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revision 1.729 by jmc, Fri Oct 6 19:44:51 2006 UTC revision 1.1029 by jmc, Wed Oct 8 00:31:29 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 pkg ggl90:
8      - in ggl90_cal.F: compute only one set of visc/diff, used to
9        step forward TKE/T/S/momentum
10      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
11        have Prandlt =1)
12    o gmredi(fm07):
13      - add lower limit on Transition layer thickness + lower limit on 1/lambda
14      - allow to set few more params from data.gmredi
15    o pkg ggl90:
16          - add missing sqrt(2) factor in computation of mixing length
17            scale in ggl90_calc.F
18            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
19    
20    checkpoint61d
21    o adjoint modifs
22      - adapt to new field rhoInSitu
23      - allow to revert from StoreDynVars2D, StoreDynVars3D
24        to individual fields
25        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
26    o store 3-D (in-situ) density in commom block (DYNVARS.h)
27     - save 1 rho computation.
28     - no longer modify T & S inland when using down_slope pkg.
29    o gad_som : allow to switch to SOM advection for T & S without corresponding
30      pickup files (using new S/R: MDS_CHECK4FILE).
31    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
32      (for useSingleCpuIO to work in multi-threaded)
33    o pkg/shelfice:
34     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
35       with SHELFICEtopoFile in data.shelfice
36     - move code for reading ice shelf topography and modifying hFacC into separate
37       subroutines of the shelfice package
38     - separate initialisation of "fixed" and "variable" variables
39     - kTopC is not (yet) replaced by kSurfC, although this is possible
40    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
41    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
42      and rename:
43      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
44      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
45    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
46    
47    checkpoint61c
48    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
49      to add mass source/sink of fluid in the interior (3-D generalisation
50      of oceanic real-fresh water flux).
51    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
52    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
53    o new pkg: down_slope
54      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
55      - presently, modify T & S inland (dwnslp_calc_rho.F).
56        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
57      - implementation for ocean in P-coords not tested.
58      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
59    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
60      (to facilitate conversion of oceanic pkg to p-coordinate).
61    o change FIND_RHO to FIND_RHO_2D :
62      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
63    o new pkg: cheapaml
64    
65    checkpoint61b
66    o exch2:
67      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
68      - no longer depend on the order sequence (N,S,E,W).
69      - 3rd exchange no longer needed (tested with 24 tiles).
70      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
71      - exch_UV_A-grid readily available (but not yet tested).
72      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
73      (both are no longer needed) in exch_uv: no effect in forward run; but
74       get truncation error differences with adjoint exch.
75    o exch2:
76     - change index-bounds storage (moved from target to local tile,
77       more intuitive this way) ; rename/remove some variables.
78     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
79    
80    checkpoint61a
81    o exch2/matlab-topology-generator:
82      fix bug in index bounds for N-S internal exchange (hard to tell if this
83      had any effect on the solution).
84    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
85      is exceeded
86    o testreport: modify syntax of awk, so that it works also with
87      awk, and not only with nawk and gawk
88    
89    checkpoint61
90    o autodiff
91      Change default for TAF usage by removing argument '-nonew_arg'
92      This changes TAF subroutine argument list (ordering of active var.)
93      Omission of this flag leads to incompatibility w.r.t. TAMC
94      To restore TAMC-compatibility, need following modifs:
95      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
96      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
97      Tested TAF version is 1.9.22
98      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
99    
100    checkpoint60
101    --->>> This is the last checkpoint for which generating the adjoint
102    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
103    --->>> by default.
104    --->>> Future checkpoints will ommit this flag by default.
105    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
106    o pkg/grdchk: Add gradient check to etan0 perturbations.
107    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
108    o pkg/autodiff: more flexibility in zeroadj.
109      model/src: modifying do_oceanic_phys.F accordingly.
110    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
111    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
112      special setup of gmredi for which the adjoint is stable
113      enough for parameter optimization.
114    o bridging the gap between eddy stress and GM.
115      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
116          along with a change in CPP option (now ALLOW_EDDYPSI).
117      -> when using GM w/ GM_AdvForm:
118          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
119          is applied either in the tracer Eq. or in momentum Eq.
120          depending on data.gmredi (intro. GM_InMomAsStress).
121      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
122      The key modifications are in model/src/taueddy_external_forcing.F
123      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
124    
125    checkpoint59r
126    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
127      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
128      fix option to read coriolis(@ cell-corner) from files with CS-grid.
129    o pkg/mnc: add some attributes to standard 1D-coordinate variables
130    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
131      mass points, when using mnc for output
132      - add runtime parameter (missing_value, missing_value_int) to override
133        default (which is the value of getcon('UNDEF'))
134    o pkg/mnc: prepare mnc for the actual use of missing values with the
135      diagnostics package: small fix in mnc_cw_readwrite.template and more
136      initialisation of never used fields
137      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
138      versions
139    o pkg/thsice/thsice_ini_vars.F added default initial values so that
140      thermodynamics sea ice solver does not blow up when some initial fields
141      are missing.
142    o move from external_forcing_surf.F to ini_forcing.F
143      the p-coord. hack consisting in using pLoad to set phi0surf ;
144      update output of tutorial_global_oce_in_p (affected @ truncation level).
145    o Freshen up a bit hs94.1x64x5, notably:
146      remove rotationPeriod and tRef=5*0. (adjoint only), and add
147      exactConserv=.TRUE.
148    o pkg/generic_advdiff:
149      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
150      applies to files where Temperature & Salinity 2nd Order moments are used.
151    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
152      this uses a dynamically allocated internal state data structure
153      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
154      and requires a fortran 90 compiler
155    
156    checkpoint59q
157    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
158       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
159    o Refresh tutorial_global_oce_biogeo, notably:
160      - change bathymetry (put back seamounts in ACC, use hFacs)
161      - change EOS (POLY3 --> JMD95Z)
162      - use Bryan-Lewis vertical diffusivity
163      - use multidimensional advection
164      - remove old virtual virtual in dic pkg, now done through ptracer pkg
165      - change a couple of parameters in dic pkg
166    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
167    o pkg/obcs: change default to OBCSfixTopo = .true.,
168      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
169      - replace "debugMode" with "debugLevel .GE. debLevB"
170    o implementation of TAF directives for gchem,cfc,dic
171    o remove "exp5" (replaced by tutorial_deep_convection).
172    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
173      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
174      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
175      --> changes results in exp4, seaice_obcs
176    o tutorial_deep_convection :
177      update the set-up and increase resolution and domain size ; start
178      from pseudo initial conditions = output at t=120mn in order to see
179      something happening when running testreport.
180    o pkg/seaice: add os7mp as an advection scheme
181                  add check for advection schemes
182                  add a flag for restoring T and S underneath sea ice
183    o pkg/my82: add netcdf-support and diagnostics
184    o thsice pkg:
185      - Now hsMax limits snow height by turning it into ice following
186        flooding scheme (and now conserving energy)
187      - Slight rewriting of the formula in thsice_calc_thick.F
188      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
189      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
190    
191    checkpoint59p
192    o gchem / dic / cfc :
193      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
194      - add new parameter files: "data.dic" & "data.cfc" ;
195      - various re-arrangement in initialisation & header file ;
196      - fix tutorial_global_oce_biogeo for multi-threaded test.
197    o pkg/dic: test for "pickup_dic" file when restarting ;
198      if no pickup-file, can restart with a re-initialised pH (same as it did
199      before) providing pickupStrictlyMatch is set to False.
200    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
201      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
202    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
203      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
204    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
205     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
206       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
207    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
208       scheme to use for vorticty-term ;
209     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
210       (with default selectVortScheme, return to original discretisation)
211     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
212    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
213    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
214      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
215      also fix diagnostics VISCAHW & VISCA4W.
216    
217    checkpoint59o
218    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
219    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
220      move a few statemens out the main loop into separate loops
221    o pkg/shelfice:
222      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
223        (kg/m^2/s), does not break tests, because in verification/isomip,
224        rhoConstFresh=rhoConst (by accident)
225      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
226      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
227        new file model/src/seawater.F, so that they are available for all pkgs.
228      - convert potential temperature into in-situ temperature. This changes the
229        isomip tests => update tests
230    o add a flag writePickupAtEnd (default=true) to be able to suppress
231      writing a pickup at the last timestep
232    o tools/mpack-1.6 :
233      - disable automake (not working) and autoconf (not needed).
234      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
235        also cleaner with much less compilation warnings.
236    o pkg/profiles:
237      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
238      (for "less than 32 characters name" compiler requirement)
239    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
240      conditions that have a different sampling frequency than S/T/U/V obcs
241    o pkg/diagnostics (stats-diags):
242      - fix global Min/Max in case 1 processor get only empty tiles
243    o genmake2: replace (4 times)
244         make genmake_tc_1.o >> genmake_warnings 2>&1
245      with
246         COMM="$CC $CFLAGS -c genmake_tc_1.c"
247         echo $COMM >> genmake_warnings
248         $COMM >> genmake_warnings 2>&1
249      to make genmake2 always see the value of CC as specified in the optfile.
250    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
251      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
252      - modify verification advect_cs test to test SOM-advection on CS-grid.
253    o pkg/ctrl:
254      - Rewrite of ctrl_map_ini_ecco.F,
255        introducing a generic routine (ctrl_map_ini_gen.F).
256      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
257    
258    checkpoint59n
259    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
260      number in dedicate array "hdiag":
261      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
262        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
263      - many small changes (integer format) for large number of diagnostics
264      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
265        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
266    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
267      usingSphericalGrid, this allows to define the rotated grid coordinates
268      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
269      geographical coordinates according to the inverse of the rotation defined
270      by the Euler angles, so that Coriolis parameter and online-interpolation by
271      exf works with the geographical coordinates on XC/YC/XG/YG.
272      Naturally, this feature does not work with all packages, so some
273      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
274      profiles), because there the coordinates are assumed to be regular
275      spherical grid coordinates.
276    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
277      - introduce isopycnal diffusion coefficient control.
278    o tools/adjoint_options:
279      - additional control vector components.
280    o pkg/mnc: have mnc create marginally meaning full coordinate variables
281      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
282    o pkg/mypackage:
283      - add example of read/write pickup for state-var ;
284      - add entry points to the main code for state-vars diags & write-pickup.
285    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
286      transitions for useExfYearlyFields
287      - add new subroutine that determines the file to read from for
288        use*YearlyFields = .TRUE. and .FALSE.
289      - add a verification experiment to global_with_exf that tests
290        useExfYearlyFields with USE_EXF_INTERPOLATION defined
291    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
292      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
293      subroutines (which could be generated from a template, because they are
294      almost identical), for now they are included in obcs_prescribe_read.F for
295      simplicity
296    o pkg/exf:
297      - add a little more diagnostic to exf_interp_read (in analogy to
298        mds_read_field, can be turned off with debugLevel < debugLevA=1)
299      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
300        ugly but fast by unrolling short inner loops, inserting a unroll=8
301        directive in routine lagran, and splitting a loop and making do while the
302        outermost loop (the latter requires the intoduction of index arrays)
303    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
304    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
305      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
306    o verification/seaice_obcs: updated for restart test and latest options
307    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
308      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
309      for now this is only available for the C-grid code and also within
310      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
311    
312    checkpoint59m
313    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
314      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
315    o gad_som : fix flux output (& diagnostics) to have same units as other  
316      advection scheme fluxes (was previously multiplied by deltaT).  
317    o added verification/seaice_obcs both to test seaice open boundaries
318      and to provide an example matlab scrpt for generating them
319    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
320    o pkg/salt_plume: clean up salt_plume_frac.F to
321      remove redundancy in PlumeMethod 1 and 4
322    o pkg/kpp: added saltplume diagnostics
323    o pkg/obcs and pkg/seaice:
324      - do not set uice and vice to zero when OB*icefile are unspecified
325      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
326      - moved seaice tracer obcs after call to seaice_growth
327    o pkg/salt_plume: added various options for salt plume depth
328      criterion and for vertical distribution of the salt
329    
330    checkpoint59l
331    o pkg/ptracers: new version of ptracers pickup:
332      read meta file and write only fields which are needed to restart.
333      ( same logic as main pickup file ; also using pickupStrictlyMatch )
334    o pkg/seaice:
335      - add timescale for melting due to warm mixed layer as a means of
336        setting SEAICE_availHeatFrac more conveniently
337      - add a CPP-flag/runtime parameter check for flooding algorithm
338      - reformulated availHeat in seaice_growth.F to be independent of AREA
339    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
340      unit changes
341    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
342    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
343      SX vector computer.
344    o pkg/seaice:
345      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
346        seaice forcing fields can now be read only through pkg/exf
347      - removed some unused halos
348    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
349    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
350      or U/VICE from U/VWIND before computing U/VSTRESS
351    
352    checkpoint59k
353    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
354      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
355    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
356      all experiments pass when compile with un-initialised var. checking option.
357    o added pkg/salt_plume
358    o script to test restart (for now, in MITgcm_contrib/jmc_script)
359    o pkg/seaice: new read/write pickup version.
360      read meta file and write only fields which are needed to restart.
361      ( same logic as main pickup file ; also using pickupStrictlyMatch )
362    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
363    o lab_sea.hb87: modify the domain & update output.hb87.txt :
364      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
365      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
366      process. Fixed here by closing the domain at the Northern boundary.
367    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
368    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
369      a set of consecutive levels in/from a 3-D array.
370    o pkg/ptracers:
371      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
372      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
373    
374    checkpoint59j
375    o in pkgs: dic, obcs, offline, rbcs:
376      standard way to compute coeff. for time interpolation between 2 time reccords
377      which retains full precision (& make results less dependent on compiler).
378      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
379    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
380      packages instead of reading ice cover and wind speed separately
381    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
382     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
383      to allow to compile customized code before the update)
384    o cleaning-up:
385      - fix CPP instruction syntax in pkg/obcs
386      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
387        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
388      - fix some threads issue in IO parts.
389    o pkg/dic:
390      - add tons of "_d 0" (--> much better testreports !)
391       and then update outputs of tutorial_global_oce_biogeo
392    o pkg/mom_fluxform:
393      add a special version of momentum advection intended to conserve momentum
394      next to a bathymetry step or a coastline edge. (default = off = #undef)
395    o new read/write pickup version:
396      - for now, only implemented for main (mdsio) pickup file.
397      - write out only what is needed to restart; merge pickup_nh , pickup_ph
398        and main pickup together.
399      - read meta file; read only what is needed to restart; stop if a field
400        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
401        if it make sense (even if the restart is not perfect).
402      - if no meta file, assume that pickup to read corresponds exactly to
403        a pickup that would currently be written.
404      - read pickup written in the old format (until checkpoint59i) if it
405        recognizes an old meta file (no field-list).
406      - add a meta file in exp. which starts from a pickup: 2 cases:
407        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
408         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
409        b) a meta file describing the content of the associated pickup file
410         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
411    o pkg/mdsio & pkg/rw:
412      - new routine to read a meta file ; new set of routine to read
413        Multiple-fields file (with meta file).
414    o added open boundary conditions capability for seaice
415        HSNOW, HSALT, UICE, and VICE
416    
417    checkpoint59i
418    o adjoint:
419      * fix multiDimAdvection adjoint
420        (partial recomputation problem by TAF for fVerT(:,:,kDown)
421        and comlev1 size definition (maxpass vs. max. number of tracers)
422      * verification/global_ocean.90x45x15 adjoint now tests
423        NLFS and multiDimAdvection using DST3 (=30)
424      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
425    o pkg/kpp: add "_d 0" to real constant (if missing);
426      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
427      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
428    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
429      for internal parameters related to restart process (formerly from PARAMS.h)
430      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
431    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
432      as argument. (only atm2d & obcs write_pickup have not yet been updated)
433    o pkg/monitor:
434      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
435      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
436      - account for deep Atmosphere factor and density factor (anelastic)
437    o added open boundary conditions capability for seaice HEFF and AREA
438    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
439      thermodynamics
440      - requires a little reorganization, which affects the testreport results
441        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
442        so that now the conservative form is tested
443      - add a few comments
444    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
445    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
446    o add new diagnostics to seaice: advective, diffusive fluxes (only for
447      multidim-advection, for scheme 2 they are not filled) and transports,
448      thermodynamic growth rates
449    o change units of EmPmR (inside the code, + within coupling interface)
450      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
451      Affects results @ truncation level (cg2d match) and update output of
452       experiments: lab_sea(6), global_ocean.90x40x15(10),
453      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
454      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
455      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
456      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
457    
458    checkpoint59h
459    o pkg/exf:
460      - improve vectorization by moving if-statement out of loops in
461        exf_mapfields, exf_radiation
462      - exf_bulkformulae.F: introduce 2D fields and vectorize code
463    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
464    o testreport:
465      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
466        monitor & update offline_exf_seaice exp. output.
467      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
468    o pkg/seaice:
469      - bug fix in the evp solver: boundary conditions were affected be
470        masking of zMax/zMin (changes results)
471      - minor bug fix in boundary conditions in seaice_calc_strainrates
472        (changes results for no_slip)
473      - seaice_lsr.F: make interpolation of eta dependent on boundaries
474      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
475      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
476        stress formulation and no-slip boundary conditions
477    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
478      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
479    o pkg/seaice: a first HSALT time stepping equation has been checked in
480    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
481      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
482      without requiring DO-IF statements
483    o pkg/thsice:
484      use continuous power-law function for partition of energy between lateral
485      melting/freezing and thinning/thickening ; old code using step function
486      still available with #undef THSICE_FRACEN_POWERLAW
487      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
488    o testreport: change AD testing : check against results/output_adm.txt
489      using same scripts as for forward test.
490    
491    checkpoint59g
492    o adjoint testing: in preparation for changing testreport:
493      - output format: cost and grad written on separated lines
494      - ad output results in directory "results" (instead of "results_ad")
495    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
496    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
497    o pkg/ecco: allow user defined cost function contributions
498    o testreport:
499      Allow to choose (per experiment) the list of tested output variables
500       and the main variable (used to issue a pass/FAIL ) ;
501      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
502      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
503      Also modify printing of summary:
504       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
505       b) echo the list of tested variables in the individual summary.txt of
506          each experiment.
507    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
508      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
509      (but still depend on the tile decompostion of the domain).
510    o pkg/seaice: change a discretization detail to make the B-grid code
511      "more symmetric". This change is likely to remove all "ridges/leads" that
512      where quasi-aligned with the grid in B-grid solutions. It may also be
513      the solution to the stress coupling issues with the B-grid.
514    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
515      remove .cvsignore from input dir. (since testreport no longer run here).
516    o pkg/thsice:
517     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
518     - fix reshaping of sea-ice just after advection:
519       melt all the ice only if ice-volume is too small.
520     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
521       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
522     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
523    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
524      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
525    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
526      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
527      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
528      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
529      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
530      -> update output.txt
531    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
532     this affects truncation error: -> update output.txt of exp:
533      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
534      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
535    
536    checkpoint59f
537    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
538    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
539      a bounded range (in forward mode)
540    o pkg/ecco, ctrl, autodiff and mom_common:
541     internal parameter controls, completements of implementations
542    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
543    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
544      (not seem any difference in testing results).
545    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
546       at face corners.
547    o pkg/generic_advdiff:
548     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
549      loop range indices for computing vertical advection tendency
550      and do the calculation in the interior only (no overlap) ;
551      for now, only implemented for SOM advection (to save CPU time).
552     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
553    o exch2 adjoint
554      First set of changes:
555      - add exch2 hand-written adjoint templates
556      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
557        This will require cleanup in pkg/autodiff/*.F
558        (changed routines currently kept separate in verif. code/)
559      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
560        that used to hide exch2 or cubed-sphere specific code
561        (commented via 'cph-exch2')
562    o pkg/seaice
563      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
564    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
565       output of global_ocean.cs32x15.thsice .
566    
567    checkpoint59e
568    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
569      for B-grid vector (not yet tested) and C-grid vector (<- only used
570      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
571    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
572      (#ifdef ALLOW_SALT_PLUME)
573    o gather_2d/scatter_2d: removed halo regions
574    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
575      scheme and the corresponding test case (under front_relax dir). For now,
576      only available with Skew-flux form and not yet tested in realistic set-up.
577      adjoint: store directives updated, but gradient checks deteriorated,
578      so maybe GM/Redi adjoint is now broken.
579    o seaice adjoint
580      * add AREA, HEFF, HSNOW as control variable
581        (should not change lab_sea results)
582      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
583    o pkg/seaice:
584      * added computation of saltFlux in seaice_growth;
585        For time being, sea ice salinity is assumed constant
586        contribution of snow flooding to freshening of sea ice is neglected.
587        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
588        defaults to 0.0 in order to maintain backward compatibility.
589        Typical values for SEAICE_salinity are 4 to 10 g/kg.
590      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
591      * added SEAICE_availHeatFrac, which specifies fraction of surface level
592        heat content used to melt or grow ice
593      * commented out cap of HICE: it helps keep ice thinner
594      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
595      * applied OBCS T/S mask to HEFFM sea ice mask
596    
597    checkpoint59d
598    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
599     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
600     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
601    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
602     and change default value of parameter "GM_Small_Number";
603     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
604       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
605       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
606    o pkg/ecco: cost function when applying pkg/smooth to controls
607    o pkg/ctrl: add forcingPrecond run time parameter
608    o pkg/seaice:
609     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
610     - fix bug in metric terms of u-equation in LSR solver (implicit part),
611       changes verification/lab_sea
612     - rearrange implicit part of u-equation in LSR solver to make it easier to
613       read, understand, and debug. This causes changes at the truncation level.
614     - fix (serious) bug in the boundary conditions (sign error in the implicit
615       part) of the LSR solver. Changes all LSR results.
616     - fixed problem with HSNOW initialization to avoid thick snow when AREA
617       is initilized with small values - does not change lab_sea results.
618     - added HsnowFile initialization capability
619    o pkg/smooth: addition to model/src and pkg/ctrl so allow
620     initialization of pkg/smooth and application to control vector
621    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
622    o dependencies: pkg/profiles requires pkg/cal
623    o pkg/profiles:
624     - added option ALLOW_PROFILES_GENERICGRID
625         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
626         that interpolation information (grid points and coefficients) is provided
627         within the netcdf input files.
628         -> sample matlab scripts can be found in MITgcm_contrib/gael
629         that allow you to prepare netcdf input files.
630     - also modified: cleaner include statements, cleaner error print statements,
631       cleaner stops when error, and more tests of the netcdf input files consistency.
632    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
633    o pkg/seaice:
634     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
635       requires a new routine: seaice_diagnostics_fill.F
636     - make sure that seaice does not move if not forced (pressure replacement
637       method, Hibler and Ip, 1995), changes results
638     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
639     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
640       It is turned off by default (=-1.), because it changes the results.
641     - make it possible to read AREA from a file, too.
642    
643    checkpoint59c
644    o add S/R and diagnostics for oceanic mixed-layer depth
645    o move GMRedi call after all vertical mixing schemes (including KPP)
646    o pkg/thsice:
647     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
648      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
649    o pkg/obcs:
650     - bug fix for balance code
651    o pkg/seaice:
652      - allow values of SEAICE_elasticParm > 1
653      - add new parameter SEAICE_evpTauRelax as an alternative
654        to SEAICE_elasticParm
655      - make lsr boundary conditions free slip (by default), changes result
656      - add code for no slip boundary conditions for lsr
657      - set minimum of zeta to zero (and not 4e8) (changes results)
658      - add a cap on AREA after advecting AREA if seaice_growth is not called
659    o change calculation of Visbeck K:
660      - no longer depend on tapering scheme; instead, compute slope (limited
661        by GM_maxSlope). this is equivalent to what was comuted before with
662        clipping or linear tappering.
663      - fix vertical averaging (wrong by 1/2 level)
664      - leave the old version (but will not be maintained) within
665        #ifdef OLD_VISBECK_CALC / #endif
666      - update output of exp. ideal_2D_oce
667    o change error catch in calc_r_star to improve vectorization
668    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
669      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
670    o adjoint:
671      Re-organized adjoint checkpointing according to Matt Mazloff
672      (but with modifs/completions/cleanups)
673      Storing is now bundled into large arrays to optimized I/O
674      (and second step in cleanup of the_main_loop)
675    
676    checkpoint59b
677    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
678      - export/import (between ocean & coupler) fields needed for ocean DIC.
679    o pkg/seaice:
680      - get rid of three more exchanges seaice_calc_viscosities (required
681        different loop boundaries in seaice_lsr and seaice_ocean_stress)
682      - bug fix in seaice_ocean_stress (update of lab_sea required)
683      - reduce loop boundaries to necessary minimum also in seaice_evp
684      - go back to the old way of computing deltaC/Z as the adjoint likes that
685        better
686    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
687      passive tracer to an Age Tracer) + update output.txt
688    o pkg/exf:
689      - implement A-grid / C-grid selection for wind-stress input files.
690      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
691      for now, in exf_bulk_largeyeager04.F only :
692      - change implementation for case where windspeed + 2. components wind-stress
693        are read-in. AND use rhoConstFresh to convert evap.
694    o pkg/seaice:
695      - use correct EXCH_UV for wind-forcing (on A-grid).
696      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
697        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
698    o pkg/exf:
699      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
700      EXF_INTERPOLATION:
701      - merge global_with_exf/code version of exf_interp_read.F
702        to the main code ;
703      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
704        reading the file ; Important: This options needs to be defined to recover
705        previous code.
706        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
707      - no longer loose real*8 precision along the way when using exf_iprec=64.
708    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
709      - change discretisation of evp-solver in order to avoid another exchange
710        (changes lab_sea) and clean up a little
711      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
712        help the adjoint (this also changes the results slightly)
713      - add a few "_d 0" where they had been missing in seaice_evp.F
714      - cleaning up: remove unused seaice_calc_rhs.F
715    o pkg/exf: some cleaning-up:
716      - change various "constants" into runtime parameters
717      - cleaned-up Large&Yeager04 routine which should eventually
718        replace exf_bulkformulae.F (changed names of S/R and CPP)
719        and merged various ALLOW_ATM_WIND options
720     only used with thsice pkg (in thsice_get_exf.F):
721      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
722        which are used when useStabilityFct_overIce=TRUE (= the default)
723      - change default values of ice & snow emissivity and scale downward LW
724        by ice & snow emissivity.
725    o pkg/thsice:
726     fix few little problems, in thsice_calc_thickn.F:
727      - growth vertically (and not laterally) if iceFrac == iceMaskMax
728      - melt only laterally if hIce < hThinIce (as the comments say)
729      and in thsice_extend.F:
730      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
731      - start to form ice as soon as the minimum ice-volume is reachable.
732     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
733      and cpl_aim+ocn
734    o pkg/kpp
735     - move computation of surface related input fields to KPP into a new
736       subroutine kpp_forcing_surf.F
737     - remove wrong (within bi,bj loops) EXCH calls.
738     - little cleaning (add argument myThid in last position, cvs header ...)
739     - for now, fix conservation problem by exchanging KPPviscAz (may not
740       be the best fix)
741    o pkg/seaice
742     - check for inconsistent evp parameter/cpp-flag combination
743     - remove leftover errIO flat for obsolete name list error handling
744    o OpenAD
745     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
746    
747    checkpoint59a
748    o pkg/seaice: some parameter clarifications and a little bit of clean up
749    o pkg/thsice: rename run-time parameters:
750       himin       -> hIceMin
751       himin0      -> hThinIce
752       hihig       -> hThickIce
753       i0          -> i0swFrac
754       transCoef   -> bMeltCoef
755       frac_energy -> fracMelting
756      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
757       with default values (for now) that do not change the results.
758      remove old version of thsice vars advection in pkg/seaice.
759    o in FFIELDS.h:
760      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
761      - make pLoad & sIceLoad always available (but still only used if
762         ATMOSPHERIC_LOADING is #define).
763    o pkg/kpp: replaced _KPP_RL with _RL
764    o bug fixes for vertical diffusivity computations when both KPP and
765        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
766        are no longer updating the vertical diffusivity array
767        (passed as argument) but are (re-) setting those arrays.
768    o pkg/seaice: fix bug in evp solver, while doing that
769      - change (improve?) discretization of stress computations for both
770        cgrid-lsr and evp solver
771      - add a new routine to compute strain rates
772      - the above changes lab_sea results
773      - add no slip conditions for evp solver (off by default), lsr-version
774        may follow
775      - fix exchange for shear at Z-points (does not change lab_sea)
776      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
777        (to force the user to pick a time step since there is not "safe" way
778        of choosing it)
779      - add principal stress diagnostics
780      - rearrange fields for evp a little to avoid having to call a: too many
781        exchanges and b: exchanges for stress trensor components which we do
782        not have.
783      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
784        of evp, complete rewrite for lsr case (latter is does not yet work
785        in all cases)
786    o pkg/kpp: add code to have mixing in shelf ice caverns
787      - add myThid to all kpp routines (long overdue)
788    
789    checkpoint59
790    o pkg/exf:
791      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
792        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
793      - move exf header files from lower_case.h to UPPER_CASE.h ;
794        add missing cvs Header & Name
795      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
796      - add namelist param. selectStressGridPosition, exf_monFreq
797      - retire many _CLIM routines, and remove data.exf_clim
798        + params moved to data.exf
799        + climsst, climsss now handled by exf_set_gen, i.e.
800          climss?period=0 refers to constant field,
801          climss?period=-12 to monthly forcing
802      - split up namelists in data.exf
803    o pkg/seaice:
804      - remove seaice_exch and seaice_exch_uv
805      - remove superfluous exchange of theta
806      - add myThid to seaice_budget_ocean/ice
807      - add new interface for atmospheric wind forcing (C-grid only)
808        + new routine
809        + two new field (taux, tauy for stress over ice)
810        + removed one global field (DAIRN) for C-grid case only
811    o pkg/thsise
812      - 2nd set of modifs for thsice adjoint in conjunction with exf
813    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
814    
815    checkpoint58y_post
816    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
817      vertical diffusivity, similar to that in MOM4; turned on using
818      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
819      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
820    o Added capability for 3D specification of background vertical diffusion
821      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
822      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
823      "data" file that contains the 3D vertical diffusivity coefficients.
824    o ice dynamics (pkg/seaice) with thsice thermodynamics:
825      - add code within pkg thsice to advect & diffuse sea-ice fields
826      similar to (and will replace) what has been added in  seaice_advdiff.F,
827      but: - conserving Mass, Heat & Salt.
828           - better when using non-linear advection scheme (not yet fully tested)
829           - can also be used in atmospheric set-up (for now, only the diffusion).
830    
831    checkpoint58x_post
832    o IO option for global-file compact format:
833      - add options when generating topology (utils/exch2/matlab-topology-generator)
834      - add I/O capability (pkg/mdsio).
835      - adapt utils/matlab/rdmds.m to read this format.
836      for now long-line format not yet supported by pkg/mdsio (& exch2).
837    o shelfice: add a few diagnostics
838    
839    checkpoint58w_post
840    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
841      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
842      (and replace horiVertRatio in NH code).
843      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
844                         and tutorial_plume_on_slope (sensitive to truncation)
845    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
846      directly to drive seaice model (C-grid only)
847    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
848     - reintroduce computation of wind from stress,
849     - compute tau (in exf_bulkformulae.F) from windstress averaged to
850       mass points to avoid tau = 0
851     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
852    o rdmnc.m: make it work with "global" files created with gluemnc
853    o rdmnc.m : some improvements in dealing with singleton dimension
854      (tested on all testreport mnc output files).
855    o genmake2: disable pkg/profiles if netcdf test fails.
856    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
857    o move call to cal_readparms up to make calendar parameters/variable available
858      to all packages
859    
860    checkpoint58v_post
861    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
862      useDynP_inEos_Zc tested.
863    o pkg/exf: changes to properly interpolate/mask/scale initial fields
864    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
865      and portions thereof.  See read_cs.txt for description and examples.
866    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
867      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
868      following the great-circle arc between those 2 points.
869    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
870      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
871    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
872     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
873     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
874     - still needs work (not working with some options ; efficiency to improve)
875       and serious testing.
876     - use this scheme for temperature & salinity in 2 advection test exp.:
877       advect_xy & advect_xz, respectively.
878    
879    checkpoint58u_post
880    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
881    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
882    o testreport: add option "-skipdir" to skip some test.
883    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
884      momentum calculation.
885    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
886    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
887      remove checkpoint.F and the_correction_step.F (no longer used);
888      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
889    o add option (linFSConserveTr) to correct for tracer source/sink due to
890      Linear Free surface
891    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
892    o pkg/thsice: fix reading mnc-pickups
893    
894    checkpoint58t_post
895    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
896    o pkg/mdsio:
897     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
898       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
899       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
900     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
901     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
902       either MDS_READ_FIELD or MDS_WRITE_FIELD )
903     - new S/R (to replace MDSWRITEMETA), which allows to write more
904       informations (variable names, time ...) to meta files.
905     - modify rdmds.m to give back the meta file content.
906    o pkg/diagnostics: change vertical interpolation to be safer, and more
907       flexible (define p-levels to interpolate to in data.diagnostics);
908      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
909       diagnostic pointer.
910    o pkg/seaice: more cleaning up of seaice_growth, added many comments
911    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
912    o fix multi-category seaice:
913     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
914       SEAICE_MULTICATEGORY
915     - fix short wave heat flux
916    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
917       and allow to use EVP solver. Change forward lab_sea: test both EVP
918       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
919    o Initial check-in of lab_sea adjoint
920      (very similar to natl_box_adjoint/code_seaice)
921      * used C-grid and EVP solver
922      * used KPP, GM/Redi
923      * uses inAdExact=.TRUE.
924      * gradient checks fail for both ADM and TLM
925        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
926        f.d. gradients actually seem more problematic than ADM, TLM gradients;
927        issue is related to forward mismatch between g77 an ifort
928    o pkg/seaice: overhaul of thermodynamics
929     - growth.F and groatb.F are replaced by new routine seaice_growth.F
930     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
931     - move a few global fields out of SEAICE.h into seaice_growth.F and
932       make them 2D (FICE/QNETO/ ...)
933     - remove FO (it is the same as QNETO)
934     - introduce a few local fields to avoid modifying external fields such
935       as atemp, etc.
936    
937    checkpoint58s_post
938    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
939      changed exf_set_gen.F so that
940        genperiod=0 means input file is one time-constant field and
941        genperiod=-12 means input file contains 12 monthly means
942    o CG2D: use pre-computed solver main-diagonal (stored in common block);
943      this affects truncation error ; generate new output file for exp. which
944      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
945        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
946        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
947        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
948        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
949        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
950    o start implementation of deep-atmosphere and anelastic formulation
951    o verification: remove 2nd copy of input files and use script "prepare_run"
952      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
953    o mom_common/vecinv/fluxform: fix a few initialisation isssues
954    o profiles: fix for multithreaded case
955    
956    o diagnostics: rename few diags:
957      s/'PRESSURE'/'RCENTER '/g
958      s/'TICE    '/'oceFreez'/g
959      s/'TAUX    '/'oceTAUX '/g
960      s/'TAUY    '/'oceTAUY '/g
961      s/'SWFLUX  '/'oceQsw  '/g
962      s/DIFx/DFxE/g
963      s/DIFy/DFyE/g
964      and add few ocean-forcing diagnostics:
965      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
966    o modifications to pkg/seaice/growth.F and budget.F, which change results of
967      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
968      as actual snow thickness.  It now refers everywhere to effective snow
969      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
970    
971    checkpoint58r_post
972    o modifications to pkg/seaice/growth.F, which change results of
973      lab_sea experiment: fixes pertain to melting snow over open water, to
974      masking EVAP under sea ice, and to using the correct AREA variable for
975      computations of EVAP, PRECIP, HSNOW, and GHEFF
976    o add ability to read bathy, salt, and theta using MNC (off by def)
977    o add flooding algorithm and advection of HSNOW for pkg/seaice;
978      both are turned off by default and do no change any results
979    o seaice advection with pkg/thsice: a step toward the use of non-linear
980      advection scheme, but #ifdef or commented out for now (requires more EXCH).
981    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
982      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
983      in natl_box (affects results @ truncation level: update output.txt)
984    o multi-threading and IO:
985      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
986      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
987        (needed to work with SingleCpuIO): tested in all verif. exp.
988    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
989      affects the results (but none of the verification test uses this scheme).
990    o Adding some pkg/diagnostics capability to pkg/seaice
991      (will certainly be subject to changes)
992    o ctrl: adding new control variables:
993      lwflux, lwdown, evap, snowprecip, apressure, runoff
994    
995    checkpoint58q_post
996    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
997      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
998      high_res_cube configuration by 4% on Columbia.
999    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
1000      add (in global_with_exf/code) a version of EXF_INTERP_READ without
1001      dynamical allocation (seems to work in multi-threaded).
1002    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
1003      single CPU io) so that TAF does not have to see EESUPPORT.h
1004  o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)  o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
1005    
1006  checkpoint58p_post  checkpoint58p_post
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