 1
656      - add new parameter SEAICE_evpTauRelax as an alternative
657        to SEAICE_elasticParm
658      - make lsr boundary conditions free slip (by default), changes result
659      - add code for no slip boundary conditions for lsr
660      - set minimum of zeta to zero (and not 4e8) (changes results)
661      - add a cap on AREA after advecting AREA if seaice_growth is not called
662    o change calculation of Visbeck K:
663      - no longer depend on tapering scheme; instead, compute slope (limited
664        by GM_maxSlope). this is equivalent to what was comuted before with
665        clipping or linear tappering.
666      - fix vertical averaging (wrong by 1/2 level)
667      - leave the old version (but will not be maintained) within
668        #ifdef OLD_VISBECK_CALC / #endif
669      - update output of exp. ideal_2D_oce
670    o change error catch in calc_r_star to improve vectorization
671    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
672      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
673    o adjoint:
674      Re-organized adjoint checkpointing according to Matt Mazloff
675      (but with modifs/completions/cleanups)
676      Storing is now bundled into large arrays to optimized I/O
677      (and second step in cleanup of the_main_loop)
678    
679    checkpoint59b
680    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
681      - export/import (between ocean & coupler) fields needed for ocean DIC.
682    o pkg/seaice:
683      - get rid of three more exchanges seaice_calc_viscosities (required
684        different loop boundaries in seaice_lsr and seaice_ocean_stress)
685      - bug fix in seaice_ocean_stress (update of lab_sea required)
686      - reduce loop boundaries to necessary minimum also in seaice_evp
687      - go back to the old way of computing deltaC/Z as the adjoint likes that
688        better
689    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
690      passive tracer to an Age Tracer) + update output.txt
691    o pkg/exf:
692      - implement A-grid / C-grid selection for wind-stress input files.
693      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
694      for now, in exf_bulk_largeyeager04.F only :
695      - change implementation for case where windspeed + 2. components wind-stress
696        are read-in. AND use rhoConstFresh to convert evap.
697    o pkg/seaice:
698      - use correct EXCH_UV for wind-forcing (on A-grid).
699      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
700        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
701    o pkg/exf:
702      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
703      EXF_INTERPOLATION:
704      - merge global_with_exf/code version of exf_interp_read.F
705        to the main code ;
706      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
707        reading the file ; Important: This options needs to be defined to recover
708        previous code.
709        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
710      - no longer loose real*8 precision along the way when using exf_iprec=64.
711    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
712      - change discretisation of evp-solver in order to avoid another exchange
713        (changes lab_sea) and clean up a little
714      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
715        help the adjoint (this also changes the results slightly)
716      - add a few "_d 0" where they had been missing in seaice_evp.F
717      - cleaning up: remove unused seaice_calc_rhs.F
718    o pkg/exf: some cleaning-up:
719      - change various "constants" into runtime parameters
720      - cleaned-up Large&Yeager04 routine which should eventually
721        replace exf_bulkformulae.F (changed names of S/R and CPP)
722        and merged various ALLOW_ATM_WIND options
723     only used with thsice pkg (in thsice_get_exf.F):
724      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
725        which are used when useStabilityFct_overIce=TRUE (= the default)
726      - change default values of ice & snow emissivity and scale downward LW
727        by ice & snow emissivity.
728    o pkg/thsice:
729     fix few little problems, in thsice_calc_thickn.F:
730      - growth vertically (and not laterally) if iceFrac == iceMaskMax
731      - melt only laterally if hIce < hThinIce (as the comments say)
732      and in thsice_extend.F:
733      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
734      - start to form ice as soon as the minimum ice-volume is reachable.
735     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
736      and cpl_aim+ocn
737    o pkg/kpp
738     - move computation of surface related input fields to KPP into a new
739       subroutine kpp_forcing_surf.F
740     - remove wrong (within bi,bj loops) EXCH calls.
741     - little cleaning (add argument myThid in last position, cvs header ...)
742     - for now, fix conservation problem by exchanging KPPviscAz (may not
743       be the best fix)
744    o pkg/seaice
745     - check for inconsistent evp parameter/cpp-flag combination
746     - remove leftover errIO flat for obsolete name list error handling
747    o OpenAD
748     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
749    
750    checkpoint59a
751    o pkg/seaice: some parameter clarifications and a little bit of clean up
752    o pkg/thsice: rename run-time parameters:
753       himin       -> hIceMin
754       himin0      -> hThinIce
755       hihig       -> hThickIce
756       i0          -> i0swFrac
757       transCoef   -> bMeltCoef
758       frac_energy -> fracMelting
759      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
760       with default values (for now) that do not change the results.
761      remove old version of thsice vars advection in pkg/seaice.
762    o in FFIELDS.h:
763      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
764      - make pLoad & sIceLoad always available (but still only used if
765         ATMOSPHERIC_LOADING is #define).
766    o pkg/kpp: replaced _KPP_RL with _RL
767    o bug fixes for vertical diffusivity computations when both KPP and
768        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
769        are no longer updating the vertical diffusivity array
770        (passed as argument) but are (re-) setting those arrays.
771    o pkg/seaice: fix bug in evp solver, while doing that
772      - change (improve?) discretization of stress computations for both
773        cgrid-lsr and evp solver
774      - add a new routine to compute strain rates
775      - the above changes lab_sea results
776      - add no slip conditions for evp solver (off by default), lsr-version
777        may follow
778      - fix exchange for shear at Z-points (does not change lab_sea)
779      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
780        (to force the user to pick a time step since there is not "safe" way
781        of choosing it)
782      - add principal stress diagnostics
783      - rearrange fields for evp a little to avoid having to call a: too many
784        exchanges and b: exchanges for stress trensor components which we do
785        not have.
786      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
787        of evp, complete rewrite for lsr case (latter is does not yet work
788        in all cases)
789    o pkg/kpp: add code to have mixing in shelf ice caverns
790      - add myThid to all kpp routines (long overdue)
791    
792    checkpoint59
793    o pkg/exf:
794      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
795        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
796      - move exf header files from lower_case.h to UPPER_CASE.h ;
797        add missing cvs Header & Name
798      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
799      - add namelist param. selectStressGridPosition, exf_monFreq
800      - retire many _CLIM routines, and remove data.exf_clim
801        + params moved to data.exf
802        + climsst, climsss now handled by exf_set_gen, i.e.
803          climss?period=0 refers to constant field,
804          climss?period=-12 to monthly forcing
805      - split up namelists in data.exf
806    o pkg/seaice:
807      - remove seaice_exch and seaice_exch_uv
808      - remove superfluous exchange of theta
809      - add myThid to seaice_budget_ocean/ice
810      - add new interface for atmospheric wind forcing (C-grid only)
811        + new routine
812        + two new field (taux, tauy for stress over ice)
813        + removed one global field (DAIRN) for C-grid case only
814    o pkg/thsise
815      - 2nd set of modifs for thsice adjoint in conjunction with exf
816    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
817    
818    checkpoint58y_post
819    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
820      vertical diffusivity, similar to that in MOM4; turned on using
821      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
822      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
823    o Added capability for 3D specification of background vertical diffusion
824      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
825      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
826      "data" file that contains the 3D vertical diffusivity coefficients.
827    o ice dynamics (pkg/seaice) with thsice thermodynamics:
828      - add code within pkg thsice to advect & diffuse sea-ice fields
829      similar to (and will replace) what has been added in  seaice_advdiff.F,
830      but: - conserving Mass, Heat & Salt.
831           - better when using non-linear advection scheme (not yet fully tested)
832           - can also be used in atmospheric set-up (for now, only the diffusion).
833    
834    checkpoint58x_post
835    o IO option for global-file compact format:
836      - add options when generating topology (utils/exch2/matlab-topology-generator)
837      - add I/O capability (pkg/mdsio).
838      - adapt utils/matlab/rdmds.m to read this format.
839      for now long-line format not yet supported by pkg/mdsio (& exch2).
840    o shelfice: add a few diagnostics
841    
842    checkpoint58w_post
843    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
844      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
845      (and replace horiVertRatio in NH code).
846      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
847                         and tutorial_plume_on_slope (sensitive to truncation)
848    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
849      directly to drive seaice model (C-grid only)
850    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
851     - reintroduce computation of wind from stress,
852     - compute tau (in exf_bulkformulae.F) from windstress averaged to
853       mass points to avoid tau = 0
854     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
855    o rdmnc.m: make it work with "global" files created with gluemnc
856    o rdmnc.m : some improvements in dealing with singleton dimension
857      (tested on all testreport mnc output files).
858    o genmake2: disable pkg/profiles if netcdf test fails.
859    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
860    o move call to cal_readparms up to make calendar parameters/variable available
861      to all packages
862    
863    checkpoint58v_post
864    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
865      useDynP_inEos_Zc tested.
866    o pkg/exf: changes to properly interpolate/mask/scale initial fields
867    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
868      and portions thereof.  See read_cs.txt for description and examples.
869    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
870      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
871      following the great-circle arc between those 2 points.
872    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
873      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
874    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
875     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
876     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
877     - still needs work (not working with some options ; efficiency to improve)
878       and serious testing.
879     - use this scheme for temperature & salinity in 2 advection test exp.:
880       advect_xy & advect_xz, respectively.
881    
882    checkpoint58u_post
883    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
884    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
885    o testreport: add option "-skipdir" to skip some test.
886    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
887      momentum calculation.
888    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
889    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
890      remove checkpoint.F and the_correction_step.F (no longer used);
891      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
892    o add option (linFSConserveTr) to correct for tracer source/sink due to
893      Linear Free surface
894    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
895    o pkg/thsice: fix reading mnc-pickups
896    
897    checkpoint58t_post
898    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
899    o pkg/mdsio:
900     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
901       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
902       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
903     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
904     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
905       either MDS_READ_FIELD or MDS_WRITE_FIELD )
906     - new S/R (to replace MDSWRITEMETA), which allows to write more
907       informations (variable names, time ...) to meta files.
908     - modify rdmds.m to give back the meta file content.
909    o pkg/diagnostics: change vertical interpolation to be safer, and more
910       flexible (define p-levels to interpolate to in data.diagnostics);
911      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
912       diagnostic pointer.
913    o pkg/seaice: more cleaning up of seaice_growth, added many comments
914    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
915    o fix multi-category seaice:
916     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
917       SEAICE_MULTICATEGORY
918     - fix short wave heat flux
919    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
920       and allow to use EVP solver. Change forward lab_sea: test both EVP
921       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
922    o Initial check-in of lab_sea adjoint
923      (very similar to natl_box_adjoint/code_seaice)
924      * used C-grid and EVP solver
925      * used KPP, GM/Redi
926      * uses inAdExact=.TRUE.
927      * gradient checks fail for both ADM and TLM
928        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
929        f.d. gradients actually seem more problematic than ADM, TLM gradients;
930        issue is related to forward mismatch between g77 an ifort
931    o pkg/seaice: overhaul of thermodynamics
932     - growth.F and groatb.F are replaced by new routine seaice_growth.F
933     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
934     - move a few global fields out of SEAICE.h into seaice_growth.F and
935       make them 2D (FICE/QNETO/ ...)
936     - remove FO (it is the same as QNETO)
937     - introduce a few local fields to avoid modifying external fields such
938       as atemp, etc.
939    
940    checkpoint58s_post
941    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
942      changed exf_set_gen.F so that
943        genperiod=0 means input file is one time-constant field and
944        genperiod=-12 means input file contains 12 monthly means
945    o CG2D: use pre-computed solver main-diagonal (stored in common block);
946      this affects truncation error ; generate new output file for exp. which
947      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
948        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
949        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
950        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
951        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
952        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
953    o start implementation of deep-atmosphere and anelastic formulation
954    o verification: remove 2nd copy of input files and use script "prepare_run"
955      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
956    o mom_common/vecinv/fluxform: fix a few initialisation isssues
957    o profiles: fix for multithreaded case
958    
959    o diagnostics: rename few diags:
960      s/'PRESSURE'/'RCENTER '/g
961      s/'TICE    '/'oceFreez'/g
962      s/'TAUX    '/'oceTAUX '/g
963      s/'TAUY    '/'oceTAUY '/g
964      s/'SWFLUX  '/'oceQsw  '/g
965      s/DIFx/DFxE/g
966      s/DIFy/DFyE/g
967      and add few ocean-forcing diagnostics:
968      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
969    o modifications to pkg/seaice/growth.F and budget.F, which change results of
970      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
971      as actual snow thickness.  It now refers everywhere to effective snow
972      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
973    
974    checkpoint58r_post
975    o modifications to pkg/seaice/growth.F, which change results of
976      lab_sea experiment: fixes pertain to melting snow over open water, to
977      masking EVAP under sea ice, and to using the correct AREA variable for
978      computations of EVAP, PRECIP, HSNOW, and GHEFF
979    o add ability to read bathy, salt, and theta using MNC (off by def)
980    o add flooding algorithm and advection of HSNOW for pkg/seaice;
981      both are turned off by default and do no change any results
982    o seaice advection with pkg/thsice: a step toward the use of non-linear
983      advection scheme, but #ifdef or commented out for now (requires more EXCH).
984    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
985      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
986      in natl_box (affects results @ truncation level: update output.txt)
987    o multi-threading and IO:
988      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
989      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
990        (needed to work with SingleCpuIO): tested in all verif. exp.
991    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
992      affects the results (but none of the verification test uses this scheme).
993    o Adding some pkg/diagnostics capability to pkg/seaice
994      (will certainly be subject to changes)
995    o ctrl: adding new control variables:
996      lwflux, lwdown, evap, snowprecip, apressure, runoff
997    
998    checkpoint58q_post
999    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
1000      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
1001      high_res_cube configuration by 4% on Columbia.
1002    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
1003      add (in global_with_exf/code) a version of EXF_INTERP_READ without
1004      dynamical allocation (seems to work in multi-threaded).
1005    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
1006      single CPU io) so that TAF does not have to see EESUPPORT.h
1007    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
1008    
1009    checkpoint58p_post
1010    o obcs: stop if obcs is used with useCDscheme = .true.
1011    o shelfice:
1012     - fix a sign error so that no slip at shelfice interface works
1013     - remove stop for combination non-hydrostatic code and shelfice. That does
1014       not mean, that the results are correct, but at least they are numerically
1015       stable
1016    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
1017    o added adjoint exch routined for all exch*3d* routines
1018      and updated flow directives
1019    
1020    checkpoint58o_post
1021    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
1022      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
1023    o change controling S/R for writing pickup file (new S/R do_write_pickup)
1024      and clean-up reading/writing of pickup files.
1025    o fix local version of read/write pickup (NH part) in rotating_tank/code
1026    o simplify EXCH interface:
1027     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
1028     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
1029    o added the regrid package
1030    o shelfice:
1031     - add a simple boundary layer scheme to reduce noise
1032     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
1033    
1034  checkpoint58n_post  checkpoint58n_post
1035  o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to  o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
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