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revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.1040 by jmc, Mon Nov 17 23:13:41 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 adding precip control xx_precip  o pkg/exf: add parameter for extrapolation of temp up to the surface
8  o moved ptracer ctrl index 17 -> 32     and option to prevent negative evap (in bulk_largeyeager04 only).
9    o Prather Advection scheme: fix tracer conservation for divergent flow
10      (e.g., when using NonLin Free-Surface).
11    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
12    o gmredi (Visbeck-variable-K):
13     - add more parameters to Visbeck-variable-K.
14     - use a 5 points average for dSigmaR in Visbeck-K calculation
15       (more "homogenous": same stencil and same weights as in dSigmaH)
16     - update output of ideal_2D_oce experiment.
17    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
18      (#undef REAL4_IS_SLOW)
19     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
20       coordinate variable
21     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
22       (surface forcing fields), removes some of the functionality
23     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
24     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
25       probably not all: copy _RS surface flux fields to RL field before
26       calling DIAGNOSTICS_FILL
27     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
28       real*4 (CALL EXCH_*_RS) versions.
29     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
30       (generate new output).
31    
32    checkpoint61e
33    o gmredi (Visbeck-variable-K):
34      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
35      - change computation of Visbeck-K where Slope > Smax :        
36        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
37        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
38    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
39      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
40    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
41    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
42      does not become too large (to avoid precision problems in implicit-diffusion
43      solver); update ideal_2D_oce output.
44    o pkg ggl90:
45      - in ggl90_cal.F: compute only one set of visc/diff, used to
46        step forward TKE/T/S/momentum
47      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
48        have Prandlt =1)
49    o gmredi (fm07):
50      - add lower limit on Transition layer thickness + lower limit on 1/lambda
51      - allow to set few more params from data.gmredi
52    o pkg ggl90:
53          - add missing sqrt(2) factor in computation of mixing length
54            scale in ggl90_calc.F
55            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
56    
57    checkpoint61d
58    o adjoint modifs
59      - adapt to new field rhoInSitu
60      - allow to revert from StoreDynVars2D, StoreDynVars3D
61        to individual fields
62        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
63    o store 3-D (in-situ) density in commom block (DYNVARS.h)
64     - save 1 rho computation.
65     - no longer modify T & S inland when using down_slope pkg.
66    o gad_som : allow to switch to SOM advection for T & S without corresponding
67      pickup files (using new S/R: MDS_CHECK4FILE).
68    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
69      (for useSingleCpuIO to work in multi-threaded)
70    o pkg/shelfice:
71     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
72       with SHELFICEtopoFile in data.shelfice
73     - move code for reading ice shelf topography and modifying hFacC into separate
74       subroutines of the shelfice package
75     - separate initialisation of "fixed" and "variable" variables
76     - kTopC is not (yet) replaced by kSurfC, although this is possible
77    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
78    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
79      and rename:
80      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
81      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
82    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
83    
84    checkpoint61c
85    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
86      to add mass source/sink of fluid in the interior (3-D generalisation
87      of oceanic real-fresh water flux).
88    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
89    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
90    o new pkg: down_slope
91      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
92      - presently, modify T & S inland (dwnslp_calc_rho.F).
93        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
94      - implementation for ocean in P-coords not tested.
95      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
96    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
97      (to facilitate conversion of oceanic pkg to p-coordinate).
98    o change FIND_RHO to FIND_RHO_2D :
99      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
100    o new pkg: cheapaml
101    
102    checkpoint61b
103    o exch2:
104      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
105      - no longer depend on the order sequence (N,S,E,W).
106      - 3rd exchange no longer needed (tested with 24 tiles).
107      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
108      - exch_UV_A-grid readily available (but not yet tested).
109      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
110      (both are no longer needed) in exch_uv: no effect in forward run; but
111       get truncation error differences with adjoint exch.
112    o exch2:
113     - change index-bounds storage (moved from target to local tile,
114       more intuitive this way) ; rename/remove some variables.
115     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
116    
117    checkpoint61a
118    o exch2/matlab-topology-generator:
119      fix bug in index bounds for N-S internal exchange (hard to tell if this
120      had any effect on the solution).
121    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
122      is exceeded
123    o testreport: modify syntax of awk, so that it works also with
124      awk, and not only with nawk and gawk
125    
126    checkpoint61
127    o autodiff
128      Change default for TAF usage by removing argument '-nonew_arg'
129      This changes TAF subroutine argument list (ordering of active var.)
130      Omission of this flag leads to incompatibility w.r.t. TAMC
131      To restore TAMC-compatibility, need following modifs:
132      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
133      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
134      Tested TAF version is 1.9.22
135      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
136    
137    checkpoint60
138    --->>> This is the last checkpoint for which generating the adjoint
139    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
140    --->>> by default.
141    --->>> Future checkpoints will ommit this flag by default.
142    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
143    o pkg/grdchk: Add gradient check to etan0 perturbations.
144    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
145    o pkg/autodiff: more flexibility in zeroadj.
146      model/src: modifying do_oceanic_phys.F accordingly.
147    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
148    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
149      special setup of gmredi for which the adjoint is stable
150      enough for parameter optimization.
151    o bridging the gap between eddy stress and GM.
152      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
153          along with a change in CPP option (now ALLOW_EDDYPSI).
154      -> when using GM w/ GM_AdvForm:
155          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
156          is applied either in the tracer Eq. or in momentum Eq.
157          depending on data.gmredi (intro. GM_InMomAsStress).
158      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
159      The key modifications are in model/src/taueddy_external_forcing.F
160      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
161    
162    checkpoint59r
163    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
164      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
165      fix option to read coriolis(@ cell-corner) from files with CS-grid.
166    o pkg/mnc: add some attributes to standard 1D-coordinate variables
167    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
168      mass points, when using mnc for output
169      - add runtime parameter (missing_value, missing_value_int) to override
170        default (which is the value of getcon('UNDEF'))
171    o pkg/mnc: prepare mnc for the actual use of missing values with the
172      diagnostics package: small fix in mnc_cw_readwrite.template and more
173      initialisation of never used fields
174      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
175      versions
176    o pkg/thsice/thsice_ini_vars.F added default initial values so that
177      thermodynamics sea ice solver does not blow up when some initial fields
178      are missing.
179    o move from external_forcing_surf.F to ini_forcing.F
180      the p-coord. hack consisting in using pLoad to set phi0surf ;
181      update output of tutorial_global_oce_in_p (affected @ truncation level).
182    o Freshen up a bit hs94.1x64x5, notably:
183      remove rotationPeriod and tRef=5*0. (adjoint only), and add
184      exactConserv=.TRUE.
185    o pkg/generic_advdiff:
186      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
187      applies to files where Temperature & Salinity 2nd Order moments are used.
188    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
189      this uses a dynamically allocated internal state data structure
190      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
191      and requires a fortran 90 compiler
192    
193    checkpoint59q
194    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
195       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
196    o Refresh tutorial_global_oce_biogeo, notably:
197      - change bathymetry (put back seamounts in ACC, use hFacs)
198      - change EOS (POLY3 --> JMD95Z)
199      - use Bryan-Lewis vertical diffusivity
200      - use multidimensional advection
201      - remove old virtual virtual in dic pkg, now done through ptracer pkg
202      - change a couple of parameters in dic pkg
203    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
204    o pkg/obcs: change default to OBCSfixTopo = .true.,
205      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
206      - replace "debugMode" with "debugLevel .GE. debLevB"
207    o implementation of TAF directives for gchem,cfc,dic
208    o remove "exp5" (replaced by tutorial_deep_convection).
209    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
210      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
211      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
212      --> changes results in exp4, seaice_obcs
213    o tutorial_deep_convection :
214      update the set-up and increase resolution and domain size ; start
215      from pseudo initial conditions = output at t=120mn in order to see
216      something happening when running testreport.
217    o pkg/seaice: add os7mp as an advection scheme
218                  add check for advection schemes
219                  add a flag for restoring T and S underneath sea ice
220    o pkg/my82: add netcdf-support and diagnostics
221    o thsice pkg:
222      - Now hsMax limits snow height by turning it into ice following
223        flooding scheme (and now conserving energy)
224      - Slight rewriting of the formula in thsice_calc_thick.F
225      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
226      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
227    
228    checkpoint59p
229    o gchem / dic / cfc :
230      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
231      - add new parameter files: "data.dic" & "data.cfc" ;
232      - various re-arrangement in initialisation & header file ;
233      - fix tutorial_global_oce_biogeo for multi-threaded test.
234    o pkg/dic: test for "pickup_dic" file when restarting ;
235      if no pickup-file, can restart with a re-initialised pH (same as it did
236      before) providing pickupStrictlyMatch is set to False.
237    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
238      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
239    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
240      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
241    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
242     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
243       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
244    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
245       scheme to use for vorticty-term ;
246     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
247       (with default selectVortScheme, return to original discretisation)
248     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
249    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
250    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
251      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
252      also fix diagnostics VISCAHW & VISCA4W.
253    
254    checkpoint59o
255    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
256    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
257      move a few statemens out the main loop into separate loops
258    o pkg/shelfice:
259      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
260        (kg/m^2/s), does not break tests, because in verification/isomip,
261        rhoConstFresh=rhoConst (by accident)
262      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
263      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
264        new file model/src/seawater.F, so that they are available for all pkgs.
265      - convert potential temperature into in-situ temperature. This changes the
266        isomip tests => update tests
267    o add a flag writePickupAtEnd (default=true) to be able to suppress
268      writing a pickup at the last timestep
269    o tools/mpack-1.6 :
270      - disable automake (not working) and autoconf (not needed).
271      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
272        also cleaner with much less compilation warnings.
273    o pkg/profiles:
274      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
275      (for "less than 32 characters name" compiler requirement)
276    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
277      conditions that have a different sampling frequency than S/T/U/V obcs
278    o pkg/diagnostics (stats-diags):
279      - fix global Min/Max in case 1 processor get only empty tiles
280    o genmake2: replace (4 times)
281         make genmake_tc_1.o >> genmake_warnings 2>&1
282      with
283         COMM="$CC $CFLAGS -c genmake_tc_1.c"
284         echo $COMM >> genmake_warnings
285         $COMM >> genmake_warnings 2>&1
286      to make genmake2 always see the value of CC as specified in the optfile.
287    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
288      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
289      - modify verification advect_cs test to test SOM-advection on CS-grid.
290    o pkg/ctrl:
291      - Rewrite of ctrl_map_ini_ecco.F,
292        introducing a generic routine (ctrl_map_ini_gen.F).
293      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
294    
295    checkpoint59n
296    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
297      number in dedicate array "hdiag":
298      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
299        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
300      - many small changes (integer format) for large number of diagnostics
301      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
302        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
303    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
304      usingSphericalGrid, this allows to define the rotated grid coordinates
305      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
306      geographical coordinates according to the inverse of the rotation defined
307      by the Euler angles, so that Coriolis parameter and online-interpolation by
308      exf works with the geographical coordinates on XC/YC/XG/YG.
309      Naturally, this feature does not work with all packages, so some
310      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
311      profiles), because there the coordinates are assumed to be regular
312      spherical grid coordinates.
313    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
314      - introduce isopycnal diffusion coefficient control.
315    o tools/adjoint_options:
316      - additional control vector components.
317    o pkg/mnc: have mnc create marginally meaning full coordinate variables
318      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
319    o pkg/mypackage:
320      - add example of read/write pickup for state-var ;
321      - add entry points to the main code for state-vars diags & write-pickup.
322    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
323      transitions for useExfYearlyFields
324      - add new subroutine that determines the file to read from for
325        use*YearlyFields = .TRUE. and .FALSE.
326      - add a verification experiment to global_with_exf that tests
327        useExfYearlyFields with USE_EXF_INTERPOLATION defined
328    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
329      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
330      subroutines (which could be generated from a template, because they are
331      almost identical), for now they are included in obcs_prescribe_read.F for
332      simplicity
333    o pkg/exf:
334      - add a little more diagnostic to exf_interp_read (in analogy to
335        mds_read_field, can be turned off with debugLevel < debugLevA=1)
336      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
337        ugly but fast by unrolling short inner loops, inserting a unroll=8
338        directive in routine lagran, and splitting a loop and making do while the
339        outermost loop (the latter requires the intoduction of index arrays)
340    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
341    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
342      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
343    o verification/seaice_obcs: updated for restart test and latest options
344    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
345      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
346      for now this is only available for the C-grid code and also within
347      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
348    
349    checkpoint59m
350    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
351      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
352    o gad_som : fix flux output (& diagnostics) to have same units as other  
353      advection scheme fluxes (was previously multiplied by deltaT).  
354    o added verification/seaice_obcs both to test seaice open boundaries
355      and to provide an example matlab scrpt for generating them
356    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
357    o pkg/salt_plume: clean up salt_plume_frac.F to
358      remove redundancy in PlumeMethod 1 and 4
359    o pkg/kpp: added saltplume diagnostics
360    o pkg/obcs and pkg/seaice:
361      - do not set uice and vice to zero when OB*icefile are unspecified
362      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
363      - moved seaice tracer obcs after call to seaice_growth
364    o pkg/salt_plume: added various options for salt plume depth
365      criterion and for vertical distribution of the salt
366    
367    checkpoint59l
368    o pkg/ptracers: new version of ptracers pickup:
369      read meta file and write only fields which are needed to restart.
370      ( same logic as main pickup file ; also using pickupStrictlyMatch )
371    o pkg/seaice:
372      - add timescale for melting due to warm mixed layer as a means of
373        setting SEAICE_availHeatFrac more conveniently
374      - add a CPP-flag/runtime parameter check for flooding algorithm
375      - reformulated availHeat in seaice_growth.F to be independent of AREA
376    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
377      unit changes
378    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
379    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
380      SX vector computer.
381    o pkg/seaice:
382      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
383        seaice forcing fields can now be read only through pkg/exf
384      - removed some unused halos
385    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
386    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
387      or U/VICE from U/VWIND before computing U/VSTRESS
388    
389    checkpoint59k
390    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
391      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
392    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
393      all experiments pass when compile with un-initialised var. checking option.
394    o added pkg/salt_plume
395    o script to test restart (for now, in MITgcm_contrib/jmc_script)
396    o pkg/seaice: new read/write pickup version.
397      read meta file and write only fields which are needed to restart.
398      ( same logic as main pickup file ; also using pickupStrictlyMatch )
399    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
400    o lab_sea.hb87: modify the domain & update output.hb87.txt :
401      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
402      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
403      process. Fixed here by closing the domain at the Northern boundary.
404    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
405    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
406      a set of consecutive levels in/from a 3-D array.
407    o pkg/ptracers:
408      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
409      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
410    
411    checkpoint59j
412    o in pkgs: dic, obcs, offline, rbcs:
413      standard way to compute coeff. for time interpolation between 2 time reccords
414      which retains full precision (& make results less dependent on compiler).
415      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
416    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
417      packages instead of reading ice cover and wind speed separately
418    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
419     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
420      to allow to compile customized code before the update)
421    o cleaning-up:
422      - fix CPP instruction syntax in pkg/obcs
423      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
424        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
425      - fix some threads issue in IO parts.
426    o pkg/dic:
427      - add tons of "_d 0" (--> much better testreports !)
428       and then update outputs of tutorial_global_oce_biogeo
429    o pkg/mom_fluxform:
430      add a special version of momentum advection intended to conserve momentum
431      next to a bathymetry step or a coastline edge. (default = off = #undef)
432    o new read/write pickup version:
433      - for now, only implemented for main (mdsio) pickup file.
434      - write out only what is needed to restart; merge pickup_nh , pickup_ph
435        and main pickup together.
436      - read meta file; read only what is needed to restart; stop if a field
437        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
438        if it make sense (even if the restart is not perfect).
439      - if no meta file, assume that pickup to read corresponds exactly to
440        a pickup that would currently be written.
441      - read pickup written in the old format (until checkpoint59i) if it
442        recognizes an old meta file (no field-list).
443      - add a meta file in exp. which starts from a pickup: 2 cases:
444        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
445         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
446        b) a meta file describing the content of the associated pickup file
447         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
448    o pkg/mdsio & pkg/rw:
449      - new routine to read a meta file ; new set of routine to read
450        Multiple-fields file (with meta file).
451    o added open boundary conditions capability for seaice
452        HSNOW, HSALT, UICE, and VICE
453    
454    checkpoint59i
455    o adjoint:
456      * fix multiDimAdvection adjoint
457        (partial recomputation problem by TAF for fVerT(:,:,kDown)
458        and comlev1 size definition (maxpass vs. max. number of tracers)
459      * verification/global_ocean.90x45x15 adjoint now tests
460        NLFS and multiDimAdvection using DST3 (=30)
461      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
462    o pkg/kpp: add "_d 0" to real constant (if missing);
463      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
464      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
465    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
466      for internal parameters related to restart process (formerly from PARAMS.h)
467      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
468    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
469      as argument. (only atm2d & obcs write_pickup have not yet been updated)
470    o pkg/monitor:
471      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
472      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
473      - account for deep Atmosphere factor and density factor (anelastic)
474    o added open boundary conditions capability for seaice HEFF and AREA
475    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
476      thermodynamics
477      - requires a little reorganization, which affects the testreport results
478        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
479        so that now the conservative form is tested
480      - add a few comments
481    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
482    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
483    o add new diagnostics to seaice: advective, diffusive fluxes (only for
484      multidim-advection, for scheme 2 they are not filled) and transports,
485      thermodynamic growth rates
486    o change units of EmPmR (inside the code, + within coupling interface)
487      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
488      Affects results @ truncation level (cg2d match) and update output of
489       experiments: lab_sea(6), global_ocean.90x40x15(10),
490      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
491      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
492      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
493      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
494    
495    checkpoint59h
496    o pkg/exf:
497      - improve vectorization by moving if-statement out of loops in
498        exf_mapfields, exf_radiation
499      - exf_bulkformulae.F: introduce 2D fields and vectorize code
500    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
501    o testreport:
502      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
503        monitor & update offline_exf_seaice exp. output.
504      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
505    o pkg/seaice:
506      - bug fix in the evp solver: boundary conditions were affected be
507        masking of zMax/zMin (changes results)
508      - minor bug fix in boundary conditions in seaice_calc_strainrates
509        (changes results for no_slip)
510      - seaice_lsr.F: make interpolation of eta dependent on boundaries
511      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
512      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
513        stress formulation and no-slip boundary conditions
514    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
515      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
516    o pkg/seaice: a first HSALT time stepping equation has been checked in
517    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
518      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
519      without requiring DO-IF statements
520    o pkg/thsice:
521      use continuous power-law function for partition of energy between lateral
522      melting/freezing and thinning/thickening ; old code using step function
523      still available with #undef THSICE_FRACEN_POWERLAW
524      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
525    o testreport: change AD testing : check against results/output_adm.txt
526      using same scripts as for forward test.
527    
528    checkpoint59g
529    o adjoint testing: in preparation for changing testreport:
530      - output format: cost and grad written on separated lines
531      - ad output results in directory "results" (instead of "results_ad")
532    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
533    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
534    o pkg/ecco: allow user defined cost function contributions
535    o testreport:
536      Allow to choose (per experiment) the list of tested output variables
537       and the main variable (used to issue a pass/FAIL ) ;
538      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
539      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
540      Also modify printing of summary:
541       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
542       b) echo the list of tested variables in the individual summary.txt of
543          each experiment.
544    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
545      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
546      (but still depend on the tile decompostion of the domain).
547    o pkg/seaice: change a discretization detail to make the B-grid code
548      "more symmetric". This change is likely to remove all "ridges/leads" that
549      where quasi-aligned with the grid in B-grid solutions. It may also be
550      the solution to the stress coupling issues with the B-grid.
551    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
552      remove .cvsignore from input dir. (since testreport no longer run here).
553    o pkg/thsice:
554     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
555     - fix reshaping of sea-ice just after advection:
556       melt all the ice only if ice-volume is too small.
557     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
558       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
559     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
560    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
561      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
562    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
563      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
564      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
565      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
566      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
567      -> update output.txt
568    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
569     this affects truncation error: -> update output.txt of exp:
570      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
571      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
572    
573    checkpoint59f
574    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
575    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
576      a bounded range (in forward mode)
577    o pkg/ecco, ctrl, autodiff and mom_common:
578     internal parameter controls, completements of implementations
579    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
580    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
581      (not seem any difference in testing results).
582    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
583       at face corners.
584    o pkg/generic_advdiff:
585     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
586      loop range indices for computing vertical advection tendency
587      and do the calculation in the interior only (no overlap) ;
588      for now, only implemented for SOM advection (to save CPU time).
589     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
590    o exch2 adjoint
591      First set of changes:
592      - add exch2 hand-written adjoint templates
593      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
594        This will require cleanup in pkg/autodiff/*.F
595        (changed routines currently kept separate in verif. code/)
596      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
597        that used to hide exch2 or cubed-sphere specific code
598        (commented via 'cph-exch2')
599    o pkg/seaice
600      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
601    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
602       output of global_ocean.cs32x15.thsice .
603    
604    checkpoint59e
605    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
606      for B-grid vector (not yet tested) and C-grid vector (<- only used
607      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
608    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
609      (#ifdef ALLOW_SALT_PLUME)
610    o gather_2d/scatter_2d: removed halo regions
611    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
612      scheme and the corresponding test case (under front_relax dir). For now,
613      only available with Skew-flux form and not yet tested in realistic set-up.
614      adjoint: store directives updated, but gradient checks deteriorated,
615      so maybe GM/Redi adjoint is now broken.
616    o seaice adjoint
617      * add AREA, HEFF, HSNOW as control variable
618        (should not change lab_sea results)
619      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
620    o pkg/seaice:
621      * added computation of saltFlux in seaice_growth;
622        For time being, sea ice salinity is assumed constant
623        contribution of snow flooding to freshening of sea ice is neglected.
624        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
625        defaults to 0.0 in order to maintain backward compatibility.
626        Typical values for SEAICE_salinity are 4 to 10 g/kg.
627      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
628      * added SEAICE_availHeatFrac, which specifies fraction of surface level
629        heat content used to melt or grow ice
630      * commented out cap of HICE: it helps keep ice thinner
631      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
632      * applied OBCS T/S mask to HEFFM sea ice mask
633    
634    checkpoint59d
635    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
636     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
637     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
638    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
639     and change default value of parameter "GM_Small_Number";
640     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
641       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
642       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
643    o pkg/ecco: cost function when applying pkg/smooth to controls
644    o pkg/ctrl: add forcingPrecond run time parameter
645    o pkg/seaice:
646     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
647     - fix bug in metric terms of u-equation in LSR solver (implicit part),
648       changes verification/lab_sea
649     - rearrange implicit part of u-equation in LSR solver to make it easier to
650       read, understand, and debug. This causes changes at the truncation level.
651     - fix (serious) bug in the boundary conditions (sign error in the implicit
652       part) of the LSR solver. Changes all LSR results.
653     - fixed problem with HSNOW initialization to avoid thick snow when AREA
654       is initilized with small values - does not change lab_sea results.
655     - added HsnowFile initialization capability
656    o pkg/smooth: addition to model/src and pkg/ctrl so allow
657     initialization of pkg/smooth and application to control vector
658    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
659    o dependencies: pkg/profiles requires pkg/cal
660    o pkg/profiles:
661     - added option ALLOW_PROFILES_GENERICGRID
662         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
663         that interpolation information (grid points and coefficients) is provided
664         within the netcdf input files.
665         -> sample matlab scripts can be found in MITgcm_contrib/gael
666         that allow you to prepare netcdf input files.
667     - also modified: cleaner include statements, cleaner error print statements,
668       cleaner stops when error, and more tests of the netcdf input files consistency.
669    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
670    o pkg/seaice:
671     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
672       requires a new routine: seaice_diagnostics_fill.F
673     - make sure that seaice does not move if not forced (pressure replacement
674       method, Hibler and Ip, 1995), changes results
675     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
676     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
677       It is turned off by default (=-1.), because it changes the results.
678     - make it possible to read AREA from a file, too.
679    
680    checkpoint59c
681    o add S/R and diagnostics for oceanic mixed-layer depth
682    o move GMRedi call after all vertical mixing schemes (including KPP)
683    o pkg/thsice:
684     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
685      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
686    o pkg/obcs:
687     - bug fix for balance code
688    o pkg/seaice:
689      - allow values of SEAICE_elasticParm > 1
690      - add new parameter SEAICE_evpTauRelax as an alternative
691        to SEAICE_elasticParm
692      - make lsr boundary conditions free slip (by default), changes result
693      - add code for no slip boundary conditions for lsr
694      - set minimum of zeta to zero (and not 4e8) (changes results)
695      - add a cap on AREA after advecting AREA if seaice_growth is not called
696    o change calculation of Visbeck K:
697      - no longer depend on tapering scheme; instead, compute slope (limited
698        by GM_maxSlope). this is equivalent to what was comuted before with
699        clipping or linear tappering.
700      - fix vertical averaging (wrong by 1/2 level)
701      - leave the old version (but will not be maintained) within
702        #ifdef OLD_VISBECK_CALC / #endif
703      - update output of exp. ideal_2D_oce
704    o change error catch in calc_r_star to improve vectorization
705    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
706      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
707    o adjoint:
708      Re-organized adjoint checkpointing according to Matt Mazloff
709      (but with modifs/completions/cleanups)
710      Storing is now bundled into large arrays to optimized I/O
711      (and second step in cleanup of the_main_loop)
712    
713    checkpoint59b
714    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
715      - export/import (between ocean & coupler) fields needed for ocean DIC.
716    o pkg/seaice:
717      - get rid of three more exchanges seaice_calc_viscosities (required
718        different loop boundaries in seaice_lsr and seaice_ocean_stress)
719      - bug fix in seaice_ocean_stress (update of lab_sea required)
720      - reduce loop boundaries to necessary minimum also in seaice_evp
721      - go back to the old way of computing deltaC/Z as the adjoint likes that
722        better
723    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
724      passive tracer to an Age Tracer) + update output.txt
725    o pkg/exf:
726      - implement A-grid / C-grid selection for wind-stress input files.
727      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
728      for now, in exf_bulk_largeyeager04.F only :
729      - change implementation for case where windspeed + 2. components wind-stress
730        are read-in. AND use rhoConstFresh to convert evap.
731    o pkg/seaice:
732      - use correct EXCH_UV for wind-forcing (on A-grid).
733      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
734        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
735    o pkg/exf:
736      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
737      EXF_INTERPOLATION:
738      - merge global_with_exf/code version of exf_interp_read.F
739        to the main code ;
740      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
741        reading the file ; Important: This options needs to be defined to recover
742        previous code.
743        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
744      - no longer loose real*8 precision along the way when using exf_iprec=64.
745    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
746      - change discretisation of evp-solver in order to avoid another exchange
747        (changes lab_sea) and clean up a little
748      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
749        help the adjoint (this also changes the results slightly)
750      - add a few "_d 0" where they had been missing in seaice_evp.F
751      - cleaning up: remove unused seaice_calc_rhs.F
752    o pkg/exf: some cleaning-up:
753      - change various "constants" into runtime parameters
754      - cleaned-up Large&Yeager04 routine which should eventually
755        replace exf_bulkformulae.F (changed names of S/R and CPP)
756        and merged various ALLOW_ATM_WIND options
757     only used with thsice pkg (in thsice_get_exf.F):
758      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
759        which are used when useStabilityFct_overIce=TRUE (= the default)
760      - change default values of ice & snow emissivity and scale downward LW
761        by ice & snow emissivity.
762    o pkg/thsice:
763     fix few little problems, in thsice_calc_thickn.F:
764      - growth vertically (and not laterally) if iceFrac == iceMaskMax
765      - melt only laterally if hIce < hThinIce (as the comments say)
766      and in thsice_extend.F:
767      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
768      - start to form ice as soon as the minimum ice-volume is reachable.
769     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
770      and cpl_aim+ocn
771    o pkg/kpp
772     - move computation of surface related input fields to KPP into a new
773       subroutine kpp_forcing_surf.F
774     - remove wrong (within bi,bj loops) EXCH calls.
775     - little cleaning (add argument myThid in last position, cvs header ...)
776     - for now, fix conservation problem by exchanging KPPviscAz (may not
777       be the best fix)
778    o pkg/seaice
779     - check for inconsistent evp parameter/cpp-flag combination
780     - remove leftover errIO flat for obsolete name list error handling
781    o OpenAD
782     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
783    
784    checkpoint59a
785    o pkg/seaice: some parameter clarifications and a little bit of clean up
786    o pkg/thsice: rename run-time parameters:
787       himin       -> hIceMin
788       himin0      -> hThinIce
789       hihig       -> hThickIce
790       i0          -> i0swFrac
791       transCoef   -> bMeltCoef
792       frac_energy -> fracMelting
793      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
794       with default values (for now) that do not change the results.
795      remove old version of thsice vars advection in pkg/seaice.
796    o in FFIELDS.h:
797      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
798      - make pLoad & sIceLoad always available (but still only used if
799         ATMOSPHERIC_LOADING is #define).
800    o pkg/kpp: replaced _KPP_RL with _RL
801    o bug fixes for vertical diffusivity computations when both KPP and
802        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
803        are no longer updating the vertical diffusivity array
804        (passed as argument) but are (re-) setting those arrays.
805    o pkg/seaice: fix bug in evp solver, while doing that
806      - change (improve?) discretization of stress computations for both
807        cgrid-lsr and evp solver
808      - add a new routine to compute strain rates
809      - the above changes lab_sea results
810      - add no slip conditions for evp solver (off by default), lsr-version
811        may follow
812      - fix exchange for shear at Z-points (does not change lab_sea)
813      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
814        (to force the user to pick a time step since there is not "safe" way
815        of choosing it)
816      - add principal stress diagnostics
817      - rearrange fields for evp a little to avoid having to call a: too many
818        exchanges and b: exchanges for stress trensor components which we do
819        not have.
820      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
821        of evp, complete rewrite for lsr case (latter is does not yet work
822        in all cases)
823    o pkg/kpp: add code to have mixing in shelf ice caverns
824      - add myThid to all kpp routines (long overdue)
825    
826    checkpoint59
827    o pkg/exf:
828      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
829        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
830      - move exf header files from lower_case.h to UPPER_CASE.h ;
831        add missing cvs Header & Name
832      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
833      - add namelist param. selectStressGridPosition, exf_monFreq
834      - retire many _CLIM routines, and remove data.exf_clim
835        + params moved to data.exf
836        + climsst, climsss now handled by exf_set_gen, i.e.
837          climss?period=0 refers to constant field,
838          climss?period=-12 to monthly forcing
839      - split up namelists in data.exf
840    o pkg/seaice:
841      - remove seaice_exch and seaice_exch_uv
842      - remove superfluous exchange of theta
843      - add myThid to seaice_budget_ocean/ice
844      - add new interface for atmospheric wind forcing (C-grid only)
845        + new routine
846        + two new field (taux, tauy for stress over ice)
847        + removed one global field (DAIRN) for C-grid case only
848    o pkg/thsise
849      - 2nd set of modifs for thsice adjoint in conjunction with exf
850    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
851    
852    checkpoint58y_post
853    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
854      vertical diffusivity, similar to that in MOM4; turned on using
855      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
856      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
857    o Added capability for 3D specification of background vertical diffusion
858      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
859      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
860      "data" file that contains the 3D vertical diffusivity coefficients.
861    o ice dynamics (pkg/seaice) with thsice thermodynamics:
862      - add code within pkg thsice to advect & diffuse sea-ice fields
863      similar to (and will replace) what has been added in  seaice_advdiff.F,
864      but: - conserving Mass, Heat & Salt.
865           - better when using non-linear advection scheme (not yet fully tested)
866           - can also be used in atmospheric set-up (for now, only the diffusion).
867    
868    checkpoint58x_post
869    o IO option for global-file compact format:
870      - add options when generating topology (utils/exch2/matlab-topology-generator)
871      - add I/O capability (pkg/mdsio).
872      - adapt utils/matlab/rdmds.m to read this format.
873      for now long-line format not yet supported by pkg/mdsio (& exch2).
874    o shelfice: add a few diagnostics
875    
876    checkpoint58w_post
877    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
878      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
879      (and replace horiVertRatio in NH code).
880      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
881                         and tutorial_plume_on_slope (sensitive to truncation)
882    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
883      directly to drive seaice model (C-grid only)
884    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
885     - reintroduce computation of wind from stress,
886     - compute tau (in exf_bulkformulae.F) from windstress averaged to
887       mass points to avoid tau = 0
888     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
889    o rdmnc.m: make it work with "global" files created with gluemnc
890    o rdmnc.m : some improvements in dealing with singleton dimension
891      (tested on all testreport mnc output files).
892    o genmake2: disable pkg/profiles if netcdf test fails.
893    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
894    o move call to cal_readparms up to make calendar parameters/variable available
895      to all packages
896    
897    checkpoint58v_post
898    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
899      useDynP_inEos_Zc tested.
900    o pkg/exf: changes to properly interpolate/mask/scale initial fields
901    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
902      and portions thereof.  See read_cs.txt for description and examples.
903    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
904      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
905      following the great-circle arc between those 2 points.
906    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
907      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
908    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
909     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
910     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
911     - still needs work (not working with some options ; efficiency to improve)
912       and serious testing.
913     - use this scheme for temperature & salinity in 2 advection test exp.:
914       advect_xy & advect_xz, respectively.
915    
916    checkpoint58u_post
917    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
918    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
919    o testreport: add option "-skipdir" to skip some test.
920    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
921      momentum calculation.
922    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
923    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
924      remove checkpoint.F and the_correction_step.F (no longer used);
925      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
926    o add option (linFSConserveTr) to correct for tracer source/sink due to
927      Linear Free surface
928    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
929    o pkg/thsice: fix reading mnc-pickups
930    
931    checkpoint58t_post
932    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
933    o pkg/mdsio:
934     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
935       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
936       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
937     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
938     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
939       either MDS_READ_FIELD or MDS_WRITE_FIELD )
940     - new S/R (to replace MDSWRITEMETA), which allows to write more
941       informations (variable names, time ...) to meta files.
942     - modify rdmds.m to give back the meta file content.
943    o pkg/diagnostics: change vertical interpolation to be safer, and more
944       flexible (define p-levels to interpolate to in data.diagnostics);
945      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
946       diagnostic pointer.
947    o pkg/seaice: more cleaning up of seaice_growth, added many comments
948    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
949    o fix multi-category seaice:
950     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
951       SEAICE_MULTICATEGORY
952     - fix short wave heat flux
953    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
954       and allow to use EVP solver. Change forward lab_sea: test both EVP
955       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
956    o Initial check-in of lab_sea adjoint
957      (very similar to natl_box_adjoint/code_seaice)
958      * used C-grid and EVP solver
959      * used KPP, GM/Redi
960      * uses inAdExact=.TRUE.
961      * gradient checks fail for both ADM and TLM
962        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
963        f.d. gradients actually seem more problematic than ADM, TLM gradients;
964        issue is related to forward mismatch between g77 an ifort
965    o pkg/seaice: overhaul of thermodynamics
966     - growth.F and groatb.F are replaced by new routine seaice_growth.F
967     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
968     - move a few global fields out of SEAICE.h into seaice_growth.F and
969       make them 2D (FICE/QNETO/ ...)
970     - remove FO (it is the same as QNETO)
971     - introduce a few local fields to avoid modifying external fields such
972       as atemp, etc.
973    
974    checkpoint58s_post
975    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
976      changed exf_set_gen.F so that
977        genperiod=0 means input file is one time-constant field and
978        genperiod=-12 means input file contains 12 monthly means
979    o CG2D: use pre-computed solver main-diagonal (stored in common block);
980      this affects truncation error ; generate new output file for exp. which
981      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
982        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
983        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
984        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
985        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
986        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
987    o start implementation of deep-atmosphere and anelastic formulation
988    o verification: remove 2nd copy of input files and use script "prepare_run"
989      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
990    o mom_common/vecinv/fluxform: fix a few initialisation isssues
991    o profiles: fix for multithreaded case
992    
993    o diagnostics: rename few diags:
994      s/'PRESSURE'/'RCENTER '/g
995      s/'TICE    '/'oceFreez'/g
996      s/'TAUX    '/'oceTAUX '/g
997      s/'TAUY    '/'oceTAUY '/g
998      s/'SWFLUX  '/'oceQsw  '/g
999      s/DIFx/DFxE/g
1000      s/DIFy/DFyE/g
1001      and add few ocean-forcing diagnostics:
1002      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
1003    o modifications to pkg/seaice/growth.F and budget.F, which change results of
1004      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
1005      as actual snow thickness.  It now refers everywhere to effective snow
1006      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
1007    
1008    checkpoint58r_post
1009    o modifications to pkg/seaice/growth.F, which change results of
1010      lab_sea experiment: fixes pertain to melting snow over open water, to
1011      masking EVAP under sea ice, and to using the correct AREA variable for
1012      computations of EVAP, PRECIP, HSNOW, and GHEFF
1013    o add ability to read bathy, salt, and theta using MNC (off by def)
1014    o add flooding algorithm and advection of HSNOW for pkg/seaice;
1015      both are turned off by default and do no change any results
1016    o seaice advection with pkg/thsice: a step toward the use of non-linear
1017      advection scheme, but #ifdef or commented out for now (requires more EXCH).
1018    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
1019      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
1020      in natl_box (affects results @ truncation level: update output.txt)
1021    o multi-threading and IO:
1022      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
1023      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
1024        (needed to work with SingleCpuIO): tested in all verif. exp.
1025    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
1026      affects the results (but none of the verification test uses this scheme).
1027    o Adding some pkg/diagnostics capability to pkg/seaice
1028      (will certainly be subject to changes)
1029    o ctrl: adding new control variables:
1030      lwflux, lwdown, evap, snowprecip, apressure, runoff
1031    
1032    checkpoint58q_post
1033    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
1034      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
1035      high_res_cube configuration by 4% on Columbia.
1036    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
1037      add (in global_with_exf/code) a version of EXF_INTERP_READ without
1038      dynamical allocation (seems to work in multi-threaded).
1039    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
1040      single CPU io) so that TAF does not have to see EESUPPORT.h
1041    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
1042    
1043    checkpoint58p_post
1044    o obcs: stop if obcs is used with useCDscheme = .true.
1045    o shelfice:
1046     - fix a sign error so that no slip at shelfice interface works
1047     - remove stop for combination non-hydrostatic code and shelfice. That does
1048       not mean, that the results are correct, but at least they are numerically
1049       stable
1050    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
1051    o added adjoint exch routined for all exch*3d* routines
1052      and updated flow directives
1053    
1054    checkpoint58o_post
1055    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
1056      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
1057    o change controling S/R for writing pickup file (new S/R do_write_pickup)
1058      and clean-up reading/writing of pickup files.
1059    o fix local version of read/write pickup (NH part) in rotating_tank/code
1060    o simplify EXCH interface:
1061     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
1062     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
1063    o added the regrid package
1064    o shelfice:
1065     - add a simple boundary layer scheme to reduce noise
1066     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
1067    
1068    checkpoint58n_post
1069    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
1070       local variable (not in common block).
1071    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
1072      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
1073      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
1074        to work with SingleCpuIO.
1075    o add "_d 0" to real constant of pkg/cfc subroutines ;
1076       update exp. cfc_exemple & tutorial_cfc_offline output files.
1077    o multi-threading and IO:
1078      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
1079        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
1080      - barrier before and after reading.
1081      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
1082      - avoid using MDS_WRITELOCAL for LAND pkg output.
1083      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
1084        common-block variables ; Allows multi-threading with master-thread IO.
1085    o change default MAX_NO_THREADS from 32 to 4 ;
1086      and stop cleanly when MAX_NO_THREADS is too small.
1087    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
1088    
1089    checkpoint58m_post
1090    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
1091       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
1092    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
1093       keep global_ocean.90x40x15 (for AD testing) with former secondary test
1094       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
1095    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
1096        add MITgcm_tutorials (= code + all the tutorials)
1097    o ecco, option to compute cost for total ssh (mean+anom)
1098    o consistent with addition of ptracer and ssh in pkg/profiles
1099    o profiles: adding ptracer and ssh
1100    o testreport: change multi-test output-file name
1101      (from output.txt.{name} to output.{name}.txt)
1102    o profiles: now ok for mutli-tiles case
1103    o seaice: add 4 parameters for different advection schemes for area,
1104      (effective) seaice thickness, enthalphy, and snow height. Their default
1105      is the standard parameter SEAICEadvScheme
1106    o calc_gw:
1107     - add cosFacU in zonal viscous flux (harmonic.visc.).
1108     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
1109       of tutorial_plume_on_slope.
1110    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
1111    o calc_gw: true flux-form, account for horizontal grid spacing.
1112      update rotating_tank results, but not plume_on_slope (affected at
1113      truncation level, 11 digits).
1114    
1115    checkpoint58l_post
1116    o calc_gw:
1117     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
1118     - remove side-drag for now (need to fix it); update plume_on_slope results.
1119     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
1120    o commit code to make SST/SSS weights spatially variable
1121      (based on either variable in-situ or variable initial T/S weights)
1122    o pkg/ecco:
1123      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
1124        now based on horizontally varying weights wthetaLev, wsaltLev
1125      * cost_averagesflags now returns year indices in addition to day, month
1126      * sflux balance is performed on annual basis
1127        (sflxumm, sfluxmm2, bal_sfluxmm)
1128      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
1129        including separate counting and multipliers
1130    o pkg/rbcs
1131      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
1132    
1133    checkpoint58k_post
1134    o testreport:
1135     - always build in dir. "build" (if not there, mkdir build instead of building
1136       & running in input)
1137     - run in dir run (if it exists), in build otherwise.
1138     - call prepare_run (if input/prepare_run exists)
1139     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
1140    o pkg/exf modifications to interpolation and rotation routines for more
1141       reasonable treatment of North Pole singularity: for tracers North Pole
1142       value is set to northernmost zonal-mean value, for zonal velocity it is
1143       set to zero, and for meridional velocity it is set to northernmost value.
1144    o pkg/exf/exf_check_range.F
1145     - add tile index to diagnostics and move stop statement to the very
1146       end of the routine.
1147    o pkg/diagnostics: (diagnostics_main_init.F)
1148      define title of isomorphic variables according to the current config.
1149    o pkg/thsice with pkg/seaice dynamics:
1150    - fix domain of computation (interior only, required for exf) and do exchanges
1151    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
1152    o towards a standard way of dealing with multi-threading in MONITOR
1153      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
1154    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
1155       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
1156    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
1157    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
1158    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
1159       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
1160    o tracer advection:
1161     - clean-up and simplify calc_common_factors.F
1162     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
1163       advection subroutine (but still not used within DST advection S/R)
1164    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
1165    
1166    checkpoint58j_post
1167    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
1168      from file (collects calls previously in FORWARD_STEP)
1169    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
1170    o adjoint store dir. adjusted accordingly
1171    o genmake2
1172      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
1173    
1174    checkpoint58i_post
1175    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
1176      on wind stress (SEAICEstressFactor defaults to 1.)
1177    o Total number of Timers is finite (<=40): comment out 2 non-essential one
1178      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
1179    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
1180      on CS-grid: no longer loosing mass.
1181    o exf & curvilinear-grid: no longer modify longitude xC & xG.
1182    o pkg/ggl90: fix sloppy output and fix a bug
1183    o pkg/seaice: added SEAICEuseEVPpickup parameter
1184      - Set to false in order to start EVP solver with
1185        non-EVP pickup files when using SEAICEuseEVP
1186      - fix sign error in diffusion in seaice_calc_rhs
1187    
1188    checkpoint58h_post
1189    * Modifications for bottom topography control
1190      o replace hFacC by _hFacC at various places
1191      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
1192      o add non-self-adjoint cg2d_nsa
1193      o update autodiff support routines
1194      o re-initialise hfac after ctrl_depth_ini
1195      o works for 5x5 box, doesnt work for global_ocean.90x40x15
1196    * Adding verification for 5x5 box (4-layer) bottom topography control
1197    
1198    checkpoint58g_post
1199    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
1200       used for mean seasonal cycle, mean diurnal cycle); add an example
1201       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
1202    o pkg/ggl90:
1203      - add parameter (minimum surface kinetic energy)
1204      - fix bug (avoiding division by zero)
1205    o couple pkg/thsice to pkg/seaice:
1206      - modify advection in seaice to accomodate new scalar fields to be advected
1207      - only muliDimAdection scheme work with seaice/thsice
1208      - mapping of thsice-variables to seaice-variables, back and forth
1209      - does not break the verification experiments, but does not give the
1210        desired results either
1211    o pkg/seaice
1212      - make (default) second order advection a bit less confusing?
1213    
1214    checkpoint58f_post
1215    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
1216      to pkg/seaice):
1217      - new routines thsice_map_exf and thsice_get_exf provide the interface
1218      - add an additional formal parameter to thsice_solve4temp
1219    o pkg/exf:
1220      - add new fields wspeed, snowprecip (to be able to couple to thsice)
1221      - correct Stefan-Boltzmann constant
1222      - new parameter for longwave surface emittance
1223      - separate some stuff from exf_bulkformulae into new routines  
1224        exf_radiation, exf_wind
1225      - add new parameters and constants: longwave emissivity for ocean, ice
1226        and snow, evaporation parameters over ice
1227      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
1228        either wind from stress or stress from wind
1229    o pkg/thSIce:
1230    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
1231    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
1232       and THSICE_CALC_THICKN
1233    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
1234    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
1235      to make debugging easier.
1236    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
1237    o pkg/bulk_force:
1238      - clean-up comments and parameters ;
1239      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
1240    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
1241      generate new output for test-experiment: aim.5l_cs.thSI
1242    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
1243      testreport accordingly
1244    
1245    checkpoint58e_post
1246    o SEAICE_CGRID adjoint done
1247    o R_STAR adjoint implemented.
1248      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
1249      * need to sort out init. of h0facc, etc.
1250    o Make pkg/profile fully independent of ecco,cost, etc. stuff
1251      to be able to use it in pure forward.
1252    
1253    checkpoint58d_post
1254    o upgrade simple test-experiment to tutorial example:
1255     step.1: duplicate the experiment and (step.2) will remove the old copy.
1256      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
1257      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
1258      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
1259      tutorial_global_oce_biogeo    <- copy of dic_example
1260      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
1261      tutorial_plume_on_slope       <- copy of plume_on_slope
1262      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
1263      tutorial_global_oce_optim     <- empty for now (David ?)
1264      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
1265     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
1266    o correct a sign problem in cost_scat.F
1267    o obcs and ptracers: fix boundary conditions for advections schemes
1268      with larger stencil
1269    o thsice adjoint: start
1270    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
1271      completeness
1272    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
1273      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
1274    o ptracers adjoint:
1275      * avoid extensive recomputatations
1276      * fix missing re-init. of gptr (missed by TAF)
1277    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
1278      me to turn off the excessive output to STDOUT that this package produces
1279    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
1280      and add those terms in Vector-Invariant formulation.
1281    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
1282      if the control period (xx_hfluxperiod etc) is 0
1283    o in profiles pkg, clean routines and fix details
1284    o in ecco pkg, reading ssh data:
1285      fix problem in case the model does not start at iter0=0
1286    o fix mnc-pickup/restart for ptracers
1287    o new package prifiles:
1288      code to compute profile-based cost by Gael Forget
1289      (modifs in ecco, ctrl, autodiff)
1290    o Benign bug fix in initialization (spotted by M. Mazloff) of
1291      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
1292    
1293    checkpoint58c_post
1294    o adjoint: finish NLFS adjoint and provide reference output in
1295      verification/global_ocean.90x40x15/results_ad_nlfs
1296    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
1297      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
1298      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
1299      with SEAICE_CGRID defined.
1300    o move calendarDumps from "data" to "data.cal" and clean-up the code
1301      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
1302    o add useEXF & useCAL flags (for now, set in hard-coded way)
1303    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
1304      (were missing in NH mode, and wrong in quasihydrostatic mode).
1305      waiting for Chris updated version of calc_gw to add those CALLs.
1306    o fix bug in quasihydrostatic S/R ;
1307      add a test for this option: global_ocean.90x40x15.qshyd
1308    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
1309      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
1310    o add on/off flag useOffLine for package OFFLINE
1311    o seaice:
1312      - modify advection so that it works also on the C-grid
1313      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
1314        problem in multi-tile runs with C-grid
1315      - add flags for clipping ice velocities and/or masking solver forcing
1316      - fix drag (ocean on ice) formulation and a bug that caused noise in the
1317        C-grid solver
1318      - added a few comments to seaice_diffusion.F
1319      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
1320        are now exclusive)
1321      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
1322        required re-ordering the code a little:
1323       + make DAIRN global variable (defined in SEAICE)
1324       + move computation of the viscosities eta and zeta into a new separate
1325         routine (because I need to recompute them in seaice_ocean_stress.F)
1326    
1327    checkpoint58b_post
1328    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
1329      update output.txt of exp. aim.5l_cs.thSI
1330    o various mnc cleanups and improvements:
1331      + shrink lookup tables by factor of ~4
1332      + better error reporting when running out of lookup space
1333      + able to handle longer path/file names (up to 500 chars)
1334    o adjoint:
1335      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
1336      - TBD: "hidden" mom_vecinv recomp. in dynamics
1337    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
1338     (allow to differentiate between forcing components using new integer flags:
1339      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
1340     and add new flag to put Dissipation tendency out of Adams-Bashforth.
1341    o ecco
1342      - enable trend removal from SSH anomaly obs.
1343    o adjoint
1344      - a fix for PmEpR when #undef EXACT_CONSERV
1345      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
1346      - try to fix "hidden" recomp. in forward_step for NLFS
1347        (NLFS seems broken sometimes after I checked it in)
1348    o seaice:
1349     - add c-grid version of the dynamic solver:
1350       + three new routines that are the c-grid substitute lsr, dynsolver
1351         and ostres
1352       + put a few fields that were local to dynsolver into global common
1353         blocks, so that I can move the computation of stresses etc into
1354         seaice_lsr (saves coding but may break the adjoint).
1355     - replace more hardwired parameters by runtime parameters
1356     - add ice masks that mask the rhs of the implicit solvers where there
1357       is no ice (commented out in seaice_dynsolver, because i am not sure
1358       if this works properly), eventually this should replace the clipping
1359       of ice velocities in seaice_dynsolver to +/-40cm/s.
1360    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
1361      include it only where its needed
1362    o move balancing of fluxes before the call of external_forcing_surf
1363    o seaice:
1364      - correct units of turning angles (now they are really in degrees)
1365      - move computation of GWATX/Y out of main routine into dynsolver
1366      - initialize GWATX/Y in seaice_init
1367    o Apply mask on Fresh-Water flux (needed for SSH forcing).
1368      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
1369    o seaice: add runtime flags for turning angles (default to zero)
1370    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
1371      and trend from exf forcing and ctrl control adjustments
1372    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
1373      (since checkpoint57x_post)
1374    o change the default rotation period to 86164.s = the Earth rotation
1375    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
1376      and based on a reference stratification. Tested within hs94.cs-32x32x5.
1377    o seaice advection: add code for choosing between the default (2nd order
1378      central differences) and multiDim advection schemes provided by
1379      pkg/generic_advdiff
1380    o seaice:
1381      - removed all references to SEAICE_GRID.h fields from
1382        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
1383        (cubed-sphere configuration will change a little)
1384      - grid computations in seaice_init are obsolete now.
1385      - cleaned up code a little so that is easier to read (hopefully).
1386      - added new (better?) discretizations of default advection and diffusion
1387        (turn on with SEAICEuseFluxForm)
1388      - replace 1 in 3d global fields by kSurface in growth.F
1389      
1390    checkpoint58a_post
1391    o seaice:
1392      - bug fix in advect.F
1393    o shelfice:
1394      - separate shelfice load anomaly from pload (breaks with time
1395        dependent forcing), => introduce constant field shelficeLoadAnomaly.
1396        Its default is 0., but it may be computed more cleverly from (unknown)
1397        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
1398        done offline. A good approximation of the pressure load anomaly is
1399        necessary to avoid large initial adjustment processes underneath
1400        deep-reaching shelfice.
1401      - small fix in ISOMIP shelfice_thermodynamics
1402      - add more sophisticated thermodynamics of Hellmer (1989), this is
1403        now the default
1404      - give a few constants more intuitive names
1405    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
1406      if bulk formulae are used in long integration (especially EmPmR). Turn
1407      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
1408      if balancePrintMean, the imbalance that is substracted is printed to
1409      STDOUT.
1410    o fix bug (typo) in obcs_apply_eta.F
1411    o add a new package shelfice which enables us to model the circulation
1412      underneath shelf-ice with draughts of hundreds of meters.
1413     - works
1414     - to do: + include improved thermodynamics
1415              + check whether kSurfC (from model/inc/SURFACE.h) can be used
1416                instead of new field kTopC
1417              + can we use topoFile, Ro_surf and existing code in ini_depth.F
1418                instead of new field R_shelfIce and new code in ini_depth.F
1419                and ini_mask_etc.F?
1420              + adjust vertical mixing schemes?
1421    o seaice pkg:
1422     - add a cpp-flag to include a simple formula for a salinity dependent
1423       freezing point of sea water at the surface
1424     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
1425       meridional stresses are now different (and hopefully correct)
1426    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
1427       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
1428       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
1429    o pkg/diagnostics: add options and parameters for regional-statistics
1430       diagnostics ; define regions by reading a region-mask from a file
1431       (might add other options later)
1432    o pkg/bulk_force:
1433     - add option and parameters to use AIM surface-flux formulae.
1434     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
1435       others forcing fields (defined in PARM05, parameter file "data") are loaded
1436       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
1437     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
1438     - use the right EXCH call for uwind,vwind (to work on CS-grid).
1439     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
1440       and parameters (note: calcWindStress replaces .NOT.readwindstress).
1441     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
1442    
1443    checkpoint58
1444    o add "--embed-source" option to genmake2 which, when the supporting
1445      tools can be compiled (as determined by genmake2) will turn on the
1446      embed_files package which then embeds the entire MITgcm source code
1447      (*.[fFhc] + Makefile) used for the build within the executable
1448      - requested by CNH but off by default
1449      - adds a paltry <9MB to the mitgcmuv executable in most cases
1450      - only writes the output when useEMBEDSRC in eedata is true
1451    o clean up 3-dim. relaxation codes:
1452      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
1453      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
1454      * Thanks to Tom Haine for testing!
1455    
1456    checkpoint57z_post
1457    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
1458      affects output (@ truncation level) of exp. plume_on_slope ; updated.
1459    o fix the pickup behavior for obcs in combination with ptracers
1460    o fix a bug in ptracers_external_fields_load
1461    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
1462      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
1463    o transfered surface NH pressure to eta field (if exactConserv).
1464    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
1465         and update lab_sea output.txt file.
1466    o completing 3-dim. relaxation code: additional term
1467         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
1468      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
1469      * At compile time, in "EXF_OPTIONS.h" set
1470          #define  ALLOW_CLIMTEMP_RELAXATION
1471          #define  ALLOW_CLIMSALT_RELAXATION
1472      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
1473          tauThetaClimRelax3Dim = 15552000.0,
1474          tauSaltClimRelax3Dim  = 15552000.0,
1475      * 3 cases:
1476          1) Use a constant-in-time 3-dim. field
1477          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
1478          3) Real-time relax. to time-evolving prescribed field
1479    o Adding Laplacian-type smoothness constraint on
1480      initial and boundary (forcing) controls (ic, bc)
1481      * enable at compile-time via
1482        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
1483      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
1484      * Absolute scale somewhat unclear so far
1485      * no area weighting was included since no other cost term does so far
1486    
1487    checkpoint57y_post
1488    First step for a NLFS adjoint
1489    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
1490    o new init. routines for calc_r_star, calc_surf_dr
1491    o still need to deal with ini_masks_etc
1492    o testreport seemed happy
1493    checkpoint57y_pre
1494    
1495    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
1496    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
1497    o add new offset feature to offline pkg (plus minor cleanup)
1498    o cfc fixes for final year of integration
1499    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
1500      be in GCHEM_OPTIONS).
1501    
1502    checkpoint57x_post
1503    o fix testreport Pb in multiple test experiment.
1504    o cleanup our namelist syntax in verification:
1505      - make it more F95 standards compliant (some work still needed)
1506      - allows the vast majority of our tests to work with gfortran
1507    o Non-Hydrostatic:
1508     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
1509     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
1510    o Allow to apply AB on T,S rather than on AB(gT,gS):
1511     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
1512     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
1513       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
1514     - need a "clever" read_pickup to restart from the other AB formulation
1515    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
1516    o remove some unused variables (reduces number of compiler warnings)
1517    o adjoint
1518      * Disable useVariableViscosity for adjoint for time being
1519        (there are a number of extensive recomputations)
1520      * Initialize certain variables needed for adjoint
1521    
1522    checkpoint57w_post
1523    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
1524                 fix the singleCpuIO RS version of MDSWRITEFIELD
1525       and add a WARNING if using globalFiles=T with multi-processors.
1526    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
1527      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
1528    o tracer advection scheme:
1529      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
1530       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
1531       was not very convenient).
1532      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
1533       (further tests needed for the implicit DST & Flux-Limiter schemes).
1534    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
1535      and sRef for convenience, handy, when you want to initialize
1536      ptracers in a large domain with a constant non-zero value. Also,
1537      untangle ptracers_init.F a little.
1538    
1539    checkpoint57v_post
1540    o change dome exp. to use variable viscosity in side-drag terms.
1541    o remove all the files from the cfc_offline test since they are now
1542      incorporated into tutorial_cfc_offline which has been producing
1543      identical results for a few days of testing
1544    o add new parameter: sideDragFactor to enable half-slip-side BC
1545      and change side-drag S/R to use viscosity from mom_calc_visc
1546      (can switch back by setting sideDragFactor=0.); affects results at
1547      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
1548       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
1549    o vorticity & strain are now computed without masking, to account for
1550      no-slip-side BC in variable viscosity calculation ; mask is applied
1551      anyway later on, before computing advection/coriolis terms.
1552    o modify exp4 to test new obcs support for reading from external files
1553      and for passive tracers
1554    o fix behavior of ptracers_monitor when monitor output is written to a
1555      netcdf-file; still not independent of monitor.F (writes in the same
1556      file).
1557    o change default value of tRef (put a uniform, meaningful value for ocean
1558      & atmos) and initialize sRef (was missing, as Martin mentioned).
1559    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
1560      to be proportional to enstrophy dissipation length.  Thus,
1561       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
1562      This is now consistent with Smagorinsky and with the manual.
1563    
1564    checkpoint57u_post
1565    o OBCS and PTRACERS: add open boundary support for passive tracers
1566      - either use homogenous (pseudo) v.Neumann conditions or prescribe
1567        OB-values from file; this is not different from the way theta and salinity
1568        are treated
1569      - however, Orlanski-radiation conditions are not supported, and the model
1570        will stop if you use pTracers and Orlanski at the same time.
1571      - beefed up the rountine obcs_external_fields_load: now only those open
1572        boundary values are overwritten with values from files for which there
1573        are really files, otherwise the OB-fields remain untouched. This makes
1574        it possible to use different OBs at different ends of the domain (as
1575        with EXF)
1576    o reduce number of exch calls in shap_filt (s2).
1577    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
1578      truncation level) 4/5 MLAdjust test results (11&12 digits match).
1579    
1580    checkpoint57t_post
1581    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
1582    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
1583      same truncation, independent of the face number: affects affects several
1584      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
1585    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
1586      note that biharmonic viscosity + no-slip was not tested in any experiment.
1587    o fix bug in non-linear free-surf side-drag ; generate new output for
1588      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
1589    o make mnc honor the writeBinaryPrec flag for most kinds of output
1590    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
1591    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
1592      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
1593    o add brackets in multi-terms sum to get same truncation, independent of
1594      the face number (manage to get exactly same value of gU,gV at the cs-edge)
1595      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
1596    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
1597      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
1598      a maximum grid-scale Reynolds number.  Also, changes all length calculations
1599      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
1600      Suggested values of viscosity parameters found in mom_calc_visc.
1601      Many new viscosity diagnostics available.
1602    
1603    checkpoint57s_post
1604    o Add clearing-house for viscosity calculations, mom_calc_visc and
1605      correct numerous bugs in LeithD and Smagorinsky discretizations.  
1606      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
1607      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
1608      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
1609      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
1610      The Strain-Tension form is now called with useStrainTensonVisc=.true.
1611      ViscAhStrain and viscAhTension are now retired.
1612    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
1613    o In response to JMC's bug report, genmake2 now ignores any soft-links
1614      that it finds in the *current* directory when searching for files.
1615      Soft-links found in any other source directories will still work as
1616      they did before.
1617    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
1618      a C routine to unlimit the stack size
1619    o mnc-ify pkg/aim snapshot vars
1620    o mnc-ify pkg/land as requested by Daniel
1621    o various changes to mnc including:
1622      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
1623      - output can now be grouped so that all files within a group
1624          change the ITER portion of their names in lock-step together
1625      - can now read ("global") PER-FACE (in addition to PER-TILE) files
1626          and works with both EXCH1 and EXCH2 (but needs more testing)
1627      - writing works for all verification test cases w/ g77 on Linux
1628    
1629    checkpoint57r_post
1630    o make MNC variable initialization happen earlier
1631    o add diagnostics for (almost) each term of the momentum Eq.
1632    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
1633    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
1634    o remove MINIMAL_TAVE_OUTPUT option ;
1635      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
1636    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
1637      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
1638    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
1639    o add time-dependent SST, SSS control
1640    o cost terms in ecco/ modularized (new cost_generic.F)
1641    o cost_averages routines are modularized (new cost_averagesgeneric.F)
1642    o new infrastructure for seaice model vs. obs misfits in seaice/
1643      * driver from the_main_loop.F is seaice_cost_driver.F
1644      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
1645      * gradient check in Exp. 6a of natl_box_adjoint/
1646    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
1647      (see README file)
1648    
1649    checkpoint57q_post
1650    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
1651    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
1652      - bug was reported by Jean-Michel and Ian Fenty
1653    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
1654      update exp. cpl_aim+ocn output.
1655    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
1656      Needed for high-res. runs with large global files
1657      to be able to limit tapelev size
1658    o Changed some tests for adjoint:
1659      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
1660      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
1661      * global_ocean.90x40x15/ back to default 3-level checkpointing
1662    o Modifications to enable scripted COMMON to MODULE conversion
1663      * verification/OpenAD/code/ has necessary scripts and description;
1664      * converts, compiles and runs successfully;
1665    
1666    checkpoint57p_post
1667    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
1668    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
1669      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
1670    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
1671    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
1672      (was already the case for dissipation with mom_vecinv,
1673       and also the case for grad.PhiHyd when staggered-timeStep)
1674      This will allow to put dissipation out-off the AB time-stepping.
1675     Unfortunately, affects truncation error. Update output of exp. that "fails"
1676      (cg2d matching number) and leave the others for later: front_relax(10),
1677      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
1678      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
1679    
1680    checkpoint57o_post
1681    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
1682      (2) its ready to be documented during the 20050801 DocFest
1683    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
1684      for ideal_2D_oce and lab_sea on linux_ia32_g77
1685    o set to #undef CTRL_SET_OLD_MAXCVARS_30
1686      in global1x1_tot/code_seaice_adj to access indices 32, 33
1687      (worth another tag)
1688    
1689    checkpoint57n_post
1690    o adding precip control xx_precip 32
1691    o adding swflux control xx_swflux 33
1692    o Replacing 10 forcing penalty cost routines by 1 generic.
1693    o Implementing partitioning in time-mean and variable adjustment
1694      for atmos. state.
1695    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
1696  o in natl_box_adjoint:  o in natl_box_adjoint:
1697    * updated: results_bulk/    * updated exp 1 to 10
1698    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
1699    o updated global1x1/*_seaice_adj/
1700      to incorporate latest changes
1701    o enable useSingleCpuIO for mdsio vector routines
1702      (applies in particular to tapelev I/O)
1703    o removed inefficient K-loop in all active_file*control*.F
1704    
1705  checkpoint57m_post  checkpoint57m_post
1706  o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)  o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)

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