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revision 1.801 by jmc, Fri Apr 27 16:33:53 2007 UTC revision 1.1023 by jmc, Tue Sep 16 21:24:26 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 gad_som : allow to switch to SOM advection for T & S without corresponding
8      pickup files (using new S/R: MDS_CHECK4FILE).
9    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
10      (for useSingleCpuIO to work in multi-threaded)
11    o pkg/shelfice:
12     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
13       with SHELFICEtopoFile in data.shelfice
14     - move code for reading ice shelf topography and modifying hFacC into separate
15       subroutines of the shelfice package
16     - separate initialisation of "fixed" and "variable" variables
17     - kTopC is not (yet) replaced by kSurfC, although this is possible
18    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
19    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
20      and rename:
21      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
22      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
23    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
24    
25    checkpoint61c
26    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
27      to add mass source/sink of fluid in the interior (3-D generalisation
28      of oceanic real-fresh water flux).
29    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
30    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
31    o new pkg: down_slope
32      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
33      - presently, modify T & S inland (dwnslp_calc_rho.F).
34        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
35      - implementation for ocean in P-coords not tested.
36      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
37    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
38      (to facilitate conversion of oceanic pkg to p-coordinate).
39    o change FIND_RHO to FIND_RHO_2D :
40      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
41    o new pkg: cheapaml
42    
43    checkpoint61b
44    o exch2:
45      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
46      - no longer depend on the order sequence (N,S,E,W).
47      - 3rd exchange no longer needed (tested with 24 tiles).
48      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
49      - exch_UV_A-grid readily available (but not yet tested).
50      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
51      (both are no longer needed) in exch_uv: no effect in forward run; but
52       get truncation error differences with adjoint exch.
53    o exch2:
54     - change index-bounds storage (moved from target to local tile,
55       more intuitive this way) ; rename/remove some variables.
56     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
57    
58    checkpoint61a
59    o exch2/matlab-topology-generator:
60      fix bug in index bounds for N-S internal exchange (hard to tell if this
61      had any effect on the solution).
62    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
63      is exceeded
64    o testreport: modify syntax of awk, so that it works also with
65      awk, and not only with nawk and gawk
66    
67    checkpoint61
68    o autodiff
69      Change default for TAF usage by removing argument '-nonew_arg'
70      This changes TAF subroutine argument list (ordering of active var.)
71      Omission of this flag leads to incompatibility w.r.t. TAMC
72      To restore TAMC-compatibility, need following modifs:
73      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
74      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
75      Tested TAF version is 1.9.22
76      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
77    
78    checkpoint60
79    --->>> This is the last checkpoint for which generating the adjoint
80    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
81    --->>> by default.
82    --->>> Future checkpoints will ommit this flag by default.
83    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
84    o pkg/grdchk: Add gradient check to etan0 perturbations.
85    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
86    o pkg/autodiff: more flexibility in zeroadj.
87      model/src: modifying do_oceanic_phys.F accordingly.
88    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
89    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
90      special setup of gmredi for which the adjoint is stable
91      enough for parameter optimization.
92    o bridging the gap between eddy stress and GM.
93      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
94          along with a change in CPP option (now ALLOW_EDDYPSI).
95      -> when using GM w/ GM_AdvForm:
96          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
97          is applied either in the tracer Eq. or in momentum Eq.
98          depending on data.gmredi (intro. GM_InMomAsStress).
99      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
100      The key modifications are in model/src/taueddy_external_forcing.F
101      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
102    
103    checkpoint59r
104    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
105      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
106      fix option to read coriolis(@ cell-corner) from files with CS-grid.
107    o pkg/mnc: add some attributes to standard 1D-coordinate variables
108    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
109      mass points, when using mnc for output
110      - add runtime parameter (missing_value, missing_value_int) to override
111        default (which is the value of getcon('UNDEF'))
112    o pkg/mnc: prepare mnc for the actual use of missing values with the
113      diagnostics package: small fix in mnc_cw_readwrite.template and more
114      initialisation of never used fields
115      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
116      versions
117    o pkg/thsice/thsice_ini_vars.F added default initial values so that
118      thermodynamics sea ice solver does not blow up when some initial fields
119      are missing.
120    o move from external_forcing_surf.F to ini_forcing.F
121      the p-coord. hack consisting in using pLoad to set phi0surf ;
122      update output of tutorial_global_oce_in_p (affected @ truncation level).
123    o Freshen up a bit hs94.1x64x5, notably:
124      remove rotationPeriod and tRef=5*0. (adjoint only), and add
125      exactConserv=.TRUE.
126    o pkg/generic_advdiff:
127      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
128      applies to files where Temperature & Salinity 2nd Order moments are used.
129    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
130      this uses a dynamically allocated internal state data structure
131      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
132      and requires a fortran 90 compiler
133    
134    checkpoint59q
135    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
136       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
137    o Refresh tutorial_global_oce_biogeo, notably:
138      - change bathymetry (put back seamounts in ACC, use hFacs)
139      - change EOS (POLY3 --> JMD95Z)
140      - use Bryan-Lewis vertical diffusivity
141      - use multidimensional advection
142      - remove old virtual virtual in dic pkg, now done through ptracer pkg
143      - change a couple of parameters in dic pkg
144    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
145    o pkg/obcs: change default to OBCSfixTopo = .true.,
146      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
147      - replace "debugMode" with "debugLevel .GE. debLevB"
148    o implementation of TAF directives for gchem,cfc,dic
149    o remove "exp5" (replaced by tutorial_deep_convection).
150    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
151      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
152      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
153      --> changes results in exp4, seaice_obcs
154    o tutorial_deep_convection :
155      update the set-up and increase resolution and domain size ; start
156      from pseudo initial conditions = output at t=120mn in order to see
157      something happening when running testreport.
158    o pkg/seaice: add os7mp as an advection scheme
159                  add check for advection schemes
160                  add a flag for restoring T and S underneath sea ice
161    o pkg/my82: add netcdf-support and diagnostics
162    o thsice pkg:
163      - Now hsMax limits snow height by turning it into ice following
164        flooding scheme (and now conserving energy)
165      - Slight rewriting of the formula in thsice_calc_thick.F
166      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
167      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
168    
169    checkpoint59p
170    o gchem / dic / cfc :
171      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
172      - add new parameter files: "data.dic" & "data.cfc" ;
173      - various re-arrangement in initialisation & header file ;
174      - fix tutorial_global_oce_biogeo for multi-threaded test.
175    o pkg/dic: test for "pickup_dic" file when restarting ;
176      if no pickup-file, can restart with a re-initialised pH (same as it did
177      before) providing pickupStrictlyMatch is set to False.
178    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
179      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
180    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
181      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
182    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
183     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
184       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
185    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
186       scheme to use for vorticty-term ;
187     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
188       (with default selectVortScheme, return to original discretisation)
189     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
190    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
191    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
192      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
193      also fix diagnostics VISCAHW & VISCA4W.
194    
195    checkpoint59o
196    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
197    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
198      move a few statemens out the main loop into separate loops
199    o pkg/shelfice:
200      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
201        (kg/m^2/s), does not break tests, because in verification/isomip,
202        rhoConstFresh=rhoConst (by accident)
203      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
204      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
205        new file model/src/seawater.F, so that they are available for all pkgs.
206      - convert potential temperature into in-situ temperature. This changes the
207        isomip tests => update tests
208    o add a flag writePickupAtEnd (default=true) to be able to suppress
209      writing a pickup at the last timestep
210    o tools/mpack-1.6 :
211      - disable automake (not working) and autoconf (not needed).
212      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
213        also cleaner with much less compilation warnings.
214    o pkg/profiles:
215      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
216      (for "less than 32 characters name" compiler requirement)
217    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
218      conditions that have a different sampling frequency than S/T/U/V obcs
219    o pkg/diagnostics (stats-diags):
220      - fix global Min/Max in case 1 processor get only empty tiles
221    o genmake2: replace (4 times)
222         make genmake_tc_1.o >> genmake_warnings 2>&1
223      with
224         COMM="$CC $CFLAGS -c genmake_tc_1.c"
225         echo $COMM >> genmake_warnings
226         $COMM >> genmake_warnings 2>&1
227      to make genmake2 always see the value of CC as specified in the optfile.
228    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
229      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
230      - modify verification advect_cs test to test SOM-advection on CS-grid.
231    o pkg/ctrl:
232      - Rewrite of ctrl_map_ini_ecco.F,
233        introducing a generic routine (ctrl_map_ini_gen.F).
234      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
235    
236    checkpoint59n
237    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
238      number in dedicate array "hdiag":
239      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
240        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
241      - many small changes (integer format) for large number of diagnostics
242      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
243        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
244    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
245      usingSphericalGrid, this allows to define the rotated grid coordinates
246      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
247      geographical coordinates according to the inverse of the rotation defined
248      by the Euler angles, so that Coriolis parameter and online-interpolation by
249      exf works with the geographical coordinates on XC/YC/XG/YG.
250      Naturally, this feature does not work with all packages, so some
251      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
252      profiles), because there the coordinates are assumed to be regular
253      spherical grid coordinates.
254    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
255      - introduce isopycnal diffusion coefficient control.
256    o tools/adjoint_options:
257      - additional control vector components.
258    o pkg/mnc: have mnc create marginally meaning full coordinate variables
259      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
260    o pkg/mypackage:
261      - add example of read/write pickup for state-var ;
262      - add entry points to the main code for state-vars diags & write-pickup.
263    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
264      transitions for useExfYearlyFields
265      - add new subroutine that determines the file to read from for
266        use*YearlyFields = .TRUE. and .FALSE.
267      - add a verification experiment to global_with_exf that tests
268        useExfYearlyFields with USE_EXF_INTERPOLATION defined
269    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
270      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
271      subroutines (which could be generated from a template, because they are
272      almost identical), for now they are included in obcs_prescribe_read.F for
273      simplicity
274    o pkg/exf:
275      - add a little more diagnostic to exf_interp_read (in analogy to
276        mds_read_field, can be turned off with debugLevel < debugLevA=1)
277      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
278        ugly but fast by unrolling short inner loops, inserting a unroll=8
279        directive in routine lagran, and splitting a loop and making do while the
280        outermost loop (the latter requires the intoduction of index arrays)
281    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
282    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
283      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
284    o verification/seaice_obcs: updated for restart test and latest options
285    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
286      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
287      for now this is only available for the C-grid code and also within
288      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
289    
290    checkpoint59m
291    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
292      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
293    o gad_som : fix flux output (& diagnostics) to have same units as other  
294      advection scheme fluxes (was previously multiplied by deltaT).  
295    o added verification/seaice_obcs both to test seaice open boundaries
296      and to provide an example matlab scrpt for generating them
297    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
298    o pkg/salt_plume: clean up salt_plume_frac.F to
299      remove redundancy in PlumeMethod 1 and 4
300    o pkg/kpp: added saltplume diagnostics
301    o pkg/obcs and pkg/seaice:
302      - do not set uice and vice to zero when OB*icefile are unspecified
303      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
304      - moved seaice tracer obcs after call to seaice_growth
305    o pkg/salt_plume: added various options for salt plume depth
306      criterion and for vertical distribution of the salt
307    
308    checkpoint59l
309    o pkg/ptracers: new version of ptracers pickup:
310      read meta file and write only fields which are needed to restart.
311      ( same logic as main pickup file ; also using pickupStrictlyMatch )
312    o pkg/seaice:
313      - add timescale for melting due to warm mixed layer as a means of
314        setting SEAICE_availHeatFrac more conveniently
315      - add a CPP-flag/runtime parameter check for flooding algorithm
316      - reformulated availHeat in seaice_growth.F to be independent of AREA
317    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
318      unit changes
319    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
320    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
321      SX vector computer.
322    o pkg/seaice:
323      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
324        seaice forcing fields can now be read only through pkg/exf
325      - removed some unused halos
326    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
327    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
328      or U/VICE from U/VWIND before computing U/VSTRESS
329    
330    checkpoint59k
331    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
332      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
333    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
334      all experiments pass when compile with un-initialised var. checking option.
335    o added pkg/salt_plume
336    o script to test restart (for now, in MITgcm_contrib/jmc_script)
337    o pkg/seaice: new read/write pickup version.
338      read meta file and write only fields which are needed to restart.
339      ( same logic as main pickup file ; also using pickupStrictlyMatch )
340    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
341    o lab_sea.hb87: modify the domain & update output.hb87.txt :
342      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
343      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
344      process. Fixed here by closing the domain at the Northern boundary.
345    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
346    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
347      a set of consecutive levels in/from a 3-D array.
348    o pkg/ptracers:
349      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
350      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
351    
352    checkpoint59j
353    o in pkgs: dic, obcs, offline, rbcs:
354      standard way to compute coeff. for time interpolation between 2 time reccords
355      which retains full precision (& make results less dependent on compiler).
356      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
357    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
358      packages instead of reading ice cover and wind speed separately
359    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
360     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
361      to allow to compile customized code before the update)
362    o cleaning-up:
363      - fix CPP instruction syntax in pkg/obcs
364      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
365        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
366      - fix some threads issue in IO parts.
367    o pkg/dic:
368      - add tons of "_d 0" (--> much better testreports !)
369       and then update outputs of tutorial_global_oce_biogeo
370    o pkg/mom_fluxform:
371      add a special version of momentum advection intended to conserve momentum
372      next to a bathymetry step or a coastline edge. (default = off = #undef)
373    o new read/write pickup version:
374      - for now, only implemented for main (mdsio) pickup file.
375      - write out only what is needed to restart; merge pickup_nh , pickup_ph
376        and main pickup together.
377      - read meta file; read only what is needed to restart; stop if a field
378        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
379        if it make sense (even if the restart is not perfect).
380      - if no meta file, assume that pickup to read corresponds exactly to
381        a pickup that would currently be written.
382      - read pickup written in the old format (until checkpoint59i) if it
383        recognizes an old meta file (no field-list).
384      - add a meta file in exp. which starts from a pickup: 2 cases:
385        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
386         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
387        b) a meta file describing the content of the associated pickup file
388         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
389    o pkg/mdsio & pkg/rw:
390      - new routine to read a meta file ; new set of routine to read
391        Multiple-fields file (with meta file).
392    o added open boundary conditions capability for seaice
393        HSNOW, HSALT, UICE, and VICE
394    
395    checkpoint59i
396    o adjoint:
397      * fix multiDimAdvection adjoint
398        (partial recomputation problem by TAF for fVerT(:,:,kDown)
399        and comlev1 size definition (maxpass vs. max. number of tracers)
400      * verification/global_ocean.90x45x15 adjoint now tests
401        NLFS and multiDimAdvection using DST3 (=30)
402      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
403    o pkg/kpp: add "_d 0" to real constant (if missing);
404      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
405      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
406    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
407      for internal parameters related to restart process (formerly from PARAMS.h)
408      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
409    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
410      as argument. (only atm2d & obcs write_pickup have not yet been updated)
411    o pkg/monitor:
412      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
413      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
414      - account for deep Atmosphere factor and density factor (anelastic)
415    o added open boundary conditions capability for seaice HEFF and AREA
416    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
417      thermodynamics
418      - requires a little reorganization, which affects the testreport results
419        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
420        so that now the conservative form is tested
421      - add a few comments
422    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
423    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
424    o add new diagnostics to seaice: advective, diffusive fluxes (only for
425      multidim-advection, for scheme 2 they are not filled) and transports,
426      thermodynamic growth rates
427    o change units of EmPmR (inside the code, + within coupling interface)
428      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
429      Affects results @ truncation level (cg2d match) and update output of
430       experiments: lab_sea(6), global_ocean.90x40x15(10),
431      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
432      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
433      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
434      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
435    
436    checkpoint59h
437    o pkg/exf:
438      - improve vectorization by moving if-statement out of loops in
439        exf_mapfields, exf_radiation
440      - exf_bulkformulae.F: introduce 2D fields and vectorize code
441    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
442    o testreport:
443      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
444        monitor & update offline_exf_seaice exp. output.
445      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
446    o pkg/seaice:
447      - bug fix in the evp solver: boundary conditions were affected be
448        masking of zMax/zMin (changes results)
449      - minor bug fix in boundary conditions in seaice_calc_strainrates
450        (changes results for no_slip)
451      - seaice_lsr.F: make interpolation of eta dependent on boundaries
452      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
453      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
454        stress formulation and no-slip boundary conditions
455    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
456      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
457    o pkg/seaice: a first HSALT time stepping equation has been checked in
458    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
459      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
460      without requiring DO-IF statements
461    o pkg/thsice:
462      use continuous power-law function for partition of energy between lateral
463      melting/freezing and thinning/thickening ; old code using step function
464      still available with #undef THSICE_FRACEN_POWERLAW
465      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
466    o testreport: change AD testing : check against results/output_adm.txt
467      using same scripts as for forward test.
468    
469    checkpoint59g
470    o adjoint testing: in preparation for changing testreport:
471      - output format: cost and grad written on separated lines
472      - ad output results in directory "results" (instead of "results_ad")
473    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
474    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
475    o pkg/ecco: allow user defined cost function contributions
476    o testreport:
477      Allow to choose (per experiment) the list of tested output variables
478       and the main variable (used to issue a pass/FAIL ) ;
479      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
480      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
481      Also modify printing of summary:
482       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
483       b) echo the list of tested variables in the individual summary.txt of
484          each experiment.
485    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
486      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
487      (but still depend on the tile decompostion of the domain).
488    o pkg/seaice: change a discretization detail to make the B-grid code
489      "more symmetric". This change is likely to remove all "ridges/leads" that
490      where quasi-aligned with the grid in B-grid solutions. It may also be
491      the solution to the stress coupling issues with the B-grid.
492    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
493      remove .cvsignore from input dir. (since testreport no longer run here).
494    o pkg/thsice:
495     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
496     - fix reshaping of sea-ice just after advection:
497       melt all the ice only if ice-volume is too small.
498     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
499       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
500     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
501    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
502      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
503    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
504      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
505      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
506      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
507      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
508      -> update output.txt
509    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
510     this affects truncation error: -> update output.txt of exp:
511      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
512      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
513    
514    checkpoint59f
515    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
516    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
517      a bounded range (in forward mode)
518    o pkg/ecco, ctrl, autodiff and mom_common:
519     internal parameter controls, completements of implementations
520    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
521    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
522      (not seem any difference in testing results).
523    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
524       at face corners.
525    o pkg/generic_advdiff:
526     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
527      loop range indices for computing vertical advection tendency
528      and do the calculation in the interior only (no overlap) ;
529      for now, only implemented for SOM advection (to save CPU time).
530     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
531    o exch2 adjoint
532      First set of changes:
533      - add exch2 hand-written adjoint templates
534      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
535        This will require cleanup in pkg/autodiff/*.F
536        (changed routines currently kept separate in verif. code/)
537      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
538        that used to hide exch2 or cubed-sphere specific code
539        (commented via 'cph-exch2')
540    o pkg/seaice
541      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
542    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
543       output of global_ocean.cs32x15.thsice .
544    
545    checkpoint59e
546    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
547      for B-grid vector (not yet tested) and C-grid vector (<- only used
548      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
549    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
550      (#ifdef ALLOW_SALT_PLUME)
551    o gather_2d/scatter_2d: removed halo regions
552    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
553      scheme and the corresponding test case (under front_relax dir). For now,
554      only available with Skew-flux form and not yet tested in realistic set-up.
555      adjoint: store directives updated, but gradient checks deteriorated,
556      so maybe GM/Redi adjoint is now broken.
557    o seaice adjoint
558      * add AREA, HEFF, HSNOW as control variable
559        (should not change lab_sea results)
560      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
561    o pkg/seaice:
562      * added computation of saltFlux in seaice_growth;
563        For time being, sea ice salinity is assumed constant
564        contribution of snow flooding to freshening of sea ice is neglected.
565        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
566        defaults to 0.0 in order to maintain backward compatibility.
567        Typical values for SEAICE_salinity are 4 to 10 g/kg.
568      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
569      * added SEAICE_availHeatFrac, which specifies fraction of surface level
570        heat content used to melt or grow ice
571      * commented out cap of HICE: it helps keep ice thinner
572      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
573      * applied OBCS T/S mask to HEFFM sea ice mask
574    
575    checkpoint59d
576    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
577     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
578     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
579    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
580     and change default value of parameter "GM_Small_Number";
581     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
582       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
583       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
584    o pkg/ecco: cost function when applying pkg/smooth to controls
585    o pkg/ctrl: add forcingPrecond run time parameter
586    o pkg/seaice:
587     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
588     - fix bug in metric terms of u-equation in LSR solver (implicit part),
589       changes verification/lab_sea
590     - rearrange implicit part of u-equation in LSR solver to make it easier to
591       read, understand, and debug. This causes changes at the truncation level.
592     - fix (serious) bug in the boundary conditions (sign error in the implicit
593       part) of the LSR solver. Changes all LSR results.
594     - fixed problem with HSNOW initialization to avoid thick snow when AREA
595       is initilized with small values - does not change lab_sea results.
596     - added HsnowFile initialization capability
597    o pkg/smooth: addition to model/src and pkg/ctrl so allow
598     initialization of pkg/smooth and application to control vector
599    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
600    o dependencies: pkg/profiles requires pkg/cal
601    o pkg/profiles:
602     - added option ALLOW_PROFILES_GENERICGRID
603         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
604         that interpolation information (grid points and coefficients) is provided
605         within the netcdf input files.
606         -> sample matlab scripts can be found in MITgcm_contrib/gael
607         that allow you to prepare netcdf input files.
608     - also modified: cleaner include statements, cleaner error print statements,
609       cleaner stops when error, and more tests of the netcdf input files consistency.
610    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
611    o pkg/seaice:
612     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
613       requires a new routine: seaice_diagnostics_fill.F
614     - make sure that seaice does not move if not forced (pressure replacement
615       method, Hibler and Ip, 1995), changes results
616     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
617     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
618       It is turned off by default (=-1.), because it changes the results.
619     - make it possible to read AREA from a file, too.
620    
621    checkpoint59c
622    o add S/R and diagnostics for oceanic mixed-layer depth
623    o move GMRedi call after all vertical mixing schemes (including KPP)
624    o pkg/thsice:
625     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
626      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
627    o pkg/obcs:
628     - bug fix for balance code
629    o pkg/seaice:
630      - allow values of SEAICE_elasticParm > 1
631      - add new parameter SEAICE_evpTauRelax as an alternative
632        to SEAICE_elasticParm
633      - make lsr boundary conditions free slip (by default), changes result
634      - add code for no slip boundary conditions for lsr
635      - set minimum of zeta to zero (and not 4e8) (changes results)
636      - add a cap on AREA after advecting AREA if seaice_growth is not called
637    o change calculation of Visbeck K:
638      - no longer depend on tapering scheme; instead, compute slope (limited
639        by GM_maxSlope). this is equivalent to what was comuted before with
640        clipping or linear tappering.
641      - fix vertical averaging (wrong by 1/2 level)
642      - leave the old version (but will not be maintained) within
643        #ifdef OLD_VISBECK_CALC / #endif
644      - update output of exp. ideal_2D_oce
645    o change error catch in calc_r_star to improve vectorization
646    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
647      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
648    o adjoint:
649      Re-organized adjoint checkpointing according to Matt Mazloff
650      (but with modifs/completions/cleanups)
651      Storing is now bundled into large arrays to optimized I/O
652      (and second step in cleanup of the_main_loop)
653    
654    checkpoint59b
655    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
656      - export/import (between ocean & coupler) fields needed for ocean DIC.
657    o pkg/seaice:
658      - get rid of three more exchanges seaice_calc_viscosities (required
659        different loop boundaries in seaice_lsr and seaice_ocean_stress)
660      - bug fix in seaice_ocean_stress (update of lab_sea required)
661      - reduce loop boundaries to necessary minimum also in seaice_evp
662      - go back to the old way of computing deltaC/Z as the adjoint likes that
663        better
664    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
665      passive tracer to an Age Tracer) + update output.txt
666    o pkg/exf:
667      - implement A-grid / C-grid selection for wind-stress input files.
668      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
669      for now, in exf_bulk_largeyeager04.F only :
670      - change implementation for case where windspeed + 2. components wind-stress
671        are read-in. AND use rhoConstFresh to convert evap.
672    o pkg/seaice:
673      - use correct EXCH_UV for wind-forcing (on A-grid).
674      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
675        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
676    o pkg/exf:
677      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
678      EXF_INTERPOLATION:
679      - merge global_with_exf/code version of exf_interp_read.F
680        to the main code ;
681      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
682        reading the file ; Important: This options needs to be defined to recover
683        previous code.
684        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
685      - no longer loose real*8 precision along the way when using exf_iprec=64.
686    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
687      - change discretisation of evp-solver in order to avoid another exchange
688        (changes lab_sea) and clean up a little
689      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
690        help the adjoint (this also changes the results slightly)
691      - add a few "_d 0" where they had been missing in seaice_evp.F
692      - cleaning up: remove unused seaice_calc_rhs.F
693    o pkg/exf: some cleaning-up:
694      - change various "constants" into runtime parameters
695      - cleaned-up Large&Yeager04 routine which should eventually
696        replace exf_bulkformulae.F (changed names of S/R and CPP)
697        and merged various ALLOW_ATM_WIND options
698     only used with thsice pkg (in thsice_get_exf.F):
699      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
700        which are used when useStabilityFct_overIce=TRUE (= the default)
701      - change default values of ice & snow emissivity and scale downward LW
702        by ice & snow emissivity.
703    o pkg/thsice:
704     fix few little problems, in thsice_calc_thickn.F:
705      - growth vertically (and not laterally) if iceFrac == iceMaskMax
706      - melt only laterally if hIce < hThinIce (as the comments say)
707      and in thsice_extend.F:
708      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
709      - start to form ice as soon as the minimum ice-volume is reachable.
710     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
711      and cpl_aim+ocn
712    o pkg/kpp
713     - move computation of surface related input fields to KPP into a new
714       subroutine kpp_forcing_surf.F
715     - remove wrong (within bi,bj loops) EXCH calls.
716     - little cleaning (add argument myThid in last position, cvs header ...)
717     - for now, fix conservation problem by exchanging KPPviscAz (may not
718       be the best fix)
719    o pkg/seaice
720     - check for inconsistent evp parameter/cpp-flag combination
721     - remove leftover errIO flat for obsolete name list error handling
722    o OpenAD
723     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
724    
725    checkpoint59a
726    o pkg/seaice: some parameter clarifications and a little bit of clean up
727    o pkg/thsice: rename run-time parameters:
728       himin       -> hIceMin
729       himin0      -> hThinIce
730       hihig       -> hThickIce
731       i0          -> i0swFrac
732       transCoef   -> bMeltCoef
733       frac_energy -> fracMelting
734      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
735       with default values (for now) that do not change the results.
736      remove old version of thsice vars advection in pkg/seaice.
737  o in FFIELDS.h:  o in FFIELDS.h:
738    - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD    - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
739    - make pLoad & sIceLoad always available (but still only used if    - make pLoad & sIceLoad always available (but still only used if
740       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
741  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
742  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
743      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
744        are no longer updating the vertical diffusivity array
745        (passed as argument) but are (re-) setting those arrays.
746  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
747    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
748      cgrid-lsr and evp solver      cgrid-lsr and evp solver
# Line 30  o pkg/seaice: fix bug in evp solver, whi Line 762  o pkg/seaice: fix bug in evp solver, whi
762      of evp, complete rewrite for lsr case (latter is does not yet work      of evp, complete rewrite for lsr case (latter is does not yet work
763      in all cases)      in all cases)
764  o pkg/kpp: add code to have mixing in shelf ice caverns  o pkg/kpp: add code to have mixing in shelf ice caverns
765      - add myThid to all kpp routines (long overdue)
766    
767  checkpoint59  checkpoint59
768  o pkg/exf:  o pkg/exf:
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