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revision 1.808 by jmc, Thu May 3 22:57:27 2007 UTC revision 1.1020 by jmc, Sat Sep 6 17:55:27 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 add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
8      and rename:
9      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
10      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
11    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
12    
13    checkpoint61c
14    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
15      to add mass source/sink of fluid in the interior (3-D generalisation
16      of oceanic real-fresh water flux).
17    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
18    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
19    o new pkg: down_slope
20      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
21      - presently, modify T & S inland (dwnslp_calc_rho.F).
22        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
23      - implementation for ocean in P-coords not tested.
24      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
25    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
26      (to facilitate conversion of oceanic pkg to p-coordinate).
27    o change FIND_RHO to FIND_RHO_2D :
28      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
29    o new pkg: cheapaml
30    
31    checkpoint61b
32    o exch2:
33      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
34      - no longer depend on the order sequence (N,S,E,W).
35      - 3rd exchange no longer needed (tested with 24 tiles).
36      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
37      - exch_UV_A-grid readily available (but not yet tested).
38      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
39      (both are no longer needed) in exch_uv: no effect in forward run; but
40       get truncation error differences with adjoint exch.
41    o exch2:
42     - change index-bounds storage (moved from target to local tile,
43       more intuitive this way) ; rename/remove some variables.
44     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
45    
46    checkpoint61a
47    o exch2/matlab-topology-generator:
48      fix bug in index bounds for N-S internal exchange (hard to tell if this
49      had any effect on the solution).
50    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
51      is exceeded
52    o testreport: modify syntax of awk, so that it works also with
53      awk, and not only with nawk and gawk
54    
55    checkpoint61
56    o autodiff
57      Change default for TAF usage by removing argument '-nonew_arg'
58      This changes TAF subroutine argument list (ordering of active var.)
59      Omission of this flag leads to incompatibility w.r.t. TAMC
60      To restore TAMC-compatibility, need following modifs:
61      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
62      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
63      Tested TAF version is 1.9.22
64      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
65    
66    checkpoint60
67    --->>> This is the last checkpoint for which generating the adjoint
68    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
69    --->>> by default.
70    --->>> Future checkpoints will ommit this flag by default.
71    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
72    o pkg/grdchk: Add gradient check to etan0 perturbations.
73    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
74    o pkg/autodiff: more flexibility in zeroadj.
75      model/src: modifying do_oceanic_phys.F accordingly.
76    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
77    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
78      special setup of gmredi for which the adjoint is stable
79      enough for parameter optimization.
80    o bridging the gap between eddy stress and GM.
81      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
82          along with a change in CPP option (now ALLOW_EDDYPSI).
83      -> when using GM w/ GM_AdvForm:
84          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
85          is applied either in the tracer Eq. or in momentum Eq.
86          depending on data.gmredi (intro. GM_InMomAsStress).
87      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
88      The key modifications are in model/src/taueddy_external_forcing.F
89      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
90    
91    checkpoint59r
92    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
93      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
94      fix option to read coriolis(@ cell-corner) from files with CS-grid.
95    o pkg/mnc: add some attributes to standard 1D-coordinate variables
96    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
97      mass points, when using mnc for output
98      - add runtime parameter (missing_value, missing_value_int) to override
99        default (which is the value of getcon('UNDEF'))
100    o pkg/mnc: prepare mnc for the actual use of missing values with the
101      diagnostics package: small fix in mnc_cw_readwrite.template and more
102      initialisation of never used fields
103      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
104      versions
105    o pkg/thsice/thsice_ini_vars.F added default initial values so that
106      thermodynamics sea ice solver does not blow up when some initial fields
107      are missing.
108    o move from external_forcing_surf.F to ini_forcing.F
109      the p-coord. hack consisting in using pLoad to set phi0surf ;
110      update output of tutorial_global_oce_in_p (affected @ truncation level).
111    o Freshen up a bit hs94.1x64x5, notably:
112      remove rotationPeriod and tRef=5*0. (adjoint only), and add
113      exactConserv=.TRUE.
114    o pkg/generic_advdiff:
115      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
116      applies to files where Temperature & Salinity 2nd Order moments are used.
117    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
118      this uses a dynamically allocated internal state data structure
119      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
120      and requires a fortran 90 compiler
121    
122    checkpoint59q
123    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
124       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
125    o Refresh tutorial_global_oce_biogeo, notably:
126      - change bathymetry (put back seamounts in ACC, use hFacs)
127      - change EOS (POLY3 --> JMD95Z)
128      - use Bryan-Lewis vertical diffusivity
129      - use multidimensional advection
130      - remove old virtual virtual in dic pkg, now done through ptracer pkg
131      - change a couple of parameters in dic pkg
132    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
133    o pkg/obcs: change default to OBCSfixTopo = .true.,
134      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
135      - replace "debugMode" with "debugLevel .GE. debLevB"
136    o implementation of TAF directives for gchem,cfc,dic
137    o remove "exp5" (replaced by tutorial_deep_convection).
138    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
139      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
140      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
141      --> changes results in exp4, seaice_obcs
142    o tutorial_deep_convection :
143      update the set-up and increase resolution and domain size ; start
144      from pseudo initial conditions = output at t=120mn in order to see
145      something happening when running testreport.
146    o pkg/seaice: add os7mp as an advection scheme
147                  add check for advection schemes
148                  add a flag for restoring T and S underneath sea ice
149    o pkg/my82: add netcdf-support and diagnostics
150    o thsice pkg:
151      - Now hsMax limits snow height by turning it into ice following
152        flooding scheme (and now conserving energy)
153      - Slight rewriting of the formula in thsice_calc_thick.F
154      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
155      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
156    
157    checkpoint59p
158    o gchem / dic / cfc :
159      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
160      - add new parameter files: "data.dic" & "data.cfc" ;
161      - various re-arrangement in initialisation & header file ;
162      - fix tutorial_global_oce_biogeo for multi-threaded test.
163    o pkg/dic: test for "pickup_dic" file when restarting ;
164      if no pickup-file, can restart with a re-initialised pH (same as it did
165      before) providing pickupStrictlyMatch is set to False.
166    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
167      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
168    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
169      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
170    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
171     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
172       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
173    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
174       scheme to use for vorticty-term ;
175     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
176       (with default selectVortScheme, return to original discretisation)
177     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
178    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
179    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
180      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
181      also fix diagnostics VISCAHW & VISCA4W.
182    
183    checkpoint59o
184    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
185    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
186      move a few statemens out the main loop into separate loops
187    o pkg/shelfice:
188      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
189        (kg/m^2/s), does not break tests, because in verification/isomip,
190        rhoConstFresh=rhoConst (by accident)
191      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
192      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
193        new file model/src/seawater.F, so that they are available for all pkgs.
194      - convert potential temperature into in-situ temperature. This changes the
195        isomip tests => update tests
196    o add a flag writePickupAtEnd (default=true) to be able to suppress
197      writing a pickup at the last timestep
198    o tools/mpack-1.6 :
199      - disable automake (not working) and autoconf (not needed).
200      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
201        also cleaner with much less compilation warnings.
202    o pkg/profiles:
203      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
204      (for "less than 32 characters name" compiler requirement)
205    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
206      conditions that have a different sampling frequency than S/T/U/V obcs
207    o pkg/diagnostics (stats-diags):
208      - fix global Min/Max in case 1 processor get only empty tiles
209    o genmake2: replace (4 times)
210         make genmake_tc_1.o >> genmake_warnings 2>&1
211      with
212         COMM="$CC $CFLAGS -c genmake_tc_1.c"
213         echo $COMM >> genmake_warnings
214         $COMM >> genmake_warnings 2>&1
215      to make genmake2 always see the value of CC as specified in the optfile.
216    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
217      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
218      - modify verification advect_cs test to test SOM-advection on CS-grid.
219    o pkg/ctrl:
220      - Rewrite of ctrl_map_ini_ecco.F,
221        introducing a generic routine (ctrl_map_ini_gen.F).
222      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
223    
224    checkpoint59n
225    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
226      number in dedicate array "hdiag":
227      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
228        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
229      - many small changes (integer format) for large number of diagnostics
230      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
231        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
232    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
233      usingSphericalGrid, this allows to define the rotated grid coordinates
234      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
235      geographical coordinates according to the inverse of the rotation defined
236      by the Euler angles, so that Coriolis parameter and online-interpolation by
237      exf works with the geographical coordinates on XC/YC/XG/YG.
238      Naturally, this feature does not work with all packages, so some
239      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
240      profiles), because there the coordinates are assumed to be regular
241      spherical grid coordinates.
242    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
243      - introduce isopycnal diffusion coefficient control.
244    o tools/adjoint_options:
245      - additional control vector components.
246    o pkg/mnc: have mnc create marginally meaning full coordinate variables
247      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
248    o pkg/mypackage:
249      - add example of read/write pickup for state-var ;
250      - add entry points to the main code for state-vars diags & write-pickup.
251    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
252      transitions for useExfYearlyFields
253      - add new subroutine that determines the file to read from for
254        use*YearlyFields = .TRUE. and .FALSE.
255      - add a verification experiment to global_with_exf that tests
256        useExfYearlyFields with USE_EXF_INTERPOLATION defined
257    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
258      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
259      subroutines (which could be generated from a template, because they are
260      almost identical), for now they are included in obcs_prescribe_read.F for
261      simplicity
262    o pkg/exf:
263      - add a little more diagnostic to exf_interp_read (in analogy to
264        mds_read_field, can be turned off with debugLevel < debugLevA=1)
265      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
266        ugly but fast by unrolling short inner loops, inserting a unroll=8
267        directive in routine lagran, and splitting a loop and making do while the
268        outermost loop (the latter requires the intoduction of index arrays)
269    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
270    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
271      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
272    o verification/seaice_obcs: updated for restart test and latest options
273    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
274      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
275      for now this is only available for the C-grid code and also within
276      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
277    
278    checkpoint59m
279    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
280      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
281    o gad_som : fix flux output (& diagnostics) to have same units as other  
282      advection scheme fluxes (was previously multiplied by deltaT).  
283    o added verification/seaice_obcs both to test seaice open boundaries
284      and to provide an example matlab scrpt for generating them
285    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
286    o pkg/salt_plume: clean up salt_plume_frac.F to
287      remove redundancy in PlumeMethod 1 and 4
288    o pkg/kpp: added saltplume diagnostics
289    o pkg/obcs and pkg/seaice:
290      - do not set uice and vice to zero when OB*icefile are unspecified
291      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
292      - moved seaice tracer obcs after call to seaice_growth
293    o pkg/salt_plume: added various options for salt plume depth
294      criterion and for vertical distribution of the salt
295    
296    checkpoint59l
297    o pkg/ptracers: new version of ptracers pickup:
298      read meta file and write only fields which are needed to restart.
299      ( same logic as main pickup file ; also using pickupStrictlyMatch )
300    o pkg/seaice:
301      - add timescale for melting due to warm mixed layer as a means of
302        setting SEAICE_availHeatFrac more conveniently
303      - add a CPP-flag/runtime parameter check for flooding algorithm
304      - reformulated availHeat in seaice_growth.F to be independent of AREA
305    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
306      unit changes
307    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
308    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
309      SX vector computer.
310    o pkg/seaice:
311      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
312        seaice forcing fields can now be read only through pkg/exf
313      - removed some unused halos
314    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
315    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
316      or U/VICE from U/VWIND before computing U/VSTRESS
317    
318    checkpoint59k
319    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
320      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
321    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
322      all experiments pass when compile with un-initialised var. checking option.
323    o added pkg/salt_plume
324    o script to test restart (for now, in MITgcm_contrib/jmc_script)
325    o pkg/seaice: new read/write pickup version.
326      read meta file and write only fields which are needed to restart.
327      ( same logic as main pickup file ; also using pickupStrictlyMatch )
328    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
329    o lab_sea.hb87: modify the domain & update output.hb87.txt :
330      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
331      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
332      process. Fixed here by closing the domain at the Northern boundary.
333    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
334    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
335      a set of consecutive levels in/from a 3-D array.
336    o pkg/ptracers:
337      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
338      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
339    
340    checkpoint59j
341    o in pkgs: dic, obcs, offline, rbcs:
342      standard way to compute coeff. for time interpolation between 2 time reccords
343      which retains full precision (& make results less dependent on compiler).
344      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
345    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
346      packages instead of reading ice cover and wind speed separately
347    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
348     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
349      to allow to compile customized code before the update)
350    o cleaning-up:
351      - fix CPP instruction syntax in pkg/obcs
352      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
353        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
354      - fix some threads issue in IO parts.
355    o pkg/dic:
356      - add tons of "_d 0" (--> much better testreports !)
357       and then update outputs of tutorial_global_oce_biogeo
358    o pkg/mom_fluxform:
359      add a special version of momentum advection intended to conserve momentum
360      next to a bathymetry step or a coastline edge. (default = off = #undef)
361    o new read/write pickup version:
362      - for now, only implemented for main (mdsio) pickup file.
363      - write out only what is needed to restart; merge pickup_nh , pickup_ph
364        and main pickup together.
365      - read meta file; read only what is needed to restart; stop if a field
366        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
367        if it make sense (even if the restart is not perfect).
368      - if no meta file, assume that pickup to read corresponds exactly to
369        a pickup that would currently be written.
370      - read pickup written in the old format (until checkpoint59i) if it
371        recognizes an old meta file (no field-list).
372      - add a meta file in exp. which starts from a pickup: 2 cases:
373        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
374         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
375        b) a meta file describing the content of the associated pickup file
376         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
377    o pkg/mdsio & pkg/rw:
378      - new routine to read a meta file ; new set of routine to read
379        Multiple-fields file (with meta file).
380    o added open boundary conditions capability for seaice
381        HSNOW, HSALT, UICE, and VICE
382    
383    checkpoint59i
384    o adjoint:
385      * fix multiDimAdvection adjoint
386        (partial recomputation problem by TAF for fVerT(:,:,kDown)
387        and comlev1 size definition (maxpass vs. max. number of tracers)
388      * verification/global_ocean.90x45x15 adjoint now tests
389        NLFS and multiDimAdvection using DST3 (=30)
390      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
391    o pkg/kpp: add "_d 0" to real constant (if missing);
392      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
393      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
394    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
395      for internal parameters related to restart process (formerly from PARAMS.h)
396      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
397    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
398      as argument. (only atm2d & obcs write_pickup have not yet been updated)
399    o pkg/monitor:
400      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
401      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
402      - account for deep Atmosphere factor and density factor (anelastic)
403    o added open boundary conditions capability for seaice HEFF and AREA
404    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
405      thermodynamics
406      - requires a little reorganization, which affects the testreport results
407        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
408        so that now the conservative form is tested
409      - add a few comments
410    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
411    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
412    o add new diagnostics to seaice: advective, diffusive fluxes (only for
413      multidim-advection, for scheme 2 they are not filled) and transports,
414      thermodynamic growth rates
415    o change units of EmPmR (inside the code, + within coupling interface)
416      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
417      Affects results @ truncation level (cg2d match) and update output of
418       experiments: lab_sea(6), global_ocean.90x40x15(10),
419      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
420      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
421      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
422      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
423    
424    checkpoint59h
425    o pkg/exf:
426      - improve vectorization by moving if-statement out of loops in
427        exf_mapfields, exf_radiation
428      - exf_bulkformulae.F: introduce 2D fields and vectorize code
429    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
430    o testreport:
431      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
432        monitor & update offline_exf_seaice exp. output.
433      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
434    o pkg/seaice:
435      - bug fix in the evp solver: boundary conditions were affected be
436        masking of zMax/zMin (changes results)
437      - minor bug fix in boundary conditions in seaice_calc_strainrates
438        (changes results for no_slip)
439      - seaice_lsr.F: make interpolation of eta dependent on boundaries
440      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
441      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
442        stress formulation and no-slip boundary conditions
443    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
444      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
445    o pkg/seaice: a first HSALT time stepping equation has been checked in
446    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
447      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
448      without requiring DO-IF statements
449    o pkg/thsice:
450      use continuous power-law function for partition of energy between lateral
451      melting/freezing and thinning/thickening ; old code using step function
452      still available with #undef THSICE_FRACEN_POWERLAW
453      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
454    o testreport: change AD testing : check against results/output_adm.txt
455      using same scripts as for forward test.
456    
457    checkpoint59g
458    o adjoint testing: in preparation for changing testreport:
459      - output format: cost and grad written on separated lines
460      - ad output results in directory "results" (instead of "results_ad")
461    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
462    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
463    o pkg/ecco: allow user defined cost function contributions
464    o testreport:
465      Allow to choose (per experiment) the list of tested output variables
466       and the main variable (used to issue a pass/FAIL ) ;
467      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
468      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
469      Also modify printing of summary:
470       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
471       b) echo the list of tested variables in the individual summary.txt of
472          each experiment.
473    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
474      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
475      (but still depend on the tile decompostion of the domain).
476    o pkg/seaice: change a discretization detail to make the B-grid code
477      "more symmetric". This change is likely to remove all "ridges/leads" that
478      where quasi-aligned with the grid in B-grid solutions. It may also be
479      the solution to the stress coupling issues with the B-grid.
480    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
481      remove .cvsignore from input dir. (since testreport no longer run here).
482    o pkg/thsice:
483     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
484     - fix reshaping of sea-ice just after advection:
485       melt all the ice only if ice-volume is too small.
486     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
487       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
488     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
489    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
490      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
491    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
492      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
493      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
494      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
495      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
496      -> update output.txt
497    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
498     this affects truncation error: -> update output.txt of exp:
499      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
500      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
501    
502    checkpoint59f
503    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
504    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
505      a bounded range (in forward mode)
506    o pkg/ecco, ctrl, autodiff and mom_common:
507     internal parameter controls, completements of implementations
508    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
509    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
510      (not seem any difference in testing results).
511    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
512       at face corners.
513    o pkg/generic_advdiff:
514     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
515      loop range indices for computing vertical advection tendency
516      and do the calculation in the interior only (no overlap) ;
517      for now, only implemented for SOM advection (to save CPU time).
518     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
519    o exch2 adjoint
520      First set of changes:
521      - add exch2 hand-written adjoint templates
522      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
523        This will require cleanup in pkg/autodiff/*.F
524        (changed routines currently kept separate in verif. code/)
525      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
526        that used to hide exch2 or cubed-sphere specific code
527        (commented via 'cph-exch2')
528    o pkg/seaice
529      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
530    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
531       output of global_ocean.cs32x15.thsice .
532    
533    checkpoint59e
534    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
535      for B-grid vector (not yet tested) and C-grid vector (<- only used
536      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
537    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
538      (#ifdef ALLOW_SALT_PLUME)
539    o gather_2d/scatter_2d: removed halo regions
540    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
541      scheme and the corresponding test case (under front_relax dir). For now,
542      only available with Skew-flux form and not yet tested in realistic set-up.
543      adjoint: store directives updated, but gradient checks deteriorated,
544      so maybe GM/Redi adjoint is now broken.
545    o seaice adjoint
546      * add AREA, HEFF, HSNOW as control variable
547        (should not change lab_sea results)
548      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
549    o pkg/seaice:
550      * added computation of saltFlux in seaice_growth;
551        For time being, sea ice salinity is assumed constant
552        contribution of snow flooding to freshening of sea ice is neglected.
553        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
554        defaults to 0.0 in order to maintain backward compatibility.
555        Typical values for SEAICE_salinity are 4 to 10 g/kg.
556      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
557      * added SEAICE_availHeatFrac, which specifies fraction of surface level
558        heat content used to melt or grow ice
559      * commented out cap of HICE: it helps keep ice thinner
560      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
561      * applied OBCS T/S mask to HEFFM sea ice mask
562    
563    checkpoint59d
564    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
565     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
566     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
567    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
568     and change default value of parameter "GM_Small_Number";
569     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
570       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
571       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
572    o pkg/ecco: cost function when applying pkg/smooth to controls
573    o pkg/ctrl: add forcingPrecond run time parameter
574    o pkg/seaice:
575     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
576     - fix bug in metric terms of u-equation in LSR solver (implicit part),
577       changes verification/lab_sea
578     - rearrange implicit part of u-equation in LSR solver to make it easier to
579       read, understand, and debug. This causes changes at the truncation level.
580     - fix (serious) bug in the boundary conditions (sign error in the implicit
581       part) of the LSR solver. Changes all LSR results.
582     - fixed problem with HSNOW initialization to avoid thick snow when AREA
583       is initilized with small values - does not change lab_sea results.
584     - added HsnowFile initialization capability
585    o pkg/smooth: addition to model/src and pkg/ctrl so allow
586     initialization of pkg/smooth and application to control vector
587    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
588    o dependencies: pkg/profiles requires pkg/cal
589    o pkg/profiles:
590     - added option ALLOW_PROFILES_GENERICGRID
591         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
592         that interpolation information (grid points and coefficients) is provided
593         within the netcdf input files.
594         -> sample matlab scripts can be found in MITgcm_contrib/gael
595         that allow you to prepare netcdf input files.
596     - also modified: cleaner include statements, cleaner error print statements,
597       cleaner stops when error, and more tests of the netcdf input files consistency.
598    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
599    o pkg/seaice:
600     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
601       requires a new routine: seaice_diagnostics_fill.F
602     - make sure that seaice does not move if not forced (pressure replacement
603       method, Hibler and Ip, 1995), changes results
604     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
605     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
606       It is turned off by default (=-1.), because it changes the results.
607     - make it possible to read AREA from a file, too.
608    
609    checkpoint59c
610    o add S/R and diagnostics for oceanic mixed-layer depth
611    o move GMRedi call after all vertical mixing schemes (including KPP)
612    o pkg/thsice:
613     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
614      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
615    o pkg/obcs:
616     - bug fix for balance code
617    o pkg/seaice:
618      - allow values of SEAICE_elasticParm > 1
619      - add new parameter SEAICE_evpTauRelax as an alternative
620        to SEAICE_elasticParm
621      - make lsr boundary conditions free slip (by default), changes result
622      - add code for no slip boundary conditions for lsr
623      - set minimum of zeta to zero (and not 4e8) (changes results)
624      - add a cap on AREA after advecting AREA if seaice_growth is not called
625    o change calculation of Visbeck K:
626      - no longer depend on tapering scheme; instead, compute slope (limited
627        by GM_maxSlope). this is equivalent to what was comuted before with
628        clipping or linear tappering.
629      - fix vertical averaging (wrong by 1/2 level)
630      - leave the old version (but will not be maintained) within
631        #ifdef OLD_VISBECK_CALC / #endif
632      - update output of exp. ideal_2D_oce
633    o change error catch in calc_r_star to improve vectorization
634    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
635      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
636    o adjoint:
637      Re-organized adjoint checkpointing according to Matt Mazloff
638      (but with modifs/completions/cleanups)
639      Storing is now bundled into large arrays to optimized I/O
640      (and second step in cleanup of the_main_loop)
641    
642    checkpoint59b
643    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
644      - export/import (between ocean & coupler) fields needed for ocean DIC.
645    o pkg/seaice:
646      - get rid of three more exchanges seaice_calc_viscosities (required
647        different loop boundaries in seaice_lsr and seaice_ocean_stress)
648      - bug fix in seaice_ocean_stress (update of lab_sea required)
649      - reduce loop boundaries to necessary minimum also in seaice_evp
650      - go back to the old way of computing deltaC/Z as the adjoint likes that
651        better
652    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
653      passive tracer to an Age Tracer) + update output.txt
654    o pkg/exf:
655      - implement A-grid / C-grid selection for wind-stress input files.
656      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
657      for now, in exf_bulk_largeyeager04.F only :
658      - change implementation for case where windspeed + 2. components wind-stress
659        are read-in. AND use rhoConstFresh to convert evap.
660    o pkg/seaice:
661      - use correct EXCH_UV for wind-forcing (on A-grid).
662      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
663        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
664    o pkg/exf:
665      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
666      EXF_INTERPOLATION:
667      - merge global_with_exf/code version of exf_interp_read.F
668        to the main code ;
669      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
670        reading the file ; Important: This options needs to be defined to recover
671        previous code.
672        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
673      - no longer loose real*8 precision along the way when using exf_iprec=64.
674    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
675      - change discretisation of evp-solver in order to avoid another exchange
676        (changes lab_sea) and clean up a little
677      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
678        help the adjoint (this also changes the results slightly)
679      - add a few "_d 0" where they had been missing in seaice_evp.F
680      - cleaning up: remove unused seaice_calc_rhs.F
681    o pkg/exf: some cleaning-up:
682      - change various "constants" into runtime parameters
683      - cleaned-up Large&Yeager04 routine which should eventually
684        replace exf_bulkformulae.F (changed names of S/R and CPP)
685        and merged various ALLOW_ATM_WIND options
686     only used with thsice pkg (in thsice_get_exf.F):
687      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
688        which are used when useStabilityFct_overIce=TRUE (= the default)
689      - change default values of ice & snow emissivity and scale downward LW
690        by ice & snow emissivity.
691    o pkg/thsice:
692     fix few little problems, in thsice_calc_thickn.F:
693      - growth vertically (and not laterally) if iceFrac == iceMaskMax
694      - melt only laterally if hIce < hThinIce (as the comments say)
695      and in thsice_extend.F:
696      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
697      - start to form ice as soon as the minimum ice-volume is reachable.
698     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
699      and cpl_aim+ocn
700  o pkg/kpp  o pkg/kpp
  - remove wrong (within bi,bj loops) EXCH calls.  
  - little cleaning (add argument myThid in last position, cvs header ...)  
701   - move computation of surface related input fields to KPP into a new   - move computation of surface related input fields to KPP into a new
702     subroutine kpp_forcing_surf.F     subroutine kpp_forcing_surf.F
703     - remove wrong (within bi,bj loops) EXCH calls.
704     - little cleaning (add argument myThid in last position, cvs header ...)
705     - for now, fix conservation problem by exchanging KPPviscAz (may not
706       be the best fix)
707  o pkg/seaice  o pkg/seaice
708   - check for inconsistent evp parameter/cpp-flag combination   - check for inconsistent evp parameter/cpp-flag combination
709   - remove leftover errIO flat for obsolete name list error handling   - remove leftover errIO flat for obsolete name list error handling
710    o OpenAD
711     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
712    
713  checkpoint59a  checkpoint59a
714  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 31  o in FFIELDS.h: Line 728  o in FFIELDS.h:
728       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
729  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
730  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
731      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
732        are no longer updating the vertical diffusivity array
733        (passed as argument) but are (re-) setting those arrays.
734  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
735    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
736      cgrid-lsr and evp solver      cgrid-lsr and evp solver
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