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revision 1.811 by mlosch, Wed May 9 14:32:05 2007 UTC revision 1.1027 by jmc, Tue Oct 7 20:59:20 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 gmredi(fm07):
8      - add lower limit on Transition layer thickness D + lower limit on D/lambda
9      - allow to set few more params from data.gmredi
10    o pkg ggl90:
11          - add missing sqrt(2) factor in computation of mixing length
12            scale in ggl90_calc.F
13            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
14    
15    checkpoint61d
16    o adjoint modifs
17      - adapt to new field rhoInSitu
18      - allow to revert from StoreDynVars2D, StoreDynVars3D
19        to individual fields
20        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
21    o store 3-D (in-situ) density in commom block (DYNVARS.h)
22     - save 1 rho computation.
23     - no longer modify T & S inland when using down_slope pkg.
24    o gad_som : allow to switch to SOM advection for T & S without corresponding
25      pickup files (using new S/R: MDS_CHECK4FILE).
26    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
27      (for useSingleCpuIO to work in multi-threaded)
28    o pkg/shelfice:
29     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
30       with SHELFICEtopoFile in data.shelfice
31     - move code for reading ice shelf topography and modifying hFacC into separate
32       subroutines of the shelfice package
33     - separate initialisation of "fixed" and "variable" variables
34     - kTopC is not (yet) replaced by kSurfC, although this is possible
35    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
36    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
37      and rename:
38      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
39      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
40    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
41    
42    checkpoint61c
43    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
44      to add mass source/sink of fluid in the interior (3-D generalisation
45      of oceanic real-fresh water flux).
46    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
47    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
48    o new pkg: down_slope
49      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
50      - presently, modify T & S inland (dwnslp_calc_rho.F).
51        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
52      - implementation for ocean in P-coords not tested.
53      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
54    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
55      (to facilitate conversion of oceanic pkg to p-coordinate).
56    o change FIND_RHO to FIND_RHO_2D :
57      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
58    o new pkg: cheapaml
59    
60    checkpoint61b
61    o exch2:
62      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
63      - no longer depend on the order sequence (N,S,E,W).
64      - 3rd exchange no longer needed (tested with 24 tiles).
65      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
66      - exch_UV_A-grid readily available (but not yet tested).
67      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
68      (both are no longer needed) in exch_uv: no effect in forward run; but
69       get truncation error differences with adjoint exch.
70    o exch2:
71     - change index-bounds storage (moved from target to local tile,
72       more intuitive this way) ; rename/remove some variables.
73     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
74    
75    checkpoint61a
76    o exch2/matlab-topology-generator:
77      fix bug in index bounds for N-S internal exchange (hard to tell if this
78      had any effect on the solution).
79    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
80      is exceeded
81    o testreport: modify syntax of awk, so that it works also with
82      awk, and not only with nawk and gawk
83    
84    checkpoint61
85    o autodiff
86      Change default for TAF usage by removing argument '-nonew_arg'
87      This changes TAF subroutine argument list (ordering of active var.)
88      Omission of this flag leads to incompatibility w.r.t. TAMC
89      To restore TAMC-compatibility, need following modifs:
90      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
91      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
92      Tested TAF version is 1.9.22
93      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
94    
95    checkpoint60
96    --->>> This is the last checkpoint for which generating the adjoint
97    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
98    --->>> by default.
99    --->>> Future checkpoints will ommit this flag by default.
100    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
101    o pkg/grdchk: Add gradient check to etan0 perturbations.
102    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
103    o pkg/autodiff: more flexibility in zeroadj.
104      model/src: modifying do_oceanic_phys.F accordingly.
105    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
106    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
107      special setup of gmredi for which the adjoint is stable
108      enough for parameter optimization.
109    o bridging the gap between eddy stress and GM.
110      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
111          along with a change in CPP option (now ALLOW_EDDYPSI).
112      -> when using GM w/ GM_AdvForm:
113          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
114          is applied either in the tracer Eq. or in momentum Eq.
115          depending on data.gmredi (intro. GM_InMomAsStress).
116      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
117      The key modifications are in model/src/taueddy_external_forcing.F
118      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
119    
120    checkpoint59r
121    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
122      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
123      fix option to read coriolis(@ cell-corner) from files with CS-grid.
124    o pkg/mnc: add some attributes to standard 1D-coordinate variables
125    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
126      mass points, when using mnc for output
127      - add runtime parameter (missing_value, missing_value_int) to override
128        default (which is the value of getcon('UNDEF'))
129    o pkg/mnc: prepare mnc for the actual use of missing values with the
130      diagnostics package: small fix in mnc_cw_readwrite.template and more
131      initialisation of never used fields
132      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
133      versions
134    o pkg/thsice/thsice_ini_vars.F added default initial values so that
135      thermodynamics sea ice solver does not blow up when some initial fields
136      are missing.
137    o move from external_forcing_surf.F to ini_forcing.F
138      the p-coord. hack consisting in using pLoad to set phi0surf ;
139      update output of tutorial_global_oce_in_p (affected @ truncation level).
140    o Freshen up a bit hs94.1x64x5, notably:
141      remove rotationPeriod and tRef=5*0. (adjoint only), and add
142      exactConserv=.TRUE.
143    o pkg/generic_advdiff:
144      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
145      applies to files where Temperature & Salinity 2nd Order moments are used.
146    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
147      this uses a dynamically allocated internal state data structure
148      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
149      and requires a fortran 90 compiler
150    
151    checkpoint59q
152    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
153       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
154    o Refresh tutorial_global_oce_biogeo, notably:
155      - change bathymetry (put back seamounts in ACC, use hFacs)
156      - change EOS (POLY3 --> JMD95Z)
157      - use Bryan-Lewis vertical diffusivity
158      - use multidimensional advection
159      - remove old virtual virtual in dic pkg, now done through ptracer pkg
160      - change a couple of parameters in dic pkg
161    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
162    o pkg/obcs: change default to OBCSfixTopo = .true.,
163      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
164      - replace "debugMode" with "debugLevel .GE. debLevB"
165    o implementation of TAF directives for gchem,cfc,dic
166    o remove "exp5" (replaced by tutorial_deep_convection).
167    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
168      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
169      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
170      --> changes results in exp4, seaice_obcs
171    o tutorial_deep_convection :
172      update the set-up and increase resolution and domain size ; start
173      from pseudo initial conditions = output at t=120mn in order to see
174      something happening when running testreport.
175    o pkg/seaice: add os7mp as an advection scheme
176                  add check for advection schemes
177                  add a flag for restoring T and S underneath sea ice
178    o pkg/my82: add netcdf-support and diagnostics
179    o thsice pkg:
180      - Now hsMax limits snow height by turning it into ice following
181        flooding scheme (and now conserving energy)
182      - Slight rewriting of the formula in thsice_calc_thick.F
183      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
184      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
185    
186    checkpoint59p
187    o gchem / dic / cfc :
188      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
189      - add new parameter files: "data.dic" & "data.cfc" ;
190      - various re-arrangement in initialisation & header file ;
191      - fix tutorial_global_oce_biogeo for multi-threaded test.
192    o pkg/dic: test for "pickup_dic" file when restarting ;
193      if no pickup-file, can restart with a re-initialised pH (same as it did
194      before) providing pickupStrictlyMatch is set to False.
195    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
196      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
197    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
198      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
199    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
200     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
201       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
202    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
203       scheme to use for vorticty-term ;
204     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
205       (with default selectVortScheme, return to original discretisation)
206     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
207    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
208    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
209      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
210      also fix diagnostics VISCAHW & VISCA4W.
211    
212    checkpoint59o
213    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
214    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
215      move a few statemens out the main loop into separate loops
216    o pkg/shelfice:
217      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
218        (kg/m^2/s), does not break tests, because in verification/isomip,
219        rhoConstFresh=rhoConst (by accident)
220      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
221      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
222        new file model/src/seawater.F, so that they are available for all pkgs.
223      - convert potential temperature into in-situ temperature. This changes the
224        isomip tests => update tests
225    o add a flag writePickupAtEnd (default=true) to be able to suppress
226      writing a pickup at the last timestep
227    o tools/mpack-1.6 :
228      - disable automake (not working) and autoconf (not needed).
229      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
230        also cleaner with much less compilation warnings.
231    o pkg/profiles:
232      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
233      (for "less than 32 characters name" compiler requirement)
234    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
235      conditions that have a different sampling frequency than S/T/U/V obcs
236    o pkg/diagnostics (stats-diags):
237      - fix global Min/Max in case 1 processor get only empty tiles
238    o genmake2: replace (4 times)
239         make genmake_tc_1.o >> genmake_warnings 2>&1
240      with
241         COMM="$CC $CFLAGS -c genmake_tc_1.c"
242         echo $COMM >> genmake_warnings
243         $COMM >> genmake_warnings 2>&1
244      to make genmake2 always see the value of CC as specified in the optfile.
245    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
246      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
247      - modify verification advect_cs test to test SOM-advection on CS-grid.
248    o pkg/ctrl:
249      - Rewrite of ctrl_map_ini_ecco.F,
250        introducing a generic routine (ctrl_map_ini_gen.F).
251      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
252    
253    checkpoint59n
254    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
255      number in dedicate array "hdiag":
256      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
257        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
258      - many small changes (integer format) for large number of diagnostics
259      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
260        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
261    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
262      usingSphericalGrid, this allows to define the rotated grid coordinates
263      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
264      geographical coordinates according to the inverse of the rotation defined
265      by the Euler angles, so that Coriolis parameter and online-interpolation by
266      exf works with the geographical coordinates on XC/YC/XG/YG.
267      Naturally, this feature does not work with all packages, so some
268      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
269      profiles), because there the coordinates are assumed to be regular
270      spherical grid coordinates.
271    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
272      - introduce isopycnal diffusion coefficient control.
273    o tools/adjoint_options:
274      - additional control vector components.
275    o pkg/mnc: have mnc create marginally meaning full coordinate variables
276      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
277    o pkg/mypackage:
278      - add example of read/write pickup for state-var ;
279      - add entry points to the main code for state-vars diags & write-pickup.
280    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
281      transitions for useExfYearlyFields
282      - add new subroutine that determines the file to read from for
283        use*YearlyFields = .TRUE. and .FALSE.
284      - add a verification experiment to global_with_exf that tests
285        useExfYearlyFields with USE_EXF_INTERPOLATION defined
286    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
287      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
288      subroutines (which could be generated from a template, because they are
289      almost identical), for now they are included in obcs_prescribe_read.F for
290      simplicity
291    o pkg/exf:
292      - add a little more diagnostic to exf_interp_read (in analogy to
293        mds_read_field, can be turned off with debugLevel < debugLevA=1)
294      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
295        ugly but fast by unrolling short inner loops, inserting a unroll=8
296        directive in routine lagran, and splitting a loop and making do while the
297        outermost loop (the latter requires the intoduction of index arrays)
298    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
299    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
300      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
301    o verification/seaice_obcs: updated for restart test and latest options
302    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
303      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
304      for now this is only available for the C-grid code and also within
305      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
306    
307    checkpoint59m
308    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
309      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
310    o gad_som : fix flux output (& diagnostics) to have same units as other  
311      advection scheme fluxes (was previously multiplied by deltaT).  
312    o added verification/seaice_obcs both to test seaice open boundaries
313      and to provide an example matlab scrpt for generating them
314    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
315    o pkg/salt_plume: clean up salt_plume_frac.F to
316      remove redundancy in PlumeMethod 1 and 4
317    o pkg/kpp: added saltplume diagnostics
318    o pkg/obcs and pkg/seaice:
319      - do not set uice and vice to zero when OB*icefile are unspecified
320      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
321      - moved seaice tracer obcs after call to seaice_growth
322    o pkg/salt_plume: added various options for salt plume depth
323      criterion and for vertical distribution of the salt
324    
325    checkpoint59l
326    o pkg/ptracers: new version of ptracers pickup:
327      read meta file and write only fields which are needed to restart.
328      ( same logic as main pickup file ; also using pickupStrictlyMatch )
329    o pkg/seaice:
330      - add timescale for melting due to warm mixed layer as a means of
331        setting SEAICE_availHeatFrac more conveniently
332      - add a CPP-flag/runtime parameter check for flooding algorithm
333      - reformulated availHeat in seaice_growth.F to be independent of AREA
334    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
335      unit changes
336    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
337    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
338      SX vector computer.
339    o pkg/seaice:
340      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
341        seaice forcing fields can now be read only through pkg/exf
342      - removed some unused halos
343    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
344    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
345      or U/VICE from U/VWIND before computing U/VSTRESS
346    
347    checkpoint59k
348    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
349      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
350    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
351      all experiments pass when compile with un-initialised var. checking option.
352    o added pkg/salt_plume
353    o script to test restart (for now, in MITgcm_contrib/jmc_script)
354    o pkg/seaice: new read/write pickup version.
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: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
358    o lab_sea.hb87: modify the domain & update output.hb87.txt :
359      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
360      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
361      process. Fixed here by closing the domain at the Northern boundary.
362    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
363    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
364      a set of consecutive levels in/from a 3-D array.
365    o pkg/ptracers:
366      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
367      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
368    
369    checkpoint59j
370    o in pkgs: dic, obcs, offline, rbcs:
371      standard way to compute coeff. for time interpolation between 2 time reccords
372      which retains full precision (& make results less dependent on compiler).
373      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
374    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
375      packages instead of reading ice cover and wind speed separately
376    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
377     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
378      to allow to compile customized code before the update)
379    o cleaning-up:
380      - fix CPP instruction syntax in pkg/obcs
381      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
382        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
383      - fix some threads issue in IO parts.
384    o pkg/dic:
385      - add tons of "_d 0" (--> much better testreports !)
386       and then update outputs of tutorial_global_oce_biogeo
387    o pkg/mom_fluxform:
388      add a special version of momentum advection intended to conserve momentum
389      next to a bathymetry step or a coastline edge. (default = off = #undef)
390    o new read/write pickup version:
391      - for now, only implemented for main (mdsio) pickup file.
392      - write out only what is needed to restart; merge pickup_nh , pickup_ph
393        and main pickup together.
394      - read meta file; read only what is needed to restart; stop if a field
395        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
396        if it make sense (even if the restart is not perfect).
397      - if no meta file, assume that pickup to read corresponds exactly to
398        a pickup that would currently be written.
399      - read pickup written in the old format (until checkpoint59i) if it
400        recognizes an old meta file (no field-list).
401      - add a meta file in exp. which starts from a pickup: 2 cases:
402        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
403         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
404        b) a meta file describing the content of the associated pickup file
405         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
406    o pkg/mdsio & pkg/rw:
407      - new routine to read a meta file ; new set of routine to read
408        Multiple-fields file (with meta file).
409    o added open boundary conditions capability for seaice
410        HSNOW, HSALT, UICE, and VICE
411    
412    checkpoint59i
413    o adjoint:
414      * fix multiDimAdvection adjoint
415        (partial recomputation problem by TAF for fVerT(:,:,kDown)
416        and comlev1 size definition (maxpass vs. max. number of tracers)
417      * verification/global_ocean.90x45x15 adjoint now tests
418        NLFS and multiDimAdvection using DST3 (=30)
419      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
420    o pkg/kpp: add "_d 0" to real constant (if missing);
421      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
422      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
423    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
424      for internal parameters related to restart process (formerly from PARAMS.h)
425      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
426    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
427      as argument. (only atm2d & obcs write_pickup have not yet been updated)
428    o pkg/monitor:
429      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
430      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
431      - account for deep Atmosphere factor and density factor (anelastic)
432    o added open boundary conditions capability for seaice HEFF and AREA
433    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
434      thermodynamics
435      - requires a little reorganization, which affects the testreport results
436        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
437        so that now the conservative form is tested
438      - add a few comments
439    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
440    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
441    o add new diagnostics to seaice: advective, diffusive fluxes (only for
442      multidim-advection, for scheme 2 they are not filled) and transports,
443      thermodynamic growth rates
444    o change units of EmPmR (inside the code, + within coupling interface)
445      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
446      Affects results @ truncation level (cg2d match) and update output of
447       experiments: lab_sea(6), global_ocean.90x40x15(10),
448      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
449      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
450      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
451      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
452    
453    checkpoint59h
454    o pkg/exf:
455      - improve vectorization by moving if-statement out of loops in
456        exf_mapfields, exf_radiation
457      - exf_bulkformulae.F: introduce 2D fields and vectorize code
458    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
459    o testreport:
460      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
461        monitor & update offline_exf_seaice exp. output.
462      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
463    o pkg/seaice:
464      - bug fix in the evp solver: boundary conditions were affected be
465        masking of zMax/zMin (changes results)
466      - minor bug fix in boundary conditions in seaice_calc_strainrates
467        (changes results for no_slip)
468      - seaice_lsr.F: make interpolation of eta dependent on boundaries
469      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
470      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
471        stress formulation and no-slip boundary conditions
472    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
473      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
474    o pkg/seaice: a first HSALT time stepping equation has been checked in
475    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
476      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
477      without requiring DO-IF statements
478    o pkg/thsice:
479      use continuous power-law function for partition of energy between lateral
480      melting/freezing and thinning/thickening ; old code using step function
481      still available with #undef THSICE_FRACEN_POWERLAW
482      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
483    o testreport: change AD testing : check against results/output_adm.txt
484      using same scripts as for forward test.
485    
486    checkpoint59g
487    o adjoint testing: in preparation for changing testreport:
488      - output format: cost and grad written on separated lines
489      - ad output results in directory "results" (instead of "results_ad")
490    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
491    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
492    o pkg/ecco: allow user defined cost function contributions
493    o testreport:
494      Allow to choose (per experiment) the list of tested output variables
495       and the main variable (used to issue a pass/FAIL ) ;
496      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
497      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
498      Also modify printing of summary:
499       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
500       b) echo the list of tested variables in the individual summary.txt of
501          each experiment.
502    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
503      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
504      (but still depend on the tile decompostion of the domain).
505    o pkg/seaice: change a discretization detail to make the B-grid code
506      "more symmetric". This change is likely to remove all "ridges/leads" that
507      where quasi-aligned with the grid in B-grid solutions. It may also be
508      the solution to the stress coupling issues with the B-grid.
509    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
510      remove .cvsignore from input dir. (since testreport no longer run here).
511    o pkg/thsice:
512     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
513     - fix reshaping of sea-ice just after advection:
514       melt all the ice only if ice-volume is too small.
515     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
516       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
517     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
518    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
519      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
520    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
521      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
522      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
523      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
524      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
525      -> update output.txt
526    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
527     this affects truncation error: -> update output.txt of exp:
528      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
529      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
530    
531    checkpoint59f
532    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
533    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
534      a bounded range (in forward mode)
535    o pkg/ecco, ctrl, autodiff and mom_common:
536     internal parameter controls, completements of implementations
537    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
538    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
539      (not seem any difference in testing results).
540    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
541       at face corners.
542    o pkg/generic_advdiff:
543     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
544      loop range indices for computing vertical advection tendency
545      and do the calculation in the interior only (no overlap) ;
546      for now, only implemented for SOM advection (to save CPU time).
547     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
548    o exch2 adjoint
549      First set of changes:
550      - add exch2 hand-written adjoint templates
551      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
552        This will require cleanup in pkg/autodiff/*.F
553        (changed routines currently kept separate in verif. code/)
554      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
555        that used to hide exch2 or cubed-sphere specific code
556        (commented via 'cph-exch2')
557    o pkg/seaice
558      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
559    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
560       output of global_ocean.cs32x15.thsice .
561    
562    checkpoint59e
563    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
564      for B-grid vector (not yet tested) and C-grid vector (<- only used
565      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
566    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
567      (#ifdef ALLOW_SALT_PLUME)
568    o gather_2d/scatter_2d: removed halo regions
569    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
570      scheme and the corresponding test case (under front_relax dir). For now,
571      only available with Skew-flux form and not yet tested in realistic set-up.
572      adjoint: store directives updated, but gradient checks deteriorated,
573      so maybe GM/Redi adjoint is now broken.
574    o seaice adjoint
575      * add AREA, HEFF, HSNOW as control variable
576        (should not change lab_sea results)
577      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
578    o pkg/seaice:
579      * added computation of saltFlux in seaice_growth;
580        For time being, sea ice salinity is assumed constant
581        contribution of snow flooding to freshening of sea ice is neglected.
582        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
583        defaults to 0.0 in order to maintain backward compatibility.
584        Typical values for SEAICE_salinity are 4 to 10 g/kg.
585      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
586      * added SEAICE_availHeatFrac, which specifies fraction of surface level
587        heat content used to melt or grow ice
588      * commented out cap of HICE: it helps keep ice thinner
589      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
590      * applied OBCS T/S mask to HEFFM sea ice mask
591    
592    checkpoint59d
593    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
594     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
595     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
596    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
597     and change default value of parameter "GM_Small_Number";
598     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
599       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
600       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
601    o pkg/ecco: cost function when applying pkg/smooth to controls
602    o pkg/ctrl: add forcingPrecond run time parameter
603    o pkg/seaice:
604     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
605     - fix bug in metric terms of u-equation in LSR solver (implicit part),
606       changes verification/lab_sea
607     - rearrange implicit part of u-equation in LSR solver to make it easier to
608       read, understand, and debug. This causes changes at the truncation level.
609     - fix (serious) bug in the boundary conditions (sign error in the implicit
610       part) of the LSR solver. Changes all LSR results.
611     - fixed problem with HSNOW initialization to avoid thick snow when AREA
612       is initilized with small values - does not change lab_sea results.
613     - added HsnowFile initialization capability
614    o pkg/smooth: addition to model/src and pkg/ctrl so allow
615     initialization of pkg/smooth and application to control vector
616    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
617    o dependencies: pkg/profiles requires pkg/cal
618    o pkg/profiles:
619     - added option ALLOW_PROFILES_GENERICGRID
620         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
621         that interpolation information (grid points and coefficients) is provided
622         within the netcdf input files.
623         -> sample matlab scripts can be found in MITgcm_contrib/gael
624         that allow you to prepare netcdf input files.
625     - also modified: cleaner include statements, cleaner error print statements,
626       cleaner stops when error, and more tests of the netcdf input files consistency.
627    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
628    o pkg/seaice:
629     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
630       requires a new routine: seaice_diagnostics_fill.F
631     - make sure that seaice does not move if not forced (pressure replacement
632       method, Hibler and Ip, 1995), changes results
633     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
634     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
635       It is turned off by default (=-1.), because it changes the results.
636     - make it possible to read AREA from a file, too.
637    
638    checkpoint59c
639    o add S/R and diagnostics for oceanic mixed-layer depth
640    o move GMRedi call after all vertical mixing schemes (including KPP)
641    o pkg/thsice:
642     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
643      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
644    o pkg/obcs:
645     - bug fix for balance code
646    o pkg/seaice:
647      - allow values of SEAICE_elasticParm > 1
648      - add new parameter SEAICE_evpTauRelax as an alternative
649        to SEAICE_elasticParm
650      - make lsr boundary conditions free slip (by default), changes result
651      - add code for no slip boundary conditions for lsr
652      - set minimum of zeta to zero (and not 4e8) (changes results)
653      - add a cap on AREA after advecting AREA if seaice_growth is not called
654    o change calculation of Visbeck K:
655      - no longer depend on tapering scheme; instead, compute slope (limited
656        by GM_maxSlope). this is equivalent to what was comuted before with
657        clipping or linear tappering.
658      - fix vertical averaging (wrong by 1/2 level)
659      - leave the old version (but will not be maintained) within
660        #ifdef OLD_VISBECK_CALC / #endif
661      - update output of exp. ideal_2D_oce
662    o change error catch in calc_r_star to improve vectorization
663    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
664      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
665    o adjoint:
666      Re-organized adjoint checkpointing according to Matt Mazloff
667      (but with modifs/completions/cleanups)
668      Storing is now bundled into large arrays to optimized I/O
669      (and second step in cleanup of the_main_loop)
670    
671    checkpoint59b
672    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
673      - export/import (between ocean & coupler) fields needed for ocean DIC.
674    o pkg/seaice:
675      - get rid of three more exchanges seaice_calc_viscosities (required
676        different loop boundaries in seaice_lsr and seaice_ocean_stress)
677      - bug fix in seaice_ocean_stress (update of lab_sea required)
678      - reduce loop boundaries to necessary minimum also in seaice_evp
679      - go back to the old way of computing deltaC/Z as the adjoint likes that
680        better
681    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
682      passive tracer to an Age Tracer) + update output.txt
683    o pkg/exf:
684      - implement A-grid / C-grid selection for wind-stress input files.
685      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
686      for now, in exf_bulk_largeyeager04.F only :
687      - change implementation for case where windspeed + 2. components wind-stress
688        are read-in. AND use rhoConstFresh to convert evap.
689    o pkg/seaice:
690      - use correct EXCH_UV for wind-forcing (on A-grid).
691      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
692        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
693    o pkg/exf:
694      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
695      EXF_INTERPOLATION:
696      - merge global_with_exf/code version of exf_interp_read.F
697        to the main code ;
698      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
699        reading the file ; Important: This options needs to be defined to recover
700        previous code.
701        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
702      - no longer loose real*8 precision along the way when using exf_iprec=64.
703  o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)  o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
704      - change discretisation of evp-solver in order to avoid another exchange
705        (changes lab_sea) and clean up a little
706      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
707        help the adjoint (this also changes the results slightly)
708      - add a few "_d 0" where they had been missing in seaice_evp.F
709      - cleaning up: remove unused seaice_calc_rhs.F
710  o pkg/exf: some cleaning-up:  o pkg/exf: some cleaning-up:
711    - change various "constants" into runtime parameters    - change various "constants" into runtime parameters
712    - cleaned-up Large&Yeager04 routine which should eventually    - cleaned-up Large&Yeager04 routine which should eventually
# Line 18  o pkg/exf: some cleaning-up: Line 720  o pkg/exf: some cleaning-up:
720  o pkg/thsice:  o pkg/thsice:
721   fix few little problems, in thsice_calc_thickn.F:   fix few little problems, in thsice_calc_thickn.F:
722    - growth vertically (and not laterally) if iceFrac == iceMaskMax    - growth vertically (and not laterally) if iceFrac == iceMaskMax
723    - melt laterally only if hIce < hThinIce (as the comments say)    - melt only laterally if hIce < hThinIce (as the comments say)
724    and in thsice_extend.F:    and in thsice_extend.F:
725    - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)    - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
726    - 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 34  o pkg/kpp Line 736  o pkg/kpp
736  o pkg/seaice  o pkg/seaice
737   - check for inconsistent evp parameter/cpp-flag combination   - check for inconsistent evp parameter/cpp-flag combination
738   - remove leftover errIO flat for obsolete name list error handling   - remove leftover errIO flat for obsolete name list error handling
739    o OpenAD
740     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
741    
742  checkpoint59a  checkpoint59a
743  o pkg/seaice: some parameter clarifications and a little bit of clean up  o pkg/seaice: some parameter clarifications and a little bit of clean up
# Line 53  o in FFIELDS.h: Line 757  o in FFIELDS.h:
757       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
758  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
759  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
760      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
761        are no longer updating the vertical diffusivity array
762        (passed as argument) but are (re-) setting those arrays.
763  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
764    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
765      cgrid-lsr and evp solver      cgrid-lsr and evp solver
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