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revision 1.826 by mlosch, Fri Jun 1 12:57:48 2007 UTC revision 1.1034 by mlosch, Sat Oct 25 20:49:22 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 fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
8      (#undef REAL4_IS_SLOW)
9     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
10       coordinate variable
11     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
12       (surface forcing fields), removes some of the functionality
13     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
14     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
15       probably not all: copy _RS surface flux fields to RL field before
16       calling DIAGNOSTICS_FILL
17    
18    checkpoint61e
19    o gmredi (Visbeck-variable-K):
20      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
21      - change computation of Visbeck-K where Slope > Smax :        
22        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
23        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
24    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
25      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
26    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
27    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
28      does not become too large (to avoid precision problems in implicit-diffusion
29      solver); update ideal_2D_oce output.
30    o pkg ggl90:
31      - in ggl90_cal.F: compute only one set of visc/diff, used to
32        step forward TKE/T/S/momentum
33      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
34        have Prandlt =1)
35    o gmredi (fm07):
36      - add lower limit on Transition layer thickness + lower limit on 1/lambda
37      - allow to set few more params from data.gmredi
38    o pkg ggl90:
39          - add missing sqrt(2) factor in computation of mixing length
40            scale in ggl90_calc.F
41            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
42    
43    checkpoint61d
44    o adjoint modifs
45      - adapt to new field rhoInSitu
46      - allow to revert from StoreDynVars2D, StoreDynVars3D
47        to individual fields
48        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
49    o store 3-D (in-situ) density in commom block (DYNVARS.h)
50     - save 1 rho computation.
51     - no longer modify T & S inland when using down_slope pkg.
52    o gad_som : allow to switch to SOM advection for T & S without corresponding
53      pickup files (using new S/R: MDS_CHECK4FILE).
54    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
55      (for useSingleCpuIO to work in multi-threaded)
56    o pkg/shelfice:
57     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
58       with SHELFICEtopoFile in data.shelfice
59     - move code for reading ice shelf topography and modifying hFacC into separate
60       subroutines of the shelfice package
61     - separate initialisation of "fixed" and "variable" variables
62     - kTopC is not (yet) replaced by kSurfC, although this is possible
63    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
64    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
65      and rename:
66      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
67      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
68    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
69    
70    checkpoint61c
71    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
72      to add mass source/sink of fluid in the interior (3-D generalisation
73      of oceanic real-fresh water flux).
74    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
75    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
76    o new pkg: down_slope
77      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
78      - presently, modify T & S inland (dwnslp_calc_rho.F).
79        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
80      - implementation for ocean in P-coords not tested.
81      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
82    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
83      (to facilitate conversion of oceanic pkg to p-coordinate).
84    o change FIND_RHO to FIND_RHO_2D :
85      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
86    o new pkg: cheapaml
87    
88    checkpoint61b
89    o exch2:
90      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
91      - no longer depend on the order sequence (N,S,E,W).
92      - 3rd exchange no longer needed (tested with 24 tiles).
93      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
94      - exch_UV_A-grid readily available (but not yet tested).
95      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
96      (both are no longer needed) in exch_uv: no effect in forward run; but
97       get truncation error differences with adjoint exch.
98    o exch2:
99     - change index-bounds storage (moved from target to local tile,
100       more intuitive this way) ; rename/remove some variables.
101     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
102    
103    checkpoint61a
104    o exch2/matlab-topology-generator:
105      fix bug in index bounds for N-S internal exchange (hard to tell if this
106      had any effect on the solution).
107    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
108      is exceeded
109    o testreport: modify syntax of awk, so that it works also with
110      awk, and not only with nawk and gawk
111    
112    checkpoint61
113    o autodiff
114      Change default for TAF usage by removing argument '-nonew_arg'
115      This changes TAF subroutine argument list (ordering of active var.)
116      Omission of this flag leads to incompatibility w.r.t. TAMC
117      To restore TAMC-compatibility, need following modifs:
118      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
119      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
120      Tested TAF version is 1.9.22
121      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
122    
123    checkpoint60
124    --->>> This is the last checkpoint for which generating the adjoint
125    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
126    --->>> by default.
127    --->>> Future checkpoints will ommit this flag by default.
128    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
129    o pkg/grdchk: Add gradient check to etan0 perturbations.
130    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
131    o pkg/autodiff: more flexibility in zeroadj.
132      model/src: modifying do_oceanic_phys.F accordingly.
133    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
134    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
135      special setup of gmredi for which the adjoint is stable
136      enough for parameter optimization.
137    o bridging the gap between eddy stress and GM.
138      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
139          along with a change in CPP option (now ALLOW_EDDYPSI).
140      -> when using GM w/ GM_AdvForm:
141          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
142          is applied either in the tracer Eq. or in momentum Eq.
143          depending on data.gmredi (intro. GM_InMomAsStress).
144      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
145      The key modifications are in model/src/taueddy_external_forcing.F
146      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
147    
148    checkpoint59r
149    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
150      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
151      fix option to read coriolis(@ cell-corner) from files with CS-grid.
152    o pkg/mnc: add some attributes to standard 1D-coordinate variables
153    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
154      mass points, when using mnc for output
155      - add runtime parameter (missing_value, missing_value_int) to override
156        default (which is the value of getcon('UNDEF'))
157    o pkg/mnc: prepare mnc for the actual use of missing values with the
158      diagnostics package: small fix in mnc_cw_readwrite.template and more
159      initialisation of never used fields
160      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
161      versions
162    o pkg/thsice/thsice_ini_vars.F added default initial values so that
163      thermodynamics sea ice solver does not blow up when some initial fields
164      are missing.
165    o move from external_forcing_surf.F to ini_forcing.F
166      the p-coord. hack consisting in using pLoad to set phi0surf ;
167      update output of tutorial_global_oce_in_p (affected @ truncation level).
168    o Freshen up a bit hs94.1x64x5, notably:
169      remove rotationPeriod and tRef=5*0. (adjoint only), and add
170      exactConserv=.TRUE.
171    o pkg/generic_advdiff:
172      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
173      applies to files where Temperature & Salinity 2nd Order moments are used.
174    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
175      this uses a dynamically allocated internal state data structure
176      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
177      and requires a fortran 90 compiler
178    
179    checkpoint59q
180    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
181       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
182    o Refresh tutorial_global_oce_biogeo, notably:
183      - change bathymetry (put back seamounts in ACC, use hFacs)
184      - change EOS (POLY3 --> JMD95Z)
185      - use Bryan-Lewis vertical diffusivity
186      - use multidimensional advection
187      - remove old virtual virtual in dic pkg, now done through ptracer pkg
188      - change a couple of parameters in dic pkg
189    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
190    o pkg/obcs: change default to OBCSfixTopo = .true.,
191      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
192      - replace "debugMode" with "debugLevel .GE. debLevB"
193    o implementation of TAF directives for gchem,cfc,dic
194    o remove "exp5" (replaced by tutorial_deep_convection).
195    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
196      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
197      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
198      --> changes results in exp4, seaice_obcs
199    o tutorial_deep_convection :
200      update the set-up and increase resolution and domain size ; start
201      from pseudo initial conditions = output at t=120mn in order to see
202      something happening when running testreport.
203    o pkg/seaice: add os7mp as an advection scheme
204                  add check for advection schemes
205                  add a flag for restoring T and S underneath sea ice
206    o pkg/my82: add netcdf-support and diagnostics
207    o thsice pkg:
208      - Now hsMax limits snow height by turning it into ice following
209        flooding scheme (and now conserving energy)
210      - Slight rewriting of the formula in thsice_calc_thick.F
211      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
212      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
213    
214    checkpoint59p
215    o gchem / dic / cfc :
216      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
217      - add new parameter files: "data.dic" & "data.cfc" ;
218      - various re-arrangement in initialisation & header file ;
219      - fix tutorial_global_oce_biogeo for multi-threaded test.
220    o pkg/dic: test for "pickup_dic" file when restarting ;
221      if no pickup-file, can restart with a re-initialised pH (same as it did
222      before) providing pickupStrictlyMatch is set to False.
223    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
224      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
225    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
226      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
227    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
228     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
229       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
230    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
231       scheme to use for vorticty-term ;
232     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
233       (with default selectVortScheme, return to original discretisation)
234     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
235    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
236    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
237      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
238      also fix diagnostics VISCAHW & VISCA4W.
239    
240    checkpoint59o
241    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
242    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
243      move a few statemens out the main loop into separate loops
244    o pkg/shelfice:
245      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
246        (kg/m^2/s), does not break tests, because in verification/isomip,
247        rhoConstFresh=rhoConst (by accident)
248      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
249      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
250        new file model/src/seawater.F, so that they are available for all pkgs.
251      - convert potential temperature into in-situ temperature. This changes the
252        isomip tests => update tests
253    o add a flag writePickupAtEnd (default=true) to be able to suppress
254      writing a pickup at the last timestep
255    o tools/mpack-1.6 :
256      - disable automake (not working) and autoconf (not needed).
257      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
258        also cleaner with much less compilation warnings.
259    o pkg/profiles:
260      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
261      (for "less than 32 characters name" compiler requirement)
262    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
263      conditions that have a different sampling frequency than S/T/U/V obcs
264    o pkg/diagnostics (stats-diags):
265      - fix global Min/Max in case 1 processor get only empty tiles
266    o genmake2: replace (4 times)
267         make genmake_tc_1.o >> genmake_warnings 2>&1
268      with
269         COMM="$CC $CFLAGS -c genmake_tc_1.c"
270         echo $COMM >> genmake_warnings
271         $COMM >> genmake_warnings 2>&1
272      to make genmake2 always see the value of CC as specified in the optfile.
273    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
274      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
275      - modify verification advect_cs test to test SOM-advection on CS-grid.
276    o pkg/ctrl:
277      - Rewrite of ctrl_map_ini_ecco.F,
278        introducing a generic routine (ctrl_map_ini_gen.F).
279      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
280    
281    checkpoint59n
282    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
283      number in dedicate array "hdiag":
284      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
285        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
286      - many small changes (integer format) for large number of diagnostics
287      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
288        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
289    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
290      usingSphericalGrid, this allows to define the rotated grid coordinates
291      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
292      geographical coordinates according to the inverse of the rotation defined
293      by the Euler angles, so that Coriolis parameter and online-interpolation by
294      exf works with the geographical coordinates on XC/YC/XG/YG.
295      Naturally, this feature does not work with all packages, so some
296      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
297      profiles), because there the coordinates are assumed to be regular
298      spherical grid coordinates.
299    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
300      - introduce isopycnal diffusion coefficient control.
301    o tools/adjoint_options:
302      - additional control vector components.
303    o pkg/mnc: have mnc create marginally meaning full coordinate variables
304      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
305    o pkg/mypackage:
306      - add example of read/write pickup for state-var ;
307      - add entry points to the main code for state-vars diags & write-pickup.
308    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
309      transitions for useExfYearlyFields
310      - add new subroutine that determines the file to read from for
311        use*YearlyFields = .TRUE. and .FALSE.
312      - add a verification experiment to global_with_exf that tests
313        useExfYearlyFields with USE_EXF_INTERPOLATION defined
314    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
315      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
316      subroutines (which could be generated from a template, because they are
317      almost identical), for now they are included in obcs_prescribe_read.F for
318      simplicity
319    o pkg/exf:
320      - add a little more diagnostic to exf_interp_read (in analogy to
321        mds_read_field, can be turned off with debugLevel < debugLevA=1)
322      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
323        ugly but fast by unrolling short inner loops, inserting a unroll=8
324        directive in routine lagran, and splitting a loop and making do while the
325        outermost loop (the latter requires the intoduction of index arrays)
326    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
327    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
328      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
329    o verification/seaice_obcs: updated for restart test and latest options
330    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
331      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
332      for now this is only available for the C-grid code and also within
333      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
334    
335    checkpoint59m
336    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
337      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
338    o gad_som : fix flux output (& diagnostics) to have same units as other  
339      advection scheme fluxes (was previously multiplied by deltaT).  
340    o added verification/seaice_obcs both to test seaice open boundaries
341      and to provide an example matlab scrpt for generating them
342    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
343    o pkg/salt_plume: clean up salt_plume_frac.F to
344      remove redundancy in PlumeMethod 1 and 4
345    o pkg/kpp: added saltplume diagnostics
346    o pkg/obcs and pkg/seaice:
347      - do not set uice and vice to zero when OB*icefile are unspecified
348      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
349      - moved seaice tracer obcs after call to seaice_growth
350    o pkg/salt_plume: added various options for salt plume depth
351      criterion and for vertical distribution of the salt
352    
353    checkpoint59l
354    o pkg/ptracers: new version of ptracers pickup:
355      read meta file and write only fields which are needed to restart.
356      ( same logic as main pickup file ; also using pickupStrictlyMatch )
357    o pkg/seaice:
358      - add timescale for melting due to warm mixed layer as a means of
359        setting SEAICE_availHeatFrac more conveniently
360      - add a CPP-flag/runtime parameter check for flooding algorithm
361      - reformulated availHeat in seaice_growth.F to be independent of AREA
362    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
363      unit changes
364    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
365    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
366      SX vector computer.
367    o pkg/seaice:
368      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
369        seaice forcing fields can now be read only through pkg/exf
370      - removed some unused halos
371    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
372    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
373      or U/VICE from U/VWIND before computing U/VSTRESS
374    
375    checkpoint59k
376    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
377      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
378    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
379      all experiments pass when compile with un-initialised var. checking option.
380    o added pkg/salt_plume
381    o script to test restart (for now, in MITgcm_contrib/jmc_script)
382    o pkg/seaice: new read/write pickup version.
383      read meta file and write only fields which are needed to restart.
384      ( same logic as main pickup file ; also using pickupStrictlyMatch )
385    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
386    o lab_sea.hb87: modify the domain & update output.hb87.txt :
387      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
388      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
389      process. Fixed here by closing the domain at the Northern boundary.
390    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
391    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
392      a set of consecutive levels in/from a 3-D array.
393    o pkg/ptracers:
394      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
395      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
396    
397    checkpoint59j
398    o in pkgs: dic, obcs, offline, rbcs:
399      standard way to compute coeff. for time interpolation between 2 time reccords
400      which retains full precision (& make results less dependent on compiler).
401      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
402    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
403      packages instead of reading ice cover and wind speed separately
404    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
405     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
406      to allow to compile customized code before the update)
407    o cleaning-up:
408      - fix CPP instruction syntax in pkg/obcs
409      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
410        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
411      - fix some threads issue in IO parts.
412    o pkg/dic:
413      - add tons of "_d 0" (--> much better testreports !)
414       and then update outputs of tutorial_global_oce_biogeo
415    o pkg/mom_fluxform:
416      add a special version of momentum advection intended to conserve momentum
417      next to a bathymetry step or a coastline edge. (default = off = #undef)
418    o new read/write pickup version:
419      - for now, only implemented for main (mdsio) pickup file.
420      - write out only what is needed to restart; merge pickup_nh , pickup_ph
421        and main pickup together.
422      - read meta file; read only what is needed to restart; stop if a field
423        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
424        if it make sense (even if the restart is not perfect).
425      - if no meta file, assume that pickup to read corresponds exactly to
426        a pickup that would currently be written.
427      - read pickup written in the old format (until checkpoint59i) if it
428        recognizes an old meta file (no field-list).
429      - add a meta file in exp. which starts from a pickup: 2 cases:
430        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
431         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
432        b) a meta file describing the content of the associated pickup file
433         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
434    o pkg/mdsio & pkg/rw:
435      - new routine to read a meta file ; new set of routine to read
436        Multiple-fields file (with meta file).
437    o added open boundary conditions capability for seaice
438        HSNOW, HSALT, UICE, and VICE
439    
440    checkpoint59i
441    o adjoint:
442      * fix multiDimAdvection adjoint
443        (partial recomputation problem by TAF for fVerT(:,:,kDown)
444        and comlev1 size definition (maxpass vs. max. number of tracers)
445      * verification/global_ocean.90x45x15 adjoint now tests
446        NLFS and multiDimAdvection using DST3 (=30)
447      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
448    o pkg/kpp: add "_d 0" to real constant (if missing);
449      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
450      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
451    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
452      for internal parameters related to restart process (formerly from PARAMS.h)
453      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
454    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
455      as argument. (only atm2d & obcs write_pickup have not yet been updated)
456    o pkg/monitor:
457      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
458      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
459      - account for deep Atmosphere factor and density factor (anelastic)
460    o added open boundary conditions capability for seaice HEFF and AREA
461    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
462      thermodynamics
463      - requires a little reorganization, which affects the testreport results
464        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
465        so that now the conservative form is tested
466      - add a few comments
467    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
468    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
469    o add new diagnostics to seaice: advective, diffusive fluxes (only for
470      multidim-advection, for scheme 2 they are not filled) and transports,
471      thermodynamic growth rates
472    o change units of EmPmR (inside the code, + within coupling interface)
473      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
474      Affects results @ truncation level (cg2d match) and update output of
475       experiments: lab_sea(6), global_ocean.90x40x15(10),
476      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
477      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
478      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
479      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
480    
481    checkpoint59h
482    o pkg/exf:
483      - improve vectorization by moving if-statement out of loops in
484        exf_mapfields, exf_radiation
485      - exf_bulkformulae.F: introduce 2D fields and vectorize code
486    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
487    o testreport:
488      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
489        monitor & update offline_exf_seaice exp. output.
490      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
491    o pkg/seaice:
492      - bug fix in the evp solver: boundary conditions were affected be
493        masking of zMax/zMin (changes results)
494      - minor bug fix in boundary conditions in seaice_calc_strainrates
495        (changes results for no_slip)
496      - seaice_lsr.F: make interpolation of eta dependent on boundaries
497      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
498      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
499        stress formulation and no-slip boundary conditions
500    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
501      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
502    o pkg/seaice: a first HSALT time stepping equation has been checked in
503    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
504      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
505      without requiring DO-IF statements
506    o pkg/thsice:
507      use continuous power-law function for partition of energy between lateral
508      melting/freezing and thinning/thickening ; old code using step function
509      still available with #undef THSICE_FRACEN_POWERLAW
510      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
511    o testreport: change AD testing : check against results/output_adm.txt
512      using same scripts as for forward test.
513    
514    checkpoint59g
515    o adjoint testing: in preparation for changing testreport:
516      - output format: cost and grad written on separated lines
517      - ad output results in directory "results" (instead of "results_ad")
518    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
519    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
520    o pkg/ecco: allow user defined cost function contributions
521    o testreport:
522      Allow to choose (per experiment) the list of tested output variables
523       and the main variable (used to issue a pass/FAIL ) ;
524      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
525      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
526      Also modify printing of summary:
527       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
528       b) echo the list of tested variables in the individual summary.txt of
529          each experiment.
530    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
531      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
532      (but still depend on the tile decompostion of the domain).
533    o pkg/seaice: change a discretization detail to make the B-grid code
534      "more symmetric". This change is likely to remove all "ridges/leads" that
535      where quasi-aligned with the grid in B-grid solutions. It may also be
536      the solution to the stress coupling issues with the B-grid.
537    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
538      remove .cvsignore from input dir. (since testreport no longer run here).
539    o pkg/thsice:
540     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
541     - fix reshaping of sea-ice just after advection:
542       melt all the ice only if ice-volume is too small.
543     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
544       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
545     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
546    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
547      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
548    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
549      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
550      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
551      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
552      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
553      -> update output.txt
554    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
555     this affects truncation error: -> update output.txt of exp:
556      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
557      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
558    
559    checkpoint59f
560    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
561    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
562      a bounded range (in forward mode)
563    o pkg/ecco, ctrl, autodiff and mom_common:
564     internal parameter controls, completements of implementations
565    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
566    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
567      (not seem any difference in testing results).
568    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
569       at face corners.
570    o pkg/generic_advdiff:
571     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
572      loop range indices for computing vertical advection tendency
573      and do the calculation in the interior only (no overlap) ;
574      for now, only implemented for SOM advection (to save CPU time).
575     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
576    o exch2 adjoint
577      First set of changes:
578      - add exch2 hand-written adjoint templates
579      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
580        This will require cleanup in pkg/autodiff/*.F
581        (changed routines currently kept separate in verif. code/)
582      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
583        that used to hide exch2 or cubed-sphere specific code
584        (commented via 'cph-exch2')
585    o pkg/seaice
586      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
587    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
588       output of global_ocean.cs32x15.thsice .
589    
590    checkpoint59e
591    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
592      for B-grid vector (not yet tested) and C-grid vector (<- only used
593      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
594    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
595      (#ifdef ALLOW_SALT_PLUME)
596    o gather_2d/scatter_2d: removed halo regions
597    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
598      scheme and the corresponding test case (under front_relax dir). For now,
599      only available with Skew-flux form and not yet tested in realistic set-up.
600      adjoint: store directives updated, but gradient checks deteriorated,
601      so maybe GM/Redi adjoint is now broken.
602    o seaice adjoint
603      * add AREA, HEFF, HSNOW as control variable
604        (should not change lab_sea results)
605      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
606    o pkg/seaice:
607      * added computation of saltFlux in seaice_growth;
608        For time being, sea ice salinity is assumed constant
609        contribution of snow flooding to freshening of sea ice is neglected.
610        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
611        defaults to 0.0 in order to maintain backward compatibility.
612        Typical values for SEAICE_salinity are 4 to 10 g/kg.
613      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
614      * added SEAICE_availHeatFrac, which specifies fraction of surface level
615        heat content used to melt or grow ice
616      * commented out cap of HICE: it helps keep ice thinner
617      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
618      * applied OBCS T/S mask to HEFFM sea ice mask
619    
620    checkpoint59d
621    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
622     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
623     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
624    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
625     and change default value of parameter "GM_Small_Number";
626     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
627       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
628       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
629    o pkg/ecco: cost function when applying pkg/smooth to controls
630    o pkg/ctrl: add forcingPrecond run time parameter
631    o pkg/seaice:
632     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
633     - fix bug in metric terms of u-equation in LSR solver (implicit part),
634       changes verification/lab_sea
635     - rearrange implicit part of u-equation in LSR solver to make it easier to
636       read, understand, and debug. This causes changes at the truncation level.
637     - fix (serious) bug in the boundary conditions (sign error in the implicit
638       part) of the LSR solver. Changes all LSR results.
639     - fixed problem with HSNOW initialization to avoid thick snow when AREA
640       is initilized with small values - does not change lab_sea results.
641     - added HsnowFile initialization capability
642    o pkg/smooth: addition to model/src and pkg/ctrl so allow
643     initialization of pkg/smooth and application to control vector
644    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
645    o dependencies: pkg/profiles requires pkg/cal
646    o pkg/profiles:
647     - added option ALLOW_PROFILES_GENERICGRID
648         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
649         that interpolation information (grid points and coefficients) is provided
650         within the netcdf input files.
651         -> sample matlab scripts can be found in MITgcm_contrib/gael
652         that allow you to prepare netcdf input files.
653     - also modified: cleaner include statements, cleaner error print statements,
654       cleaner stops when error, and more tests of the netcdf input files consistency.
655    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
656    o pkg/seaice:
657     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
658       requires a new routine: seaice_diagnostics_fill.F
659     - make sure that seaice does not move if not forced (pressure replacement
660       method, Hibler and Ip, 1995), changes results
661     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
662     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
663       It is turned off by default (=-1.), because it changes the results.
664     - make it possible to read AREA from a file, too.
665    
666    checkpoint59c
667    o add S/R and diagnostics for oceanic mixed-layer depth
668    o move GMRedi call after all vertical mixing schemes (including KPP)
669    o pkg/thsice:
670     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
671      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
672  o pkg/obcs:  o pkg/obcs:
673   - bug fix for balance code   - bug fix for balance code
674  o pkg/seaice:  o pkg/seaice:
# Line 18  o change calculation of Visbeck K: Line 683  o change calculation of Visbeck K:
683    - no longer depend on tapering scheme; instead, compute slope (limited    - no longer depend on tapering scheme; instead, compute slope (limited
684      by GM_maxSlope). this is equivalent to what was comuted before with      by GM_maxSlope). this is equivalent to what was comuted before with
685      clipping or linear tappering.      clipping or linear tappering.
686    - fix vertical averaging (wrong by 1 level)    - fix vertical averaging (wrong by 1/2 level)
687    - leave the old version (but will not be maintained) within    - leave the old version (but will not be maintained) within
688      #ifdef OLD_VISBECK_CALC / #endif      #ifdef OLD_VISBECK_CALC / #endif
689      - update output of exp. ideal_2D_oce
690  o change error catch in calc_r_star to improve vectorization  o change error catch in calc_r_star to improve vectorization
691  o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and  o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
692    add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).    add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
693    o adjoint:
694      Re-organized adjoint checkpointing according to Matt Mazloff
695      (but with modifs/completions/cleanups)
696      Storing is now bundled into large arrays to optimized I/O
697      (and second step in cleanup of the_main_loop)
698    
699  checkpoint59b  checkpoint59b
700  o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):  o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
# Line 77  o pkg/exf: some cleaning-up: Line 748  o pkg/exf: some cleaning-up:
748  o pkg/thsice:  o pkg/thsice:
749   fix few little problems, in thsice_calc_thickn.F:   fix few little problems, in thsice_calc_thickn.F:
750    - growth vertically (and not laterally) if iceFrac == iceMaskMax    - growth vertically (and not laterally) if iceFrac == iceMaskMax
751    - melt laterally only if hIce < hThinIce (as the comments say)    - melt only laterally if hIce < hThinIce (as the comments say)
752    and in thsice_extend.F:    and in thsice_extend.F:
753    - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)    - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
754    - start to form ice as soon as the minimum ice-volume is reachable.    - start to form ice as soon as the minimum ice-volume is reachable.
# Line 114  o in FFIELDS.h: Line 785  o in FFIELDS.h:
785       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
786  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
787  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
788      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
789        are no longer updating the vertical diffusivity array
790        (passed as argument) but are (re-) setting those arrays.
791  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
792    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
793      cgrid-lsr and evp solver      cgrid-lsr and evp solver
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