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revision 1.685 by baylor, Thu Jun 22 19:39:21 2006 UTC revision 1.1025 by heimbach, Thu Sep 25 16:10:48 2008 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint61d
8    o adjoint modifs
9      - adapt to new field rhoInSitu
10      - allow to revert from StoreDynVars2D, StoreDynVars3D
11        to individual fields
12        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
13    o store 3-D (in-situ) density in commom block (DYNVARS.h)
14     - save 1 rho computation.
15     - no longer modify T & S inland when using down_slope pkg.
16    o gad_som : allow to switch to SOM advection for T & S without corresponding
17      pickup files (using new S/R: MDS_CHECK4FILE).
18    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
19      (for useSingleCpuIO to work in multi-threaded)
20    o pkg/shelfice:
21     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
22       with SHELFICEtopoFile in data.shelfice
23     - move code for reading ice shelf topography and modifying hFacC into separate
24       subroutines of the shelfice package
25     - separate initialisation of "fixed" and "variable" variables
26     - kTopC is not (yet) replaced by kSurfC, although this is possible
27    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
28    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
29      and rename:
30      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
31      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
32    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
33    
34    checkpoint61c
35    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
36      to add mass source/sink of fluid in the interior (3-D generalisation
37      of oceanic real-fresh water flux).
38    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
39    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
40    o new pkg: down_slope
41      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
42      - presently, modify T & S inland (dwnslp_calc_rho.F).
43        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
44      - implementation for ocean in P-coords not tested.
45      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
46    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
47      (to facilitate conversion of oceanic pkg to p-coordinate).
48    o change FIND_RHO to FIND_RHO_2D :
49      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
50    o new pkg: cheapaml
51    
52    checkpoint61b
53    o exch2:
54      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
55      - no longer depend on the order sequence (N,S,E,W).
56      - 3rd exchange no longer needed (tested with 24 tiles).
57      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
58      - exch_UV_A-grid readily available (but not yet tested).
59      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
60      (both are no longer needed) in exch_uv: no effect in forward run; but
61       get truncation error differences with adjoint exch.
62    o exch2:
63     - change index-bounds storage (moved from target to local tile,
64       more intuitive this way) ; rename/remove some variables.
65     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
66    
67    checkpoint61a
68    o exch2/matlab-topology-generator:
69      fix bug in index bounds for N-S internal exchange (hard to tell if this
70      had any effect on the solution).
71    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
72      is exceeded
73    o testreport: modify syntax of awk, so that it works also with
74      awk, and not only with nawk and gawk
75    
76    checkpoint61
77    o autodiff
78      Change default for TAF usage by removing argument '-nonew_arg'
79      This changes TAF subroutine argument list (ordering of active var.)
80      Omission of this flag leads to incompatibility w.r.t. TAMC
81      To restore TAMC-compatibility, need following modifs:
82      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
83      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
84      Tested TAF version is 1.9.22
85      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
86    
87    checkpoint60
88    --->>> This is the last checkpoint for which generating the adjoint
89    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
90    --->>> by default.
91    --->>> Future checkpoints will ommit this flag by default.
92    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
93    o pkg/grdchk: Add gradient check to etan0 perturbations.
94    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
95    o pkg/autodiff: more flexibility in zeroadj.
96      model/src: modifying do_oceanic_phys.F accordingly.
97    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
98    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
99      special setup of gmredi for which the adjoint is stable
100      enough for parameter optimization.
101    o bridging the gap between eddy stress and GM.
102      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
103          along with a change in CPP option (now ALLOW_EDDYPSI).
104      -> when using GM w/ GM_AdvForm:
105          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
106          is applied either in the tracer Eq. or in momentum Eq.
107          depending on data.gmredi (intro. GM_InMomAsStress).
108      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
109      The key modifications are in model/src/taueddy_external_forcing.F
110      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
111    
112    checkpoint59r
113    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
114      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
115      fix option to read coriolis(@ cell-corner) from files with CS-grid.
116    o pkg/mnc: add some attributes to standard 1D-coordinate variables
117    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
118      mass points, when using mnc for output
119      - add runtime parameter (missing_value, missing_value_int) to override
120        default (which is the value of getcon('UNDEF'))
121    o pkg/mnc: prepare mnc for the actual use of missing values with the
122      diagnostics package: small fix in mnc_cw_readwrite.template and more
123      initialisation of never used fields
124      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
125      versions
126    o pkg/thsice/thsice_ini_vars.F added default initial values so that
127      thermodynamics sea ice solver does not blow up when some initial fields
128      are missing.
129    o move from external_forcing_surf.F to ini_forcing.F
130      the p-coord. hack consisting in using pLoad to set phi0surf ;
131      update output of tutorial_global_oce_in_p (affected @ truncation level).
132    o Freshen up a bit hs94.1x64x5, notably:
133      remove rotationPeriod and tRef=5*0. (adjoint only), and add
134      exactConserv=.TRUE.
135    o pkg/generic_advdiff:
136      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
137      applies to files where Temperature & Salinity 2nd Order moments are used.
138    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
139      this uses a dynamically allocated internal state data structure
140      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
141      and requires a fortran 90 compiler
142    
143    checkpoint59q
144    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
145       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
146    o Refresh tutorial_global_oce_biogeo, notably:
147      - change bathymetry (put back seamounts in ACC, use hFacs)
148      - change EOS (POLY3 --> JMD95Z)
149      - use Bryan-Lewis vertical diffusivity
150      - use multidimensional advection
151      - remove old virtual virtual in dic pkg, now done through ptracer pkg
152      - change a couple of parameters in dic pkg
153    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
154    o pkg/obcs: change default to OBCSfixTopo = .true.,
155      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
156      - replace "debugMode" with "debugLevel .GE. debLevB"
157    o implementation of TAF directives for gchem,cfc,dic
158    o remove "exp5" (replaced by tutorial_deep_convection).
159    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
160      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
161      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
162      --> changes results in exp4, seaice_obcs
163    o tutorial_deep_convection :
164      update the set-up and increase resolution and domain size ; start
165      from pseudo initial conditions = output at t=120mn in order to see
166      something happening when running testreport.
167    o pkg/seaice: add os7mp as an advection scheme
168                  add check for advection schemes
169                  add a flag for restoring T and S underneath sea ice
170    o pkg/my82: add netcdf-support and diagnostics
171    o thsice pkg:
172      - Now hsMax limits snow height by turning it into ice following
173        flooding scheme (and now conserving energy)
174      - Slight rewriting of the formula in thsice_calc_thick.F
175      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
176      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
177    
178    checkpoint59p
179    o gchem / dic / cfc :
180      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
181      - add new parameter files: "data.dic" & "data.cfc" ;
182      - various re-arrangement in initialisation & header file ;
183      - fix tutorial_global_oce_biogeo for multi-threaded test.
184    o pkg/dic: test for "pickup_dic" file when restarting ;
185      if no pickup-file, can restart with a re-initialised pH (same as it did
186      before) providing pickupStrictlyMatch is set to False.
187    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
188      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
189    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
190      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
191    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
192     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
193       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
194    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
195       scheme to use for vorticty-term ;
196     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
197       (with default selectVortScheme, return to original discretisation)
198     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
199    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
200    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
201      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
202      also fix diagnostics VISCAHW & VISCA4W.
203    
204    checkpoint59o
205    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
206    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
207      move a few statemens out the main loop into separate loops
208    o pkg/shelfice:
209      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
210        (kg/m^2/s), does not break tests, because in verification/isomip,
211        rhoConstFresh=rhoConst (by accident)
212      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
213      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
214        new file model/src/seawater.F, so that they are available for all pkgs.
215      - convert potential temperature into in-situ temperature. This changes the
216        isomip tests => update tests
217    o add a flag writePickupAtEnd (default=true) to be able to suppress
218      writing a pickup at the last timestep
219    o tools/mpack-1.6 :
220      - disable automake (not working) and autoconf (not needed).
221      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
222        also cleaner with much less compilation warnings.
223    o pkg/profiles:
224      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
225      (for "less than 32 characters name" compiler requirement)
226    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
227      conditions that have a different sampling frequency than S/T/U/V obcs
228    o pkg/diagnostics (stats-diags):
229      - fix global Min/Max in case 1 processor get only empty tiles
230    o genmake2: replace (4 times)
231         make genmake_tc_1.o >> genmake_warnings 2>&1
232      with
233         COMM="$CC $CFLAGS -c genmake_tc_1.c"
234         echo $COMM >> genmake_warnings
235         $COMM >> genmake_warnings 2>&1
236      to make genmake2 always see the value of CC as specified in the optfile.
237    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
238      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
239      - modify verification advect_cs test to test SOM-advection on CS-grid.
240    o pkg/ctrl:
241      - Rewrite of ctrl_map_ini_ecco.F,
242        introducing a generic routine (ctrl_map_ini_gen.F).
243      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
244    
245    checkpoint59n
246    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
247      number in dedicate array "hdiag":
248      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
249        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
250      - many small changes (integer format) for large number of diagnostics
251      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
252        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
253    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
254      usingSphericalGrid, this allows to define the rotated grid coordinates
255      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
256      geographical coordinates according to the inverse of the rotation defined
257      by the Euler angles, so that Coriolis parameter and online-interpolation by
258      exf works with the geographical coordinates on XC/YC/XG/YG.
259      Naturally, this feature does not work with all packages, so some
260      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
261      profiles), because there the coordinates are assumed to be regular
262      spherical grid coordinates.
263    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
264      - introduce isopycnal diffusion coefficient control.
265    o tools/adjoint_options:
266      - additional control vector components.
267    o pkg/mnc: have mnc create marginally meaning full coordinate variables
268      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
269    o pkg/mypackage:
270      - add example of read/write pickup for state-var ;
271      - add entry points to the main code for state-vars diags & write-pickup.
272    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
273      transitions for useExfYearlyFields
274      - add new subroutine that determines the file to read from for
275        use*YearlyFields = .TRUE. and .FALSE.
276      - add a verification experiment to global_with_exf that tests
277        useExfYearlyFields with USE_EXF_INTERPOLATION defined
278    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
279      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
280      subroutines (which could be generated from a template, because they are
281      almost identical), for now they are included in obcs_prescribe_read.F for
282      simplicity
283    o pkg/exf:
284      - add a little more diagnostic to exf_interp_read (in analogy to
285        mds_read_field, can be turned off with debugLevel < debugLevA=1)
286      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
287        ugly but fast by unrolling short inner loops, inserting a unroll=8
288        directive in routine lagran, and splitting a loop and making do while the
289        outermost loop (the latter requires the intoduction of index arrays)
290    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
291    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
292      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
293    o verification/seaice_obcs: updated for restart test and latest options
294    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
295      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
296      for now this is only available for the C-grid code and also within
297      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
298    
299    checkpoint59m
300    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
301      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
302    o gad_som : fix flux output (& diagnostics) to have same units as other  
303      advection scheme fluxes (was previously multiplied by deltaT).  
304    o added verification/seaice_obcs both to test seaice open boundaries
305      and to provide an example matlab scrpt for generating them
306    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
307    o pkg/salt_plume: clean up salt_plume_frac.F to
308      remove redundancy in PlumeMethod 1 and 4
309    o pkg/kpp: added saltplume diagnostics
310    o pkg/obcs and pkg/seaice:
311      - do not set uice and vice to zero when OB*icefile are unspecified
312      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
313      - moved seaice tracer obcs after call to seaice_growth
314    o pkg/salt_plume: added various options for salt plume depth
315      criterion and for vertical distribution of the salt
316    
317    checkpoint59l
318    o pkg/ptracers: new version of ptracers pickup:
319      read meta file and write only fields which are needed to restart.
320      ( same logic as main pickup file ; also using pickupStrictlyMatch )
321    o pkg/seaice:
322      - add timescale for melting due to warm mixed layer as a means of
323        setting SEAICE_availHeatFrac more conveniently
324      - add a CPP-flag/runtime parameter check for flooding algorithm
325      - reformulated availHeat in seaice_growth.F to be independent of AREA
326    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
327      unit changes
328    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
329    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
330      SX vector computer.
331    o pkg/seaice:
332      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
333        seaice forcing fields can now be read only through pkg/exf
334      - removed some unused halos
335    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
336    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
337      or U/VICE from U/VWIND before computing U/VSTRESS
338    
339    checkpoint59k
340    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
341      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
342    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
343      all experiments pass when compile with un-initialised var. checking option.
344    o added pkg/salt_plume
345    o script to test restart (for now, in MITgcm_contrib/jmc_script)
346    o pkg/seaice: new read/write pickup version.
347      read meta file and write only fields which are needed to restart.
348      ( same logic as main pickup file ; also using pickupStrictlyMatch )
349    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
350    o lab_sea.hb87: modify the domain & update output.hb87.txt :
351      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
352      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
353      process. Fixed here by closing the domain at the Northern boundary.
354    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
355    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
356      a set of consecutive levels in/from a 3-D array.
357    o pkg/ptracers:
358      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
359      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
360    
361    checkpoint59j
362    o in pkgs: dic, obcs, offline, rbcs:
363      standard way to compute coeff. for time interpolation between 2 time reccords
364      which retains full precision (& make results less dependent on compiler).
365      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
366    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
367      packages instead of reading ice cover and wind speed separately
368    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
369     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
370      to allow to compile customized code before the update)
371    o cleaning-up:
372      - fix CPP instruction syntax in pkg/obcs
373      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
374        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
375      - fix some threads issue in IO parts.
376    o pkg/dic:
377      - add tons of "_d 0" (--> much better testreports !)
378       and then update outputs of tutorial_global_oce_biogeo
379    o pkg/mom_fluxform:
380      add a special version of momentum advection intended to conserve momentum
381      next to a bathymetry step or a coastline edge. (default = off = #undef)
382    o new read/write pickup version:
383      - for now, only implemented for main (mdsio) pickup file.
384      - write out only what is needed to restart; merge pickup_nh , pickup_ph
385        and main pickup together.
386      - read meta file; read only what is needed to restart; stop if a field
387        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
388        if it make sense (even if the restart is not perfect).
389      - if no meta file, assume that pickup to read corresponds exactly to
390        a pickup that would currently be written.
391      - read pickup written in the old format (until checkpoint59i) if it
392        recognizes an old meta file (no field-list).
393      - add a meta file in exp. which starts from a pickup: 2 cases:
394        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
395         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
396        b) a meta file describing the content of the associated pickup file
397         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
398    o pkg/mdsio & pkg/rw:
399      - new routine to read a meta file ; new set of routine to read
400        Multiple-fields file (with meta file).
401    o added open boundary conditions capability for seaice
402        HSNOW, HSALT, UICE, and VICE
403    
404    checkpoint59i
405    o adjoint:
406      * fix multiDimAdvection adjoint
407        (partial recomputation problem by TAF for fVerT(:,:,kDown)
408        and comlev1 size definition (maxpass vs. max. number of tracers)
409      * verification/global_ocean.90x45x15 adjoint now tests
410        NLFS and multiDimAdvection using DST3 (=30)
411      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
412    o pkg/kpp: add "_d 0" to real constant (if missing);
413      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
414      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
415    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
416      for internal parameters related to restart process (formerly from PARAMS.h)
417      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
418    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
419      as argument. (only atm2d & obcs write_pickup have not yet been updated)
420    o pkg/monitor:
421      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
422      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
423      - account for deep Atmosphere factor and density factor (anelastic)
424    o added open boundary conditions capability for seaice HEFF and AREA
425    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
426      thermodynamics
427      - requires a little reorganization, which affects the testreport results
428        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
429        so that now the conservative form is tested
430      - add a few comments
431    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
432    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
433    o add new diagnostics to seaice: advective, diffusive fluxes (only for
434      multidim-advection, for scheme 2 they are not filled) and transports,
435      thermodynamic growth rates
436    o change units of EmPmR (inside the code, + within coupling interface)
437      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
438      Affects results @ truncation level (cg2d match) and update output of
439       experiments: lab_sea(6), global_ocean.90x40x15(10),
440      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
441      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
442      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
443      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
444    
445    checkpoint59h
446    o pkg/exf:
447      - improve vectorization by moving if-statement out of loops in
448        exf_mapfields, exf_radiation
449      - exf_bulkformulae.F: introduce 2D fields and vectorize code
450    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
451    o testreport:
452      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
453        monitor & update offline_exf_seaice exp. output.
454      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
455    o pkg/seaice:
456      - bug fix in the evp solver: boundary conditions were affected be
457        masking of zMax/zMin (changes results)
458      - minor bug fix in boundary conditions in seaice_calc_strainrates
459        (changes results for no_slip)
460      - seaice_lsr.F: make interpolation of eta dependent on boundaries
461      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
462      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
463        stress formulation and no-slip boundary conditions
464    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
465      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
466    o pkg/seaice: a first HSALT time stepping equation has been checked in
467    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
468      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
469      without requiring DO-IF statements
470    o pkg/thsice:
471      use continuous power-law function for partition of energy between lateral
472      melting/freezing and thinning/thickening ; old code using step function
473      still available with #undef THSICE_FRACEN_POWERLAW
474      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
475    o testreport: change AD testing : check against results/output_adm.txt
476      using same scripts as for forward test.
477    
478    checkpoint59g
479    o adjoint testing: in preparation for changing testreport:
480      - output format: cost and grad written on separated lines
481      - ad output results in directory "results" (instead of "results_ad")
482    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
483    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
484    o pkg/ecco: allow user defined cost function contributions
485    o testreport:
486      Allow to choose (per experiment) the list of tested output variables
487       and the main variable (used to issue a pass/FAIL ) ;
488      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
489      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
490      Also modify printing of summary:
491       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
492       b) echo the list of tested variables in the individual summary.txt of
493          each experiment.
494    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
495      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
496      (but still depend on the tile decompostion of the domain).
497    o pkg/seaice: change a discretization detail to make the B-grid code
498      "more symmetric". This change is likely to remove all "ridges/leads" that
499      where quasi-aligned with the grid in B-grid solutions. It may also be
500      the solution to the stress coupling issues with the B-grid.
501    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
502      remove .cvsignore from input dir. (since testreport no longer run here).
503    o pkg/thsice:
504     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
505     - fix reshaping of sea-ice just after advection:
506       melt all the ice only if ice-volume is too small.
507     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
508       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
509     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
510    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
511      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
512    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
513      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
514      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
515      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
516      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
517      -> update output.txt
518    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
519     this affects truncation error: -> update output.txt of exp:
520      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
521      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
522    
523    checkpoint59f
524    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
525    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
526      a bounded range (in forward mode)
527    o pkg/ecco, ctrl, autodiff and mom_common:
528     internal parameter controls, completements of implementations
529    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
530    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
531      (not seem any difference in testing results).
532    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
533       at face corners.
534    o pkg/generic_advdiff:
535     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
536      loop range indices for computing vertical advection tendency
537      and do the calculation in the interior only (no overlap) ;
538      for now, only implemented for SOM advection (to save CPU time).
539     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
540    o exch2 adjoint
541      First set of changes:
542      - add exch2 hand-written adjoint templates
543      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
544        This will require cleanup in pkg/autodiff/*.F
545        (changed routines currently kept separate in verif. code/)
546      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
547        that used to hide exch2 or cubed-sphere specific code
548        (commented via 'cph-exch2')
549    o pkg/seaice
550      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
551    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
552       output of global_ocean.cs32x15.thsice .
553    
554    checkpoint59e
555    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
556      for B-grid vector (not yet tested) and C-grid vector (<- only used
557      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
558    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
559      (#ifdef ALLOW_SALT_PLUME)
560    o gather_2d/scatter_2d: removed halo regions
561    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
562      scheme and the corresponding test case (under front_relax dir). For now,
563      only available with Skew-flux form and not yet tested in realistic set-up.
564      adjoint: store directives updated, but gradient checks deteriorated,
565      so maybe GM/Redi adjoint is now broken.
566    o seaice adjoint
567      * add AREA, HEFF, HSNOW as control variable
568        (should not change lab_sea results)
569      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
570    o pkg/seaice:
571      * added computation of saltFlux in seaice_growth;
572        For time being, sea ice salinity is assumed constant
573        contribution of snow flooding to freshening of sea ice is neglected.
574        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
575        defaults to 0.0 in order to maintain backward compatibility.
576        Typical values for SEAICE_salinity are 4 to 10 g/kg.
577      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
578      * added SEAICE_availHeatFrac, which specifies fraction of surface level
579        heat content used to melt or grow ice
580      * commented out cap of HICE: it helps keep ice thinner
581      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
582      * applied OBCS T/S mask to HEFFM sea ice mask
583    
584    checkpoint59d
585    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
586     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
587     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
588    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
589     and change default value of parameter "GM_Small_Number";
590     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
591       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
592       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
593    o pkg/ecco: cost function when applying pkg/smooth to controls
594    o pkg/ctrl: add forcingPrecond run time parameter
595    o pkg/seaice:
596     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
597     - fix bug in metric terms of u-equation in LSR solver (implicit part),
598       changes verification/lab_sea
599     - rearrange implicit part of u-equation in LSR solver to make it easier to
600       read, understand, and debug. This causes changes at the truncation level.
601     - fix (serious) bug in the boundary conditions (sign error in the implicit
602       part) of the LSR solver. Changes all LSR results.
603     - fixed problem with HSNOW initialization to avoid thick snow when AREA
604       is initilized with small values - does not change lab_sea results.
605     - added HsnowFile initialization capability
606    o pkg/smooth: addition to model/src and pkg/ctrl so allow
607     initialization of pkg/smooth and application to control vector
608    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
609    o dependencies: pkg/profiles requires pkg/cal
610    o pkg/profiles:
611     - added option ALLOW_PROFILES_GENERICGRID
612         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
613         that interpolation information (grid points and coefficients) is provided
614         within the netcdf input files.
615         -> sample matlab scripts can be found in MITgcm_contrib/gael
616         that allow you to prepare netcdf input files.
617     - also modified: cleaner include statements, cleaner error print statements,
618       cleaner stops when error, and more tests of the netcdf input files consistency.
619    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
620    o pkg/seaice:
621     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
622       requires a new routine: seaice_diagnostics_fill.F
623     - make sure that seaice does not move if not forced (pressure replacement
624       method, Hibler and Ip, 1995), changes results
625     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
626     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
627       It is turned off by default (=-1.), because it changes the results.
628     - make it possible to read AREA from a file, too.
629    
630    checkpoint59c
631    o add S/R and diagnostics for oceanic mixed-layer depth
632    o move GMRedi call after all vertical mixing schemes (including KPP)
633    o pkg/thsice:
634     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
635      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
636    o pkg/obcs:
637     - bug fix for balance code
638    o pkg/seaice:
639      - allow values of SEAICE_elasticParm > 1
640      - add new parameter SEAICE_evpTauRelax as an alternative
641        to SEAICE_elasticParm
642      - make lsr boundary conditions free slip (by default), changes result
643      - add code for no slip boundary conditions for lsr
644      - set minimum of zeta to zero (and not 4e8) (changes results)
645      - add a cap on AREA after advecting AREA if seaice_growth is not called
646    o change calculation of Visbeck K:
647      - no longer depend on tapering scheme; instead, compute slope (limited
648        by GM_maxSlope). this is equivalent to what was comuted before with
649        clipping or linear tappering.
650      - fix vertical averaging (wrong by 1/2 level)
651      - leave the old version (but will not be maintained) within
652        #ifdef OLD_VISBECK_CALC / #endif
653      - update output of exp. ideal_2D_oce
654    o change error catch in calc_r_star to improve vectorization
655    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
656      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
657    o adjoint:
658      Re-organized adjoint checkpointing according to Matt Mazloff
659      (but with modifs/completions/cleanups)
660      Storing is now bundled into large arrays to optimized I/O
661      (and second step in cleanup of the_main_loop)
662    
663    checkpoint59b
664    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
665      - export/import (between ocean & coupler) fields needed for ocean DIC.
666    o pkg/seaice:
667      - get rid of three more exchanges seaice_calc_viscosities (required
668        different loop boundaries in seaice_lsr and seaice_ocean_stress)
669      - bug fix in seaice_ocean_stress (update of lab_sea required)
670      - reduce loop boundaries to necessary minimum also in seaice_evp
671      - go back to the old way of computing deltaC/Z as the adjoint likes that
672        better
673    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
674      passive tracer to an Age Tracer) + update output.txt
675    o pkg/exf:
676      - implement A-grid / C-grid selection for wind-stress input files.
677      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
678      for now, in exf_bulk_largeyeager04.F only :
679      - change implementation for case where windspeed + 2. components wind-stress
680        are read-in. AND use rhoConstFresh to convert evap.
681    o pkg/seaice:
682      - use correct EXCH_UV for wind-forcing (on A-grid).
683      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
684        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
685    o pkg/exf:
686      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
687      EXF_INTERPOLATION:
688      - merge global_with_exf/code version of exf_interp_read.F
689        to the main code ;
690      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
691        reading the file ; Important: This options needs to be defined to recover
692        previous code.
693        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
694      - no longer loose real*8 precision along the way when using exf_iprec=64.
695    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
696      - change discretisation of evp-solver in order to avoid another exchange
697        (changes lab_sea) and clean up a little
698      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
699        help the adjoint (this also changes the results slightly)
700      - add a few "_d 0" where they had been missing in seaice_evp.F
701      - cleaning up: remove unused seaice_calc_rhs.F
702    o pkg/exf: some cleaning-up:
703      - change various "constants" into runtime parameters
704      - cleaned-up Large&Yeager04 routine which should eventually
705        replace exf_bulkformulae.F (changed names of S/R and CPP)
706        and merged various ALLOW_ATM_WIND options
707     only used with thsice pkg (in thsice_get_exf.F):
708      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
709        which are used when useStabilityFct_overIce=TRUE (= the default)
710      - change default values of ice & snow emissivity and scale downward LW
711        by ice & snow emissivity.
712    o pkg/thsice:
713     fix few little problems, in thsice_calc_thickn.F:
714      - growth vertically (and not laterally) if iceFrac == iceMaskMax
715      - melt only laterally if hIce < hThinIce (as the comments say)
716      and in thsice_extend.F:
717      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
718      - start to form ice as soon as the minimum ice-volume is reachable.
719     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
720      and cpl_aim+ocn
721    o pkg/kpp
722     - move computation of surface related input fields to KPP into a new
723       subroutine kpp_forcing_surf.F
724     - remove wrong (within bi,bj loops) EXCH calls.
725     - little cleaning (add argument myThid in last position, cvs header ...)
726     - for now, fix conservation problem by exchanging KPPviscAz (may not
727       be the best fix)
728    o pkg/seaice
729     - check for inconsistent evp parameter/cpp-flag combination
730     - remove leftover errIO flat for obsolete name list error handling
731    o OpenAD
732     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
733    
734    checkpoint59a
735    o pkg/seaice: some parameter clarifications and a little bit of clean up
736    o pkg/thsice: rename run-time parameters:
737       himin       -> hIceMin
738       himin0      -> hThinIce
739       hihig       -> hThickIce
740       i0          -> i0swFrac
741       transCoef   -> bMeltCoef
742       frac_energy -> fracMelting
743      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
744       with default values (for now) that do not change the results.
745      remove old version of thsice vars advection in pkg/seaice.
746    o in FFIELDS.h:
747      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
748      - make pLoad & sIceLoad always available (but still only used if
749         ATMOSPHERIC_LOADING is #define).
750    o pkg/kpp: replaced _KPP_RL with _RL
751    o bug fixes for vertical diffusivity computations when both KPP and
752        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
753        are no longer updating the vertical diffusivity array
754        (passed as argument) but are (re-) setting those arrays.
755    o pkg/seaice: fix bug in evp solver, while doing that
756      - change (improve?) discretization of stress computations for both
757        cgrid-lsr and evp solver
758      - add a new routine to compute strain rates
759      - the above changes lab_sea results
760      - add no slip conditions for evp solver (off by default), lsr-version
761        may follow
762      - fix exchange for shear at Z-points (does not change lab_sea)
763      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
764        (to force the user to pick a time step since there is not "safe" way
765        of choosing it)
766      - add principal stress diagnostics
767      - rearrange fields for evp a little to avoid having to call a: too many
768        exchanges and b: exchanges for stress trensor components which we do
769        not have.
770      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
771        of evp, complete rewrite for lsr case (latter is does not yet work
772        in all cases)
773    o pkg/kpp: add code to have mixing in shelf ice caverns
774      - add myThid to all kpp routines (long overdue)
775    
776    checkpoint59
777    o pkg/exf:
778      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
779        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
780      - move exf header files from lower_case.h to UPPER_CASE.h ;
781        add missing cvs Header & Name
782      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
783      - add namelist param. selectStressGridPosition, exf_monFreq
784      - retire many _CLIM routines, and remove data.exf_clim
785        + params moved to data.exf
786        + climsst, climsss now handled by exf_set_gen, i.e.
787          climss?period=0 refers to constant field,
788          climss?period=-12 to monthly forcing
789      - split up namelists in data.exf
790    o pkg/seaice:
791      - remove seaice_exch and seaice_exch_uv
792      - remove superfluous exchange of theta
793      - add myThid to seaice_budget_ocean/ice
794      - add new interface for atmospheric wind forcing (C-grid only)
795        + new routine
796        + two new field (taux, tauy for stress over ice)
797        + removed one global field (DAIRN) for C-grid case only
798    o pkg/thsise
799      - 2nd set of modifs for thsice adjoint in conjunction with exf
800    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
801    
802    checkpoint58y_post
803    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
804      vertical diffusivity, similar to that in MOM4; turned on using
805      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
806      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
807    o Added capability for 3D specification of background vertical diffusion
808      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
809      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
810      "data" file that contains the 3D vertical diffusivity coefficients.
811    o ice dynamics (pkg/seaice) with thsice thermodynamics:
812      - add code within pkg thsice to advect & diffuse sea-ice fields
813      similar to (and will replace) what has been added in  seaice_advdiff.F,
814      but: - conserving Mass, Heat & Salt.
815           - better when using non-linear advection scheme (not yet fully tested)
816           - can also be used in atmospheric set-up (for now, only the diffusion).
817    
818    checkpoint58x_post
819    o IO option for global-file compact format:
820      - add options when generating topology (utils/exch2/matlab-topology-generator)
821      - add I/O capability (pkg/mdsio).
822      - adapt utils/matlab/rdmds.m to read this format.
823      for now long-line format not yet supported by pkg/mdsio (& exch2).
824    o shelfice: add a few diagnostics
825    
826    checkpoint58w_post
827    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
828      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
829      (and replace horiVertRatio in NH code).
830      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
831                         and tutorial_plume_on_slope (sensitive to truncation)
832    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
833      directly to drive seaice model (C-grid only)
834    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
835     - reintroduce computation of wind from stress,
836     - compute tau (in exf_bulkformulae.F) from windstress averaged to
837       mass points to avoid tau = 0
838     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
839    o rdmnc.m: make it work with "global" files created with gluemnc
840    o rdmnc.m : some improvements in dealing with singleton dimension
841      (tested on all testreport mnc output files).
842    o genmake2: disable pkg/profiles if netcdf test fails.
843    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
844    o move call to cal_readparms up to make calendar parameters/variable available
845      to all packages
846    
847    checkpoint58v_post
848    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
849      useDynP_inEos_Zc tested.
850    o pkg/exf: changes to properly interpolate/mask/scale initial fields
851    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
852      and portions thereof.  See read_cs.txt for description and examples.
853    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
854      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
855      following the great-circle arc between those 2 points.
856    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
857      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
858    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
859     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
860     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
861     - still needs work (not working with some options ; efficiency to improve)
862       and serious testing.
863     - use this scheme for temperature & salinity in 2 advection test exp.:
864       advect_xy & advect_xz, respectively.
865    
866    checkpoint58u_post
867    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
868    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
869    o testreport: add option "-skipdir" to skip some test.
870    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
871      momentum calculation.
872    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
873    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
874      remove checkpoint.F and the_correction_step.F (no longer used);
875      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
876    o add option (linFSConserveTr) to correct for tracer source/sink due to
877      Linear Free surface
878    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
879    o pkg/thsice: fix reading mnc-pickups
880    
881    checkpoint58t_post
882    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
883    o pkg/mdsio:
884     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
885       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
886       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
887     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
888     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
889       either MDS_READ_FIELD or MDS_WRITE_FIELD )
890     - new S/R (to replace MDSWRITEMETA), which allows to write more
891       informations (variable names, time ...) to meta files.
892     - modify rdmds.m to give back the meta file content.
893    o pkg/diagnostics: change vertical interpolation to be safer, and more
894       flexible (define p-levels to interpolate to in data.diagnostics);
895      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
896       diagnostic pointer.
897    o pkg/seaice: more cleaning up of seaice_growth, added many comments
898    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
899    o fix multi-category seaice:
900     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
901       SEAICE_MULTICATEGORY
902     - fix short wave heat flux
903    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
904       and allow to use EVP solver. Change forward lab_sea: test both EVP
905       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
906    o Initial check-in of lab_sea adjoint
907      (very similar to natl_box_adjoint/code_seaice)
908      * used C-grid and EVP solver
909      * used KPP, GM/Redi
910      * uses inAdExact=.TRUE.
911      * gradient checks fail for both ADM and TLM
912        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
913        f.d. gradients actually seem more problematic than ADM, TLM gradients;
914        issue is related to forward mismatch between g77 an ifort
915    o pkg/seaice: overhaul of thermodynamics
916     - growth.F and groatb.F are replaced by new routine seaice_growth.F
917     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
918     - move a few global fields out of SEAICE.h into seaice_growth.F and
919       make them 2D (FICE/QNETO/ ...)
920     - remove FO (it is the same as QNETO)
921     - introduce a few local fields to avoid modifying external fields such
922       as atemp, etc.
923    
924    checkpoint58s_post
925    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
926      changed exf_set_gen.F so that
927        genperiod=0 means input file is one time-constant field and
928        genperiod=-12 means input file contains 12 monthly means
929    o CG2D: use pre-computed solver main-diagonal (stored in common block);
930      this affects truncation error ; generate new output file for exp. which
931      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
932        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
933        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
934        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
935        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
936        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
937    o start implementation of deep-atmosphere and anelastic formulation
938    o verification: remove 2nd copy of input files and use script "prepare_run"
939      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
940    o mom_common/vecinv/fluxform: fix a few initialisation isssues
941    o profiles: fix for multithreaded case
942    
943    o diagnostics: rename few diags:
944      s/'PRESSURE'/'RCENTER '/g
945      s/'TICE    '/'oceFreez'/g
946      s/'TAUX    '/'oceTAUX '/g
947      s/'TAUY    '/'oceTAUY '/g
948      s/'SWFLUX  '/'oceQsw  '/g
949      s/DIFx/DFxE/g
950      s/DIFy/DFyE/g
951      and add few ocean-forcing diagnostics:
952      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
953    o modifications to pkg/seaice/growth.F and budget.F, which change results of
954      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
955      as actual snow thickness.  It now refers everywhere to effective snow
956      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
957    
958    checkpoint58r_post
959    o modifications to pkg/seaice/growth.F, which change results of
960      lab_sea experiment: fixes pertain to melting snow over open water, to
961      masking EVAP under sea ice, and to using the correct AREA variable for
962      computations of EVAP, PRECIP, HSNOW, and GHEFF
963    o add ability to read bathy, salt, and theta using MNC (off by def)
964    o add flooding algorithm and advection of HSNOW for pkg/seaice;
965      both are turned off by default and do no change any results
966    o seaice advection with pkg/thsice: a step toward the use of non-linear
967      advection scheme, but #ifdef or commented out for now (requires more EXCH).
968    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
969      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
970      in natl_box (affects results @ truncation level: update output.txt)
971    o multi-threading and IO:
972      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
973      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
974        (needed to work with SingleCpuIO): tested in all verif. exp.
975    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
976      affects the results (but none of the verification test uses this scheme).
977    o Adding some pkg/diagnostics capability to pkg/seaice
978      (will certainly be subject to changes)
979    o ctrl: adding new control variables:
980      lwflux, lwdown, evap, snowprecip, apressure, runoff
981    
982    checkpoint58q_post
983    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
984      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
985      high_res_cube configuration by 4% on Columbia.
986    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
987      add (in global_with_exf/code) a version of EXF_INTERP_READ without
988      dynamical allocation (seems to work in multi-threaded).
989    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
990      single CPU io) so that TAF does not have to see EESUPPORT.h
991    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
992    
993    checkpoint58p_post
994    o obcs: stop if obcs is used with useCDscheme = .true.
995    o shelfice:
996     - fix a sign error so that no slip at shelfice interface works
997     - remove stop for combination non-hydrostatic code and shelfice. That does
998       not mean, that the results are correct, but at least they are numerically
999       stable
1000    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
1001    o added adjoint exch routined for all exch*3d* routines
1002      and updated flow directives
1003    
1004    checkpoint58o_post
1005    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
1006      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
1007    o change controling S/R for writing pickup file (new S/R do_write_pickup)
1008      and clean-up reading/writing of pickup files.
1009    o fix local version of read/write pickup (NH part) in rotating_tank/code
1010    o simplify EXCH interface:
1011     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
1012     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
1013    o added the regrid package
1014    o shelfice:
1015     - add a simple boundary layer scheme to reduce noise
1016     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
1017    
1018    checkpoint58n_post
1019    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
1020       local variable (not in common block).
1021    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
1022      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
1023      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
1024        to work with SingleCpuIO.
1025    o add "_d 0" to real constant of pkg/cfc subroutines ;
1026       update exp. cfc_exemple & tutorial_cfc_offline output files.
1027    o multi-threading and IO:
1028      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
1029        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
1030      - barrier before and after reading.
1031      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
1032      - avoid using MDS_WRITELOCAL for LAND pkg output.
1033      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
1034        common-block variables ; Allows multi-threading with master-thread IO.
1035    o change default MAX_NO_THREADS from 32 to 4 ;
1036      and stop cleanly when MAX_NO_THREADS is too small.
1037    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
1038    
1039    checkpoint58m_post
1040    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
1041       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
1042    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
1043       keep global_ocean.90x40x15 (for AD testing) with former secondary test
1044       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
1045    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
1046        add MITgcm_tutorials (= code + all the tutorials)
1047    o ecco, option to compute cost for total ssh (mean+anom)
1048    o consistent with addition of ptracer and ssh in pkg/profiles
1049    o profiles: adding ptracer and ssh
1050    o testreport: change multi-test output-file name
1051      (from output.txt.{name} to output.{name}.txt)
1052    o profiles: now ok for mutli-tiles case
1053    o seaice: add 4 parameters for different advection schemes for area,
1054      (effective) seaice thickness, enthalphy, and snow height. Their default
1055      is the standard parameter SEAICEadvScheme
1056    o calc_gw:
1057     - add cosFacU in zonal viscous flux (harmonic.visc.).
1058     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
1059       of tutorial_plume_on_slope.
1060    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
1061    o calc_gw: true flux-form, account for horizontal grid spacing.
1062      update rotating_tank results, but not plume_on_slope (affected at
1063      truncation level, 11 digits).
1064    
1065    checkpoint58l_post
1066    o calc_gw:
1067     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
1068     - remove side-drag for now (need to fix it); update plume_on_slope results.
1069     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
1070    o commit code to make SST/SSS weights spatially variable
1071      (based on either variable in-situ or variable initial T/S weights)
1072    o pkg/ecco:
1073      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
1074        now based on horizontally varying weights wthetaLev, wsaltLev
1075      * cost_averagesflags now returns year indices in addition to day, month
1076      * sflux balance is performed on annual basis
1077        (sflxumm, sfluxmm2, bal_sfluxmm)
1078      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
1079        including separate counting and multipliers
1080    o pkg/rbcs
1081      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
1082    
1083    checkpoint58k_post
1084    o testreport:
1085     - always build in dir. "build" (if not there, mkdir build instead of building
1086       & running in input)
1087     - run in dir run (if it exists), in build otherwise.
1088     - call prepare_run (if input/prepare_run exists)
1089     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
1090    o pkg/exf modifications to interpolation and rotation routines for more
1091       reasonable treatment of North Pole singularity: for tracers North Pole
1092       value is set to northernmost zonal-mean value, for zonal velocity it is
1093       set to zero, and for meridional velocity it is set to northernmost value.
1094    o pkg/exf/exf_check_range.F
1095     - add tile index to diagnostics and move stop statement to the very
1096       end of the routine.
1097    o pkg/diagnostics: (diagnostics_main_init.F)
1098      define title of isomorphic variables according to the current config.
1099    o pkg/thsice with pkg/seaice dynamics:
1100    - fix domain of computation (interior only, required for exf) and do exchanges
1101    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
1102    o towards a standard way of dealing with multi-threading in MONITOR
1103      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
1104  o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)  o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
1105     to W momentum equation in nonhydrostatic and quasihydrostatic runs.       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
1106  o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.  o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
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