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revision 1.696 by heimbach, Sat Jul 8 00:29:20 2006 UTC revision 1.1024 by jmc, Mon Sep 22 18:00:25 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 take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V  o store 3-D (in-situ) density in commom block (DYNVARS.h)
8     - save 1 rho computation.
9     - no longer modify T & S inland when using down_slope pkg.
10    o gad_som : allow to switch to SOM advection for T & S without corresponding
11      pickup files (using new S/R: MDS_CHECK4FILE).
12    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
13      (for useSingleCpuIO to work in multi-threaded)
14    o pkg/shelfice:
15     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
16       with SHELFICEtopoFile in data.shelfice
17     - move code for reading ice shelf topography and modifying hFacC into separate
18       subroutines of the shelfice package
19     - separate initialisation of "fixed" and "variable" variables
20     - kTopC is not (yet) replaced by kSurfC, although this is possible
21    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
22    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
23      and rename:
24      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
25      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
26    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
27    
28    checkpoint61c
29    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
30      to add mass source/sink of fluid in the interior (3-D generalisation
31      of oceanic real-fresh water flux).
32    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
33    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
34    o new pkg: down_slope
35      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
36      - presently, modify T & S inland (dwnslp_calc_rho.F).
37        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
38      - implementation for ocean in P-coords not tested.
39      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
40    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
41      (to facilitate conversion of oceanic pkg to p-coordinate).
42    o change FIND_RHO to FIND_RHO_2D :
43      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
44    o new pkg: cheapaml
45    
46    checkpoint61b
47    o exch2:
48      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
49      - no longer depend on the order sequence (N,S,E,W).
50      - 3rd exchange no longer needed (tested with 24 tiles).
51      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
52      - exch_UV_A-grid readily available (but not yet tested).
53      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
54      (both are no longer needed) in exch_uv: no effect in forward run; but
55       get truncation error differences with adjoint exch.
56    o exch2:
57     - change index-bounds storage (moved from target to local tile,
58       more intuitive this way) ; rename/remove some variables.
59     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
60    
61    checkpoint61a
62    o exch2/matlab-topology-generator:
63      fix bug in index bounds for N-S internal exchange (hard to tell if this
64      had any effect on the solution).
65    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
66      is exceeded
67    o testreport: modify syntax of awk, so that it works also with
68      awk, and not only with nawk and gawk
69    
70    checkpoint61
71    o autodiff
72      Change default for TAF usage by removing argument '-nonew_arg'
73      This changes TAF subroutine argument list (ordering of active var.)
74      Omission of this flag leads to incompatibility w.r.t. TAMC
75      To restore TAMC-compatibility, need following modifs:
76      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
77      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
78      Tested TAF version is 1.9.22
79      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
80    
81    checkpoint60
82    --->>> This is the last checkpoint for which generating the adjoint
83    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
84    --->>> by default.
85    --->>> Future checkpoints will ommit this flag by default.
86    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
87    o pkg/grdchk: Add gradient check to etan0 perturbations.
88    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
89    o pkg/autodiff: more flexibility in zeroadj.
90      model/src: modifying do_oceanic_phys.F accordingly.
91    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
92    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
93      special setup of gmredi for which the adjoint is stable
94      enough for parameter optimization.
95    o bridging the gap between eddy stress and GM.
96      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
97          along with a change in CPP option (now ALLOW_EDDYPSI).
98      -> when using GM w/ GM_AdvForm:
99          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
100          is applied either in the tracer Eq. or in momentum Eq.
101          depending on data.gmredi (intro. GM_InMomAsStress).
102      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
103      The key modifications are in model/src/taueddy_external_forcing.F
104      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
105    
106    checkpoint59r
107    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
108      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
109      fix option to read coriolis(@ cell-corner) from files with CS-grid.
110    o pkg/mnc: add some attributes to standard 1D-coordinate variables
111    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
112      mass points, when using mnc for output
113      - add runtime parameter (missing_value, missing_value_int) to override
114        default (which is the value of getcon('UNDEF'))
115    o pkg/mnc: prepare mnc for the actual use of missing values with the
116      diagnostics package: small fix in mnc_cw_readwrite.template and more
117      initialisation of never used fields
118      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
119      versions
120    o pkg/thsice/thsice_ini_vars.F added default initial values so that
121      thermodynamics sea ice solver does not blow up when some initial fields
122      are missing.
123    o move from external_forcing_surf.F to ini_forcing.F
124      the p-coord. hack consisting in using pLoad to set phi0surf ;
125      update output of tutorial_global_oce_in_p (affected @ truncation level).
126    o Freshen up a bit hs94.1x64x5, notably:
127      remove rotationPeriod and tRef=5*0. (adjoint only), and add
128      exactConserv=.TRUE.
129    o pkg/generic_advdiff:
130      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
131      applies to files where Temperature & Salinity 2nd Order moments are used.
132    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
133      this uses a dynamically allocated internal state data structure
134      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
135      and requires a fortran 90 compiler
136    
137    checkpoint59q
138    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
139       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
140    o Refresh tutorial_global_oce_biogeo, notably:
141      - change bathymetry (put back seamounts in ACC, use hFacs)
142      - change EOS (POLY3 --> JMD95Z)
143      - use Bryan-Lewis vertical diffusivity
144      - use multidimensional advection
145      - remove old virtual virtual in dic pkg, now done through ptracer pkg
146      - change a couple of parameters in dic pkg
147    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
148    o pkg/obcs: change default to OBCSfixTopo = .true.,
149      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
150      - replace "debugMode" with "debugLevel .GE. debLevB"
151    o implementation of TAF directives for gchem,cfc,dic
152    o remove "exp5" (replaced by tutorial_deep_convection).
153    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
154      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
155      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
156      --> changes results in exp4, seaice_obcs
157    o tutorial_deep_convection :
158      update the set-up and increase resolution and domain size ; start
159      from pseudo initial conditions = output at t=120mn in order to see
160      something happening when running testreport.
161    o pkg/seaice: add os7mp as an advection scheme
162                  add check for advection schemes
163                  add a flag for restoring T and S underneath sea ice
164    o pkg/my82: add netcdf-support and diagnostics
165    o thsice pkg:
166      - Now hsMax limits snow height by turning it into ice following
167        flooding scheme (and now conserving energy)
168      - Slight rewriting of the formula in thsice_calc_thick.F
169      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
170      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
171    
172    checkpoint59p
173    o gchem / dic / cfc :
174      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
175      - add new parameter files: "data.dic" & "data.cfc" ;
176      - various re-arrangement in initialisation & header file ;
177      - fix tutorial_global_oce_biogeo for multi-threaded test.
178    o pkg/dic: test for "pickup_dic" file when restarting ;
179      if no pickup-file, can restart with a re-initialised pH (same as it did
180      before) providing pickupStrictlyMatch is set to False.
181    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
182      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
183    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
184      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
185    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
186     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
187       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
188    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
189       scheme to use for vorticty-term ;
190     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
191       (with default selectVortScheme, return to original discretisation)
192     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
193    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
194    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
195      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
196      also fix diagnostics VISCAHW & VISCA4W.
197    
198    checkpoint59o
199    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
200    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
201      move a few statemens out the main loop into separate loops
202    o pkg/shelfice:
203      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
204        (kg/m^2/s), does not break tests, because in verification/isomip,
205        rhoConstFresh=rhoConst (by accident)
206      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
207      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
208        new file model/src/seawater.F, so that they are available for all pkgs.
209      - convert potential temperature into in-situ temperature. This changes the
210        isomip tests => update tests
211    o add a flag writePickupAtEnd (default=true) to be able to suppress
212      writing a pickup at the last timestep
213    o tools/mpack-1.6 :
214      - disable automake (not working) and autoconf (not needed).
215      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
216        also cleaner with much less compilation warnings.
217    o pkg/profiles:
218      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
219      (for "less than 32 characters name" compiler requirement)
220    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
221      conditions that have a different sampling frequency than S/T/U/V obcs
222    o pkg/diagnostics (stats-diags):
223      - fix global Min/Max in case 1 processor get only empty tiles
224    o genmake2: replace (4 times)
225         make genmake_tc_1.o >> genmake_warnings 2>&1
226      with
227         COMM="$CC $CFLAGS -c genmake_tc_1.c"
228         echo $COMM >> genmake_warnings
229         $COMM >> genmake_warnings 2>&1
230      to make genmake2 always see the value of CC as specified in the optfile.
231    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
232      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
233      - modify verification advect_cs test to test SOM-advection on CS-grid.
234    o pkg/ctrl:
235      - Rewrite of ctrl_map_ini_ecco.F,
236        introducing a generic routine (ctrl_map_ini_gen.F).
237      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
238    
239    checkpoint59n
240    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
241      number in dedicate array "hdiag":
242      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
243        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
244      - many small changes (integer format) for large number of diagnostics
245      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
246        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
247    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
248      usingSphericalGrid, this allows to define the rotated grid coordinates
249      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
250      geographical coordinates according to the inverse of the rotation defined
251      by the Euler angles, so that Coriolis parameter and online-interpolation by
252      exf works with the geographical coordinates on XC/YC/XG/YG.
253      Naturally, this feature does not work with all packages, so some
254      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
255      profiles), because there the coordinates are assumed to be regular
256      spherical grid coordinates.
257    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
258      - introduce isopycnal diffusion coefficient control.
259    o tools/adjoint_options:
260      - additional control vector components.
261    o pkg/mnc: have mnc create marginally meaning full coordinate variables
262      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
263    o pkg/mypackage:
264      - add example of read/write pickup for state-var ;
265      - add entry points to the main code for state-vars diags & write-pickup.
266    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
267      transitions for useExfYearlyFields
268      - add new subroutine that determines the file to read from for
269        use*YearlyFields = .TRUE. and .FALSE.
270      - add a verification experiment to global_with_exf that tests
271        useExfYearlyFields with USE_EXF_INTERPOLATION defined
272    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
273      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
274      subroutines (which could be generated from a template, because they are
275      almost identical), for now they are included in obcs_prescribe_read.F for
276      simplicity
277    o pkg/exf:
278      - add a little more diagnostic to exf_interp_read (in analogy to
279        mds_read_field, can be turned off with debugLevel < debugLevA=1)
280      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
281        ugly but fast by unrolling short inner loops, inserting a unroll=8
282        directive in routine lagran, and splitting a loop and making do while the
283        outermost loop (the latter requires the intoduction of index arrays)
284    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
285    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
286      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
287    o verification/seaice_obcs: updated for restart test and latest options
288    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
289      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
290      for now this is only available for the C-grid code and also within
291      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
292    
293    checkpoint59m
294    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
295      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
296    o gad_som : fix flux output (& diagnostics) to have same units as other  
297      advection scheme fluxes (was previously multiplied by deltaT).  
298    o added verification/seaice_obcs both to test seaice open boundaries
299      and to provide an example matlab scrpt for generating them
300    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
301    o pkg/salt_plume: clean up salt_plume_frac.F to
302      remove redundancy in PlumeMethod 1 and 4
303    o pkg/kpp: added saltplume diagnostics
304    o pkg/obcs and pkg/seaice:
305      - do not set uice and vice to zero when OB*icefile are unspecified
306      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
307      - moved seaice tracer obcs after call to seaice_growth
308    o pkg/salt_plume: added various options for salt plume depth
309      criterion and for vertical distribution of the salt
310    
311    checkpoint59l
312    o pkg/ptracers: new version of ptracers pickup:
313      read meta file and write only fields which are needed to restart.
314      ( same logic as main pickup file ; also using pickupStrictlyMatch )
315    o pkg/seaice:
316      - add timescale for melting due to warm mixed layer as a means of
317        setting SEAICE_availHeatFrac more conveniently
318      - add a CPP-flag/runtime parameter check for flooding algorithm
319      - reformulated availHeat in seaice_growth.F to be independent of AREA
320    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
321      unit changes
322    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
323    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
324      SX vector computer.
325    o pkg/seaice:
326      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
327        seaice forcing fields can now be read only through pkg/exf
328      - removed some unused halos
329    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
330    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
331      or U/VICE from U/VWIND before computing U/VSTRESS
332    
333    checkpoint59k
334    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
335      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
336    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
337      all experiments pass when compile with un-initialised var. checking option.
338    o added pkg/salt_plume
339    o script to test restart (for now, in MITgcm_contrib/jmc_script)
340    o pkg/seaice: new read/write pickup version.
341      read meta file and write only fields which are needed to restart.
342      ( same logic as main pickup file ; also using pickupStrictlyMatch )
343    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
344    o lab_sea.hb87: modify the domain & update output.hb87.txt :
345      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
346      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
347      process. Fixed here by closing the domain at the Northern boundary.
348    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
349    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
350      a set of consecutive levels in/from a 3-D array.
351    o pkg/ptracers:
352      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
353      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
354    
355    checkpoint59j
356    o in pkgs: dic, obcs, offline, rbcs:
357      standard way to compute coeff. for time interpolation between 2 time reccords
358      which retains full precision (& make results less dependent on compiler).
359      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
360    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
361      packages instead of reading ice cover and wind speed separately
362    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
363     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
364      to allow to compile customized code before the update)
365    o cleaning-up:
366      - fix CPP instruction syntax in pkg/obcs
367      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
368        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
369      - fix some threads issue in IO parts.
370    o pkg/dic:
371      - add tons of "_d 0" (--> much better testreports !)
372       and then update outputs of tutorial_global_oce_biogeo
373    o pkg/mom_fluxform:
374      add a special version of momentum advection intended to conserve momentum
375      next to a bathymetry step or a coastline edge. (default = off = #undef)
376    o new read/write pickup version:
377      - for now, only implemented for main (mdsio) pickup file.
378      - write out only what is needed to restart; merge pickup_nh , pickup_ph
379        and main pickup together.
380      - read meta file; read only what is needed to restart; stop if a field
381        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
382        if it make sense (even if the restart is not perfect).
383      - if no meta file, assume that pickup to read corresponds exactly to
384        a pickup that would currently be written.
385      - read pickup written in the old format (until checkpoint59i) if it
386        recognizes an old meta file (no field-list).
387      - add a meta file in exp. which starts from a pickup: 2 cases:
388        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
389         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
390        b) a meta file describing the content of the associated pickup file
391         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
392    o pkg/mdsio & pkg/rw:
393      - new routine to read a meta file ; new set of routine to read
394        Multiple-fields file (with meta file).
395    o added open boundary conditions capability for seaice
396        HSNOW, HSALT, UICE, and VICE
397    
398    checkpoint59i
399    o adjoint:
400      * fix multiDimAdvection adjoint
401        (partial recomputation problem by TAF for fVerT(:,:,kDown)
402        and comlev1 size definition (maxpass vs. max. number of tracers)
403      * verification/global_ocean.90x45x15 adjoint now tests
404        NLFS and multiDimAdvection using DST3 (=30)
405      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
406    o pkg/kpp: add "_d 0" to real constant (if missing);
407      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
408      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
409    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
410      for internal parameters related to restart process (formerly from PARAMS.h)
411      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
412    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
413      as argument. (only atm2d & obcs write_pickup have not yet been updated)
414    o pkg/monitor:
415      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
416      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
417      - account for deep Atmosphere factor and density factor (anelastic)
418    o added open boundary conditions capability for seaice HEFF and AREA
419    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
420      thermodynamics
421      - requires a little reorganization, which affects the testreport results
422        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
423        so that now the conservative form is tested
424      - add a few comments
425    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
426    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
427    o add new diagnostics to seaice: advective, diffusive fluxes (only for
428      multidim-advection, for scheme 2 they are not filled) and transports,
429      thermodynamic growth rates
430    o change units of EmPmR (inside the code, + within coupling interface)
431      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
432      Affects results @ truncation level (cg2d match) and update output of
433       experiments: lab_sea(6), global_ocean.90x40x15(10),
434      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
435      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
436      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
437      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
438    
439    checkpoint59h
440    o pkg/exf:
441      - improve vectorization by moving if-statement out of loops in
442        exf_mapfields, exf_radiation
443      - exf_bulkformulae.F: introduce 2D fields and vectorize code
444    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
445    o testreport:
446      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
447        monitor & update offline_exf_seaice exp. output.
448      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
449    o pkg/seaice:
450      - bug fix in the evp solver: boundary conditions were affected be
451        masking of zMax/zMin (changes results)
452      - minor bug fix in boundary conditions in seaice_calc_strainrates
453        (changes results for no_slip)
454      - seaice_lsr.F: make interpolation of eta dependent on boundaries
455      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
456      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
457        stress formulation and no-slip boundary conditions
458    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
459      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
460    o pkg/seaice: a first HSALT time stepping equation has been checked in
461    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
462      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
463      without requiring DO-IF statements
464    o pkg/thsice:
465      use continuous power-law function for partition of energy between lateral
466      melting/freezing and thinning/thickening ; old code using step function
467      still available with #undef THSICE_FRACEN_POWERLAW
468      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
469    o testreport: change AD testing : check against results/output_adm.txt
470      using same scripts as for forward test.
471    
472    checkpoint59g
473    o adjoint testing: in preparation for changing testreport:
474      - output format: cost and grad written on separated lines
475      - ad output results in directory "results" (instead of "results_ad")
476    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
477    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
478    o pkg/ecco: allow user defined cost function contributions
479    o testreport:
480      Allow to choose (per experiment) the list of tested output variables
481       and the main variable (used to issue a pass/FAIL ) ;
482      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
483      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
484      Also modify printing of summary:
485       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
486       b) echo the list of tested variables in the individual summary.txt of
487          each experiment.
488    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
489      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
490      (but still depend on the tile decompostion of the domain).
491    o pkg/seaice: change a discretization detail to make the B-grid code
492      "more symmetric". This change is likely to remove all "ridges/leads" that
493      where quasi-aligned with the grid in B-grid solutions. It may also be
494      the solution to the stress coupling issues with the B-grid.
495    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
496      remove .cvsignore from input dir. (since testreport no longer run here).
497    o pkg/thsice:
498     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
499     - fix reshaping of sea-ice just after advection:
500       melt all the ice only if ice-volume is too small.
501     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
502       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
503     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
504    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
505      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
506    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
507      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
508      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
509      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
510      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
511      -> update output.txt
512    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
513     this affects truncation error: -> update output.txt of exp:
514      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
515      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
516    
517    checkpoint59f
518    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
519    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
520      a bounded range (in forward mode)
521    o pkg/ecco, ctrl, autodiff and mom_common:
522     internal parameter controls, completements of implementations
523    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
524    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
525      (not seem any difference in testing results).
526    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
527       at face corners.
528    o pkg/generic_advdiff:
529     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
530      loop range indices for computing vertical advection tendency
531      and do the calculation in the interior only (no overlap) ;
532      for now, only implemented for SOM advection (to save CPU time).
533     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
534    o exch2 adjoint
535      First set of changes:
536      - add exch2 hand-written adjoint templates
537      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
538        This will require cleanup in pkg/autodiff/*.F
539        (changed routines currently kept separate in verif. code/)
540      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
541        that used to hide exch2 or cubed-sphere specific code
542        (commented via 'cph-exch2')
543    o pkg/seaice
544      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
545    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
546       output of global_ocean.cs32x15.thsice .
547    
548    checkpoint59e
549    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
550      for B-grid vector (not yet tested) and C-grid vector (<- only used
551      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
552    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
553      (#ifdef ALLOW_SALT_PLUME)
554    o gather_2d/scatter_2d: removed halo regions
555    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
556      scheme and the corresponding test case (under front_relax dir). For now,
557      only available with Skew-flux form and not yet tested in realistic set-up.
558      adjoint: store directives updated, but gradient checks deteriorated,
559      so maybe GM/Redi adjoint is now broken.
560    o seaice adjoint
561      * add AREA, HEFF, HSNOW as control variable
562        (should not change lab_sea results)
563      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
564    o pkg/seaice:
565      * added computation of saltFlux in seaice_growth;
566        For time being, sea ice salinity is assumed constant
567        contribution of snow flooding to freshening of sea ice is neglected.
568        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
569        defaults to 0.0 in order to maintain backward compatibility.
570        Typical values for SEAICE_salinity are 4 to 10 g/kg.
571      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
572      * added SEAICE_availHeatFrac, which specifies fraction of surface level
573        heat content used to melt or grow ice
574      * commented out cap of HICE: it helps keep ice thinner
575      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
576      * applied OBCS T/S mask to HEFFM sea ice mask
577    
578    checkpoint59d
579    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
580     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
581     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
582    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
583     and change default value of parameter "GM_Small_Number";
584     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
585       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
586       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
587    o pkg/ecco: cost function when applying pkg/smooth to controls
588    o pkg/ctrl: add forcingPrecond run time parameter
589    o pkg/seaice:
590     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
591     - fix bug in metric terms of u-equation in LSR solver (implicit part),
592       changes verification/lab_sea
593     - rearrange implicit part of u-equation in LSR solver to make it easier to
594       read, understand, and debug. This causes changes at the truncation level.
595     - fix (serious) bug in the boundary conditions (sign error in the implicit
596       part) of the LSR solver. Changes all LSR results.
597     - fixed problem with HSNOW initialization to avoid thick snow when AREA
598       is initilized with small values - does not change lab_sea results.
599     - added HsnowFile initialization capability
600    o pkg/smooth: addition to model/src and pkg/ctrl so allow
601     initialization of pkg/smooth and application to control vector
602    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
603    o dependencies: pkg/profiles requires pkg/cal
604    o pkg/profiles:
605     - added option ALLOW_PROFILES_GENERICGRID
606         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
607         that interpolation information (grid points and coefficients) is provided
608         within the netcdf input files.
609         -> sample matlab scripts can be found in MITgcm_contrib/gael
610         that allow you to prepare netcdf input files.
611     - also modified: cleaner include statements, cleaner error print statements,
612       cleaner stops when error, and more tests of the netcdf input files consistency.
613    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
614    o pkg/seaice:
615     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
616       requires a new routine: seaice_diagnostics_fill.F
617     - make sure that seaice does not move if not forced (pressure replacement
618       method, Hibler and Ip, 1995), changes results
619     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
620     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
621       It is turned off by default (=-1.), because it changes the results.
622     - make it possible to read AREA from a file, too.
623    
624    checkpoint59c
625    o add S/R and diagnostics for oceanic mixed-layer depth
626    o move GMRedi call after all vertical mixing schemes (including KPP)
627    o pkg/thsice:
628     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
629      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
630    o pkg/obcs:
631     - bug fix for balance code
632    o pkg/seaice:
633      - allow values of SEAICE_elasticParm > 1
634      - add new parameter SEAICE_evpTauRelax as an alternative
635        to SEAICE_elasticParm
636      - make lsr boundary conditions free slip (by default), changes result
637      - add code for no slip boundary conditions for lsr
638      - set minimum of zeta to zero (and not 4e8) (changes results)
639      - add a cap on AREA after advecting AREA if seaice_growth is not called
640    o change calculation of Visbeck K:
641      - no longer depend on tapering scheme; instead, compute slope (limited
642        by GM_maxSlope). this is equivalent to what was comuted before with
643        clipping or linear tappering.
644      - fix vertical averaging (wrong by 1/2 level)
645      - leave the old version (but will not be maintained) within
646        #ifdef OLD_VISBECK_CALC / #endif
647      - update output of exp. ideal_2D_oce
648    o change error catch in calc_r_star to improve vectorization
649    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
650      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
651    o adjoint:
652      Re-organized adjoint checkpointing according to Matt Mazloff
653      (but with modifs/completions/cleanups)
654      Storing is now bundled into large arrays to optimized I/O
655      (and second step in cleanup of the_main_loop)
656    
657    checkpoint59b
658    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
659      - export/import (between ocean & coupler) fields needed for ocean DIC.
660    o pkg/seaice:
661      - get rid of three more exchanges seaice_calc_viscosities (required
662        different loop boundaries in seaice_lsr and seaice_ocean_stress)
663      - bug fix in seaice_ocean_stress (update of lab_sea required)
664      - reduce loop boundaries to necessary minimum also in seaice_evp
665      - go back to the old way of computing deltaC/Z as the adjoint likes that
666        better
667    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
668      passive tracer to an Age Tracer) + update output.txt
669    o pkg/exf:
670      - implement A-grid / C-grid selection for wind-stress input files.
671      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
672      for now, in exf_bulk_largeyeager04.F only :
673      - change implementation for case where windspeed + 2. components wind-stress
674        are read-in. AND use rhoConstFresh to convert evap.
675    o pkg/seaice:
676      - use correct EXCH_UV for wind-forcing (on A-grid).
677      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
678        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
679    o pkg/exf:
680      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
681      EXF_INTERPOLATION:
682      - merge global_with_exf/code version of exf_interp_read.F
683        to the main code ;
684      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
685        reading the file ; Important: This options needs to be defined to recover
686        previous code.
687        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
688      - no longer loose real*8 precision along the way when using exf_iprec=64.
689    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
690      - change discretisation of evp-solver in order to avoid another exchange
691        (changes lab_sea) and clean up a little
692      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
693        help the adjoint (this also changes the results slightly)
694      - add a few "_d 0" where they had been missing in seaice_evp.F
695      - cleaning up: remove unused seaice_calc_rhs.F
696    o pkg/exf: some cleaning-up:
697      - change various "constants" into runtime parameters
698      - cleaned-up Large&Yeager04 routine which should eventually
699        replace exf_bulkformulae.F (changed names of S/R and CPP)
700        and merged various ALLOW_ATM_WIND options
701     only used with thsice pkg (in thsice_get_exf.F):
702      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
703        which are used when useStabilityFct_overIce=TRUE (= the default)
704      - change default values of ice & snow emissivity and scale downward LW
705        by ice & snow emissivity.
706    o pkg/thsice:
707     fix few little problems, in thsice_calc_thickn.F:
708      - growth vertically (and not laterally) if iceFrac == iceMaskMax
709      - melt only laterally if hIce < hThinIce (as the comments say)
710      and in thsice_extend.F:
711      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
712      - start to form ice as soon as the minimum ice-volume is reachable.
713     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
714      and cpl_aim+ocn
715    o pkg/kpp
716     - move computation of surface related input fields to KPP into a new
717       subroutine kpp_forcing_surf.F
718     - remove wrong (within bi,bj loops) EXCH calls.
719     - little cleaning (add argument myThid in last position, cvs header ...)
720     - for now, fix conservation problem by exchanging KPPviscAz (may not
721       be the best fix)
722    o pkg/seaice
723     - check for inconsistent evp parameter/cpp-flag combination
724     - remove leftover errIO flat for obsolete name list error handling
725    o OpenAD
726     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
727    
728    checkpoint59a
729    o pkg/seaice: some parameter clarifications and a little bit of clean up
730    o pkg/thsice: rename run-time parameters:
731       himin       -> hIceMin
732       himin0      -> hThinIce
733       hihig       -> hThickIce
734       i0          -> i0swFrac
735       transCoef   -> bMeltCoef
736       frac_energy -> fracMelting
737      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
738       with default values (for now) that do not change the results.
739      remove old version of thsice vars advection in pkg/seaice.
740    o in FFIELDS.h:
741      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
742      - make pLoad & sIceLoad always available (but still only used if
743         ATMOSPHERIC_LOADING is #define).
744    o pkg/kpp: replaced _KPP_RL with _RL
745    o bug fixes for vertical diffusivity computations when both KPP and
746        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
747        are no longer updating the vertical diffusivity array
748        (passed as argument) but are (re-) setting those arrays.
749    o pkg/seaice: fix bug in evp solver, while doing that
750      - change (improve?) discretization of stress computations for both
751        cgrid-lsr and evp solver
752      - add a new routine to compute strain rates
753      - the above changes lab_sea results
754      - add no slip conditions for evp solver (off by default), lsr-version
755        may follow
756      - fix exchange for shear at Z-points (does not change lab_sea)
757      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
758        (to force the user to pick a time step since there is not "safe" way
759        of choosing it)
760      - add principal stress diagnostics
761      - rearrange fields for evp a little to avoid having to call a: too many
762        exchanges and b: exchanges for stress trensor components which we do
763        not have.
764      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
765        of evp, complete rewrite for lsr case (latter is does not yet work
766        in all cases)
767    o pkg/kpp: add code to have mixing in shelf ice caverns
768      - add myThid to all kpp routines (long overdue)
769    
770    checkpoint59
771    o pkg/exf:
772      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
773        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
774      - move exf header files from lower_case.h to UPPER_CASE.h ;
775        add missing cvs Header & Name
776      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
777      - add namelist param. selectStressGridPosition, exf_monFreq
778      - retire many _CLIM routines, and remove data.exf_clim
779        + params moved to data.exf
780        + climsst, climsss now handled by exf_set_gen, i.e.
781          climss?period=0 refers to constant field,
782          climss?period=-12 to monthly forcing
783      - split up namelists in data.exf
784    o pkg/seaice:
785      - remove seaice_exch and seaice_exch_uv
786      - remove superfluous exchange of theta
787      - add myThid to seaice_budget_ocean/ice
788      - add new interface for atmospheric wind forcing (C-grid only)
789        + new routine
790        + two new field (taux, tauy for stress over ice)
791        + removed one global field (DAIRN) for C-grid case only
792    o pkg/thsise
793      - 2nd set of modifs for thsice adjoint in conjunction with exf
794    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
795    
796    checkpoint58y_post
797    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
798      vertical diffusivity, similar to that in MOM4; turned on using
799      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
800      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
801    o Added capability for 3D specification of background vertical diffusion
802      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
803      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
804      "data" file that contains the 3D vertical diffusivity coefficients.
805    o ice dynamics (pkg/seaice) with thsice thermodynamics:
806      - add code within pkg thsice to advect & diffuse sea-ice fields
807      similar to (and will replace) what has been added in  seaice_advdiff.F,
808      but: - conserving Mass, Heat & Salt.
809           - better when using non-linear advection scheme (not yet fully tested)
810           - can also be used in atmospheric set-up (for now, only the diffusion).
811    
812    checkpoint58x_post
813    o IO option for global-file compact format:
814      - add options when generating topology (utils/exch2/matlab-topology-generator)
815      - add I/O capability (pkg/mdsio).
816      - adapt utils/matlab/rdmds.m to read this format.
817      for now long-line format not yet supported by pkg/mdsio (& exch2).
818    o shelfice: add a few diagnostics
819    
820    checkpoint58w_post
821    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
822      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
823      (and replace horiVertRatio in NH code).
824      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
825                         and tutorial_plume_on_slope (sensitive to truncation)
826    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
827      directly to drive seaice model (C-grid only)
828    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
829     - reintroduce computation of wind from stress,
830     - compute tau (in exf_bulkformulae.F) from windstress averaged to
831       mass points to avoid tau = 0
832     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
833    o rdmnc.m: make it work with "global" files created with gluemnc
834    o rdmnc.m : some improvements in dealing with singleton dimension
835      (tested on all testreport mnc output files).
836    o genmake2: disable pkg/profiles if netcdf test fails.
837    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
838    o move call to cal_readparms up to make calendar parameters/variable available
839      to all packages
840    
841    checkpoint58v_post
842    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
843      useDynP_inEos_Zc tested.
844    o pkg/exf: changes to properly interpolate/mask/scale initial fields
845    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
846      and portions thereof.  See read_cs.txt for description and examples.
847    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
848      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
849      following the great-circle arc between those 2 points.
850    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
851      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
852    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
853     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
854     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
855     - still needs work (not working with some options ; efficiency to improve)
856       and serious testing.
857     - use this scheme for temperature & salinity in 2 advection test exp.:
858       advect_xy & advect_xz, respectively.
859    
860    checkpoint58u_post
861    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
862    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
863    o testreport: add option "-skipdir" to skip some test.
864    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
865      momentum calculation.
866    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
867    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
868      remove checkpoint.F and the_correction_step.F (no longer used);
869      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
870    o add option (linFSConserveTr) to correct for tracer source/sink due to
871      Linear Free surface
872    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
873    o pkg/thsice: fix reading mnc-pickups
874    
875    checkpoint58t_post
876    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
877    o pkg/mdsio:
878     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
879       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
880       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
881     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
882     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
883       either MDS_READ_FIELD or MDS_WRITE_FIELD )
884     - new S/R (to replace MDSWRITEMETA), which allows to write more
885       informations (variable names, time ...) to meta files.
886     - modify rdmds.m to give back the meta file content.
887    o pkg/diagnostics: change vertical interpolation to be safer, and more
888       flexible (define p-levels to interpolate to in data.diagnostics);
889      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
890       diagnostic pointer.
891    o pkg/seaice: more cleaning up of seaice_growth, added many comments
892    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
893    o fix multi-category seaice:
894     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
895       SEAICE_MULTICATEGORY
896     - fix short wave heat flux
897    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
898       and allow to use EVP solver. Change forward lab_sea: test both EVP
899       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
900    o Initial check-in of lab_sea adjoint
901      (very similar to natl_box_adjoint/code_seaice)
902      * used C-grid and EVP solver
903      * used KPP, GM/Redi
904      * uses inAdExact=.TRUE.
905      * gradient checks fail for both ADM and TLM
906        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
907        f.d. gradients actually seem more problematic than ADM, TLM gradients;
908        issue is related to forward mismatch between g77 an ifort
909    o pkg/seaice: overhaul of thermodynamics
910     - growth.F and groatb.F are replaced by new routine seaice_growth.F
911     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
912     - move a few global fields out of SEAICE.h into seaice_growth.F and
913       make them 2D (FICE/QNETO/ ...)
914     - remove FO (it is the same as QNETO)
915     - introduce a few local fields to avoid modifying external fields such
916       as atemp, etc.
917    
918    checkpoint58s_post
919    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
920      changed exf_set_gen.F so that
921        genperiod=0 means input file is one time-constant field and
922        genperiod=-12 means input file contains 12 monthly means
923    o CG2D: use pre-computed solver main-diagonal (stored in common block);
924      this affects truncation error ; generate new output file for exp. which
925      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
926        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
927        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
928        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
929        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
930        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
931    o start implementation of deep-atmosphere and anelastic formulation
932    o verification: remove 2nd copy of input files and use script "prepare_run"
933      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
934    o mom_common/vecinv/fluxform: fix a few initialisation isssues
935    o profiles: fix for multithreaded case
936    
937    o diagnostics: rename few diags:
938      s/'PRESSURE'/'RCENTER '/g
939      s/'TICE    '/'oceFreez'/g
940      s/'TAUX    '/'oceTAUX '/g
941      s/'TAUY    '/'oceTAUY '/g
942      s/'SWFLUX  '/'oceQsw  '/g
943      s/DIFx/DFxE/g
944      s/DIFy/DFyE/g
945      and add few ocean-forcing diagnostics:
946      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
947    o modifications to pkg/seaice/growth.F and budget.F, which change results of
948      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
949      as actual snow thickness.  It now refers everywhere to effective snow
950      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
951    
952    checkpoint58r_post
953    o modifications to pkg/seaice/growth.F, which change results of
954      lab_sea experiment: fixes pertain to melting snow over open water, to
955      masking EVAP under sea ice, and to using the correct AREA variable for
956      computations of EVAP, PRECIP, HSNOW, and GHEFF
957    o add ability to read bathy, salt, and theta using MNC (off by def)
958    o add flooding algorithm and advection of HSNOW for pkg/seaice;
959      both are turned off by default and do no change any results
960    o seaice advection with pkg/thsice: a step toward the use of non-linear
961      advection scheme, but #ifdef or commented out for now (requires more EXCH).
962    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
963      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
964      in natl_box (affects results @ truncation level: update output.txt)
965    o multi-threading and IO:
966      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
967      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
968        (needed to work with SingleCpuIO): tested in all verif. exp.
969    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
970      affects the results (but none of the verification test uses this scheme).
971    o Adding some pkg/diagnostics capability to pkg/seaice
972      (will certainly be subject to changes)
973    o ctrl: adding new control variables:
974      lwflux, lwdown, evap, snowprecip, apressure, runoff
975    
976    checkpoint58q_post
977    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
978      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
979      high_res_cube configuration by 4% on Columbia.
980    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
981      add (in global_with_exf/code) a version of EXF_INTERP_READ without
982      dynamical allocation (seems to work in multi-threaded).
983    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
984      single CPU io) so that TAF does not have to see EESUPPORT.h
985    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
986    
987    checkpoint58p_post
988    o obcs: stop if obcs is used with useCDscheme = .true.
989    o shelfice:
990     - fix a sign error so that no slip at shelfice interface works
991     - remove stop for combination non-hydrostatic code and shelfice. That does
992       not mean, that the results are correct, but at least they are numerically
993       stable
994    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
995    o added adjoint exch routined for all exch*3d* routines
996      and updated flow directives
997    
998    checkpoint58o_post
999    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
1000      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
1001    o change controling S/R for writing pickup file (new S/R do_write_pickup)
1002      and clean-up reading/writing of pickup files.
1003    o fix local version of read/write pickup (NH part) in rotating_tank/code
1004    o simplify EXCH interface:
1005     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
1006     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
1007    o added the regrid package
1008    o shelfice:
1009     - add a simple boundary layer scheme to reduce noise
1010     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
1011    
1012    checkpoint58n_post
1013    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
1014       local variable (not in common block).
1015    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
1016      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
1017      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
1018        to work with SingleCpuIO.
1019    o add "_d 0" to real constant of pkg/cfc subroutines ;
1020       update exp. cfc_exemple & tutorial_cfc_offline output files.
1021    o multi-threading and IO:
1022      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
1023        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
1024      - barrier before and after reading.
1025      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
1026      - avoid using MDS_WRITELOCAL for LAND pkg output.
1027      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
1028        common-block variables ; Allows multi-threading with master-thread IO.
1029    o change default MAX_NO_THREADS from 32 to 4 ;
1030      and stop cleanly when MAX_NO_THREADS is too small.
1031    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
1032    
1033    checkpoint58m_post
1034    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
1035       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
1036    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
1037       keep global_ocean.90x40x15 (for AD testing) with former secondary test
1038       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
1039    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
1040        add MITgcm_tutorials (= code + all the tutorials)
1041    o ecco, option to compute cost for total ssh (mean+anom)
1042    o consistent with addition of ptracer and ssh in pkg/profiles
1043    o profiles: adding ptracer and ssh
1044    o testreport: change multi-test output-file name
1045      (from output.txt.{name} to output.{name}.txt)
1046    o profiles: now ok for mutli-tiles case
1047    o seaice: add 4 parameters for different advection schemes for area,
1048      (effective) seaice thickness, enthalphy, and snow height. Their default
1049      is the standard parameter SEAICEadvScheme
1050    o calc_gw:
1051     - add cosFacU in zonal viscous flux (harmonic.visc.).
1052     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
1053       of tutorial_plume_on_slope.
1054    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
1055    o calc_gw: true flux-form, account for horizontal grid spacing.
1056      update rotating_tank results, but not plume_on_slope (affected at
1057      truncation level, 11 digits).
1058    
1059    checkpoint58l_post
1060    o calc_gw:
1061     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
1062     - remove side-drag for now (need to fix it); update plume_on_slope results.
1063     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
1064  o commit code to make SST/SSS weights spatially variable  o commit code to make SST/SSS weights spatially variable
1065    (based on either variable in-situ or variable initial T/S weights)    (based on either variable in-situ or variable initial T/S weights)
1066  o pkg/ecco:  o pkg/ecco:
# Line 15  o pkg/ecco: Line 1071  o pkg/ecco:
1071      (sflxumm, sfluxmm2, bal_sfluxmm)      (sflxumm, sfluxmm2, bal_sfluxmm)
1072    * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,    * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
1073      including separate counting and multipliers      including separate counting and multipliers
1074    o pkg/rbcs
1075      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
1076    
1077  checkpoint58k_post  checkpoint58k_post
1078  o testreport:  o testreport:
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