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revision 1.859 by jmc, Fri Aug 17 20:51:27 2007 UTC revision 1.1065 by heimbach, Fri Feb 13 15:05:19 2009 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/autodiff, pkg/ctrl:
8      Add flag to reduce all tapelev I/O to single-prec.
9      In data.ctrl set
10        doSinglePrecTapelev = .TRUE.
11    o model/src/ini_curvilinear_grid.F: check in hack for SX8 compiler
12      to make sure that recip_dxV and recip_dyU are never zero, until we
13      have a proper exchange for them. Most compilers do not seem
14      to mind divisions by zero in the overlaps, as long as the results are
15      not used anywhere, but sxf90 does.
16    o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
17      real fresh water flux (not yet)
18    o pkg/mdsio & rw:
19     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
20     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
21    o pkg/flt:
22     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
23       init_fixed & ini_varia.
24     - clean-up & simplify linear interpolation S/R:
25       move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
26     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
27     - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
28     - add vert. coordinate & horiz. indices to output files.
29     - change vertical position in initial condition, from index to depth [m].
30     - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
31       (easier to get to a curvilinear grid) ; delX,delY no longer used.
32    o pkg/ggl90: a few modifications:
33     - fix bottom boundary condition, and interpolation of KappaE
34       near top and bottom
35     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
36     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
37     - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
38    o rename thetaMin,phiMin -> xgOrigin,ygOrigin
39      (maintain temporary backward compatibility, until next checkpoint)
40    
41    checkpoint61h
42    o pkg/diagnostics with "periodic averaging diagnostics":
43      fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
44    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
45    o pkg/obcs: fix loop ranges for balancing code
46    o pkg/flt:
47     - improve criteria for finding which tile owns a float.
48     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
49    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
50      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
51      with ocean biogeo)
52    o pkg/flt:
53     - do some cleaning and fix the restart ;
54     - add output.txt in flt_example/results to get this pkg tested.
55    o genmake2: add an EXTENDED_SRC option and flag.
56       for now, cannot be turned on on command line (only through genmake_local)
57    o pkg/mdsio: read/write vector:
58     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
59     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
60       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
61     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
62      (drop to 4 digits matching for grad). But this test does not look very
63      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
64    
65    checkpoint61g
66    o pkg/flt:
67      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
68       + make OPTIONS file more standard.
69      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
70      - fix _BYTESWAPIO CPP-Flag
71      - standard reading of file-parameter "data.flt"
72      - fix argument list of S/R FLT_RESTART
73      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
74    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
75    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
76      a still unfixed compiler/optimization bug
77    
78    checkpoint61f
79    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
80      update results of global_ocean.cs32x15.icedyn test.
81    o move getcon.F from model/src to pkg/fizhi.
82    o pkg/exf: add parameter for extrapolation of temp up to the surface
83       and option to prevent negative evap (in bulk_largeyeager04 only).
84    o Prather Advection scheme: fix tracer conservation for divergent flow
85      (e.g., when using NonLin Free-Surface).
86    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
87    o gmredi (Visbeck-variable-K):
88     - add more parameters to Visbeck-variable-K.
89     - use a 5 points average for dSigmaR in Visbeck-K calculation
90       (more "homogenous": same stencil and same weights as in dSigmaH)
91     - update output of ideal_2D_oce experiment.
92    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
93      (#undef REAL4_IS_SLOW)
94     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
95       coordinate variable
96     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
97       (surface forcing fields), removes some of the functionality
98     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
99     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
100       probably not all: copy _RS surface flux fields to RL field before
101       calling DIAGNOSTICS_FILL
102     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
103       real*4 (CALL EXCH_*_RS) versions.
104     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
105       (generate new output).
106    
107    checkpoint61e
108    o gmredi (Visbeck-variable-K):
109      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
110      - change computation of Visbeck-K where Slope > Smax :        
111        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
112        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
113    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
114      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
115    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
116    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
117      does not become too large (to avoid precision problems in implicit-diffusion
118      solver); update ideal_2D_oce output.
119    o pkg ggl90:
120      - in ggl90_cal.F: compute only one set of visc/diff, used to
121        step forward TKE/T/S/momentum
122      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
123        have Prandlt =1)
124    o gmredi (fm07):
125      - add lower limit on Transition layer thickness + lower limit on 1/lambda
126      - allow to set few more params from data.gmredi
127    o pkg ggl90:
128          - add missing sqrt(2) factor in computation of mixing length
129            scale in ggl90_calc.F
130            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
131    
132    checkpoint61d
133    o adjoint modifs
134      - adapt to new field rhoInSitu
135      - allow to revert from StoreDynVars2D, StoreDynVars3D
136        to individual fields
137        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
138    o store 3-D (in-situ) density in commom block (DYNVARS.h)
139     - save 1 rho computation.
140     - no longer modify T & S inland when using down_slope pkg.
141    o gad_som : allow to switch to SOM advection for T & S without corresponding
142      pickup files (using new S/R: MDS_CHECK4FILE).
143    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
144      (for useSingleCpuIO to work in multi-threaded)
145    o pkg/shelfice:
146     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
147       with SHELFICEtopoFile in data.shelfice
148     - move code for reading ice shelf topography and modifying hFacC into separate
149       subroutines of the shelfice package
150     - separate initialisation of "fixed" and "variable" variables
151     - kTopC is not (yet) replaced by kSurfC, although this is possible
152    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
153    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
154      and rename:
155      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
156      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
157    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
158    
159    checkpoint61c
160    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
161      to add mass source/sink of fluid in the interior (3-D generalisation
162      of oceanic real-fresh water flux).
163    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
164    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
165    o new pkg: down_slope
166      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
167      - presently, modify T & S inland (dwnslp_calc_rho.F).
168        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
169      - implementation for ocean in P-coords not tested.
170      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
171    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
172      (to facilitate conversion of oceanic pkg to p-coordinate).
173    o change FIND_RHO to FIND_RHO_2D :
174      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
175    o new pkg: cheapaml
176    
177    checkpoint61b
178    o exch2:
179      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
180      - no longer depend on the order sequence (N,S,E,W).
181      - 3rd exchange no longer needed (tested with 24 tiles).
182      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
183      - exch_UV_A-grid readily available (but not yet tested).
184      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
185      (both are no longer needed) in exch_uv: no effect in forward run; but
186       get truncation error differences with adjoint exch.
187    o exch2:
188     - change index-bounds storage (moved from target to local tile,
189       more intuitive this way) ; rename/remove some variables.
190     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
191    
192    checkpoint61a
193    o exch2/matlab-topology-generator:
194      fix bug in index bounds for N-S internal exchange (hard to tell if this
195      had any effect on the solution).
196    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
197      is exceeded
198    o testreport: modify syntax of awk, so that it works also with
199      awk, and not only with nawk and gawk
200    
201    checkpoint61
202    o autodiff
203      Change default for TAF usage by removing argument '-nonew_arg'
204      This changes TAF subroutine argument list (ordering of active var.)
205      Omission of this flag leads to incompatibility w.r.t. TAMC
206      To restore TAMC-compatibility, need following modifs:
207      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
208      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
209      Tested TAF version is 1.9.22
210      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
211    
212    checkpoint60
213    --->>> This is the last checkpoint for which generating the adjoint
214    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
215    --->>> by default.
216    --->>> Future checkpoints will ommit this flag by default.
217    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
218    o pkg/grdchk: Add gradient check to etan0 perturbations.
219    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
220    o pkg/autodiff: more flexibility in zeroadj.
221      model/src: modifying do_oceanic_phys.F accordingly.
222    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
223    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
224      special setup of gmredi for which the adjoint is stable
225      enough for parameter optimization.
226    o bridging the gap between eddy stress and GM.
227      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
228          along with a change in CPP option (now ALLOW_EDDYPSI).
229      -> when using GM w/ GM_AdvForm:
230          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
231          is applied either in the tracer Eq. or in momentum Eq.
232          depending on data.gmredi (intro. GM_InMomAsStress).
233      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
234      The key modifications are in model/src/taueddy_external_forcing.F
235      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
236    
237    checkpoint59r
238    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
239      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
240      fix option to read coriolis(@ cell-corner) from files with CS-grid.
241    o pkg/mnc: add some attributes to standard 1D-coordinate variables
242    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
243      mass points, when using mnc for output
244      - add runtime parameter (missing_value, missing_value_int) to override
245        default (which is the value of getcon('UNDEF'))
246    o pkg/mnc: prepare mnc for the actual use of missing values with the
247      diagnostics package: small fix in mnc_cw_readwrite.template and more
248      initialisation of never used fields
249      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
250      versions
251    o pkg/thsice/thsice_ini_vars.F added default initial values so that
252      thermodynamics sea ice solver does not blow up when some initial fields
253      are missing.
254    o move from external_forcing_surf.F to ini_forcing.F
255      the p-coord. hack consisting in using pLoad to set phi0surf ;
256      update output of tutorial_global_oce_in_p (affected @ truncation level).
257    o Freshen up a bit hs94.1x64x5, notably:
258      remove rotationPeriod and tRef=5*0. (adjoint only), and add
259      exactConserv=.TRUE.
260    o pkg/generic_advdiff:
261      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
262      applies to files where Temperature & Salinity 2nd Order moments are used.
263    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
264      this uses a dynamically allocated internal state data structure
265      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
266      and requires a fortran 90 compiler
267    
268    checkpoint59q
269    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
270       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
271    o Refresh tutorial_global_oce_biogeo, notably:
272      - change bathymetry (put back seamounts in ACC, use hFacs)
273      - change EOS (POLY3 --> JMD95Z)
274      - use Bryan-Lewis vertical diffusivity
275      - use multidimensional advection
276      - remove old virtual virtual in dic pkg, now done through ptracer pkg
277      - change a couple of parameters in dic pkg
278    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
279    o pkg/obcs: change default to OBCSfixTopo = .true.,
280      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
281      - replace "debugMode" with "debugLevel .GE. debLevB"
282    o implementation of TAF directives for gchem,cfc,dic
283    o remove "exp5" (replaced by tutorial_deep_convection).
284    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
285      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
286      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
287      --> changes results in exp4, seaice_obcs
288    o tutorial_deep_convection :
289      update the set-up and increase resolution and domain size ; start
290      from pseudo initial conditions = output at t=120mn in order to see
291      something happening when running testreport.
292    o pkg/seaice: add os7mp as an advection scheme
293                  add check for advection schemes
294                  add a flag for restoring T and S underneath sea ice
295    o pkg/my82: add netcdf-support and diagnostics
296    o thsice pkg:
297      - Now hsMax limits snow height by turning it into ice following
298        flooding scheme (and now conserving energy)
299      - Slight rewriting of the formula in thsice_calc_thick.F
300      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
301      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
302    
303    checkpoint59p
304    o gchem / dic / cfc :
305      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
306      - add new parameter files: "data.dic" & "data.cfc" ;
307      - various re-arrangement in initialisation & header file ;
308      - fix tutorial_global_oce_biogeo for multi-threaded test.
309    o pkg/dic: test for "pickup_dic" file when restarting ;
310      if no pickup-file, can restart with a re-initialised pH (same as it did
311      before) providing pickupStrictlyMatch is set to False.
312    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
313      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
314    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
315      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
316    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
317     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
318       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
319    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
320       scheme to use for vorticty-term ;
321     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
322       (with default selectVortScheme, return to original discretisation)
323     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
324    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
325    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
326      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
327      also fix diagnostics VISCAHW & VISCA4W.
328    
329    checkpoint59o
330    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
331    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
332      move a few statemens out the main loop into separate loops
333    o pkg/shelfice:
334      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
335        (kg/m^2/s), does not break tests, because in verification/isomip,
336        rhoConstFresh=rhoConst (by accident)
337      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
338      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
339        new file model/src/seawater.F, so that they are available for all pkgs.
340      - convert potential temperature into in-situ temperature. This changes the
341        isomip tests => update tests
342    o add a flag writePickupAtEnd (default=true) to be able to suppress
343      writing a pickup at the last timestep
344    o tools/mpack-1.6 :
345      - disable automake (not working) and autoconf (not needed).
346      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
347        also cleaner with much less compilation warnings.
348    o pkg/profiles:
349      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
350      (for "less than 32 characters name" compiler requirement)
351    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
352      conditions that have a different sampling frequency than S/T/U/V obcs
353    o pkg/diagnostics (stats-diags):
354      - fix global Min/Max in case 1 processor get only empty tiles
355    o genmake2: replace (4 times)
356         make genmake_tc_1.o >> genmake_warnings 2>&1
357      with
358         COMM="$CC $CFLAGS -c genmake_tc_1.c"
359         echo $COMM >> genmake_warnings
360         $COMM >> genmake_warnings 2>&1
361      to make genmake2 always see the value of CC as specified in the optfile.
362    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
363      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
364      - modify verification advect_cs test to test SOM-advection on CS-grid.
365    o pkg/ctrl:
366      - Rewrite of ctrl_map_ini_ecco.F,
367        introducing a generic routine (ctrl_map_ini_gen.F).
368      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
369    
370    checkpoint59n
371    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
372      number in dedicate array "hdiag":
373      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
374        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
375      - many small changes (integer format) for large number of diagnostics
376      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
377        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
378    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
379      usingSphericalGrid, this allows to define the rotated grid coordinates
380      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
381      geographical coordinates according to the inverse of the rotation defined
382      by the Euler angles, so that Coriolis parameter and online-interpolation by
383      exf works with the geographical coordinates on XC/YC/XG/YG.
384      Naturally, this feature does not work with all packages, so some
385      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
386      profiles), because there the coordinates are assumed to be regular
387      spherical grid coordinates.
388    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
389      - introduce isopycnal diffusion coefficient control.
390    o tools/adjoint_options:
391      - additional control vector components.
392    o pkg/mnc: have mnc create marginally meaning full coordinate variables
393      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
394    o pkg/mypackage:
395      - add example of read/write pickup for state-var ;
396      - add entry points to the main code for state-vars diags & write-pickup.
397    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
398      transitions for useExfYearlyFields
399      - add new subroutine that determines the file to read from for
400        use*YearlyFields = .TRUE. and .FALSE.
401      - add a verification experiment to global_with_exf that tests
402        useExfYearlyFields with USE_EXF_INTERPOLATION defined
403    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
404      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
405      subroutines (which could be generated from a template, because they are
406      almost identical), for now they are included in obcs_prescribe_read.F for
407      simplicity
408    o pkg/exf:
409      - add a little more diagnostic to exf_interp_read (in analogy to
410        mds_read_field, can be turned off with debugLevel < debugLevA=1)
411      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
412        ugly but fast by unrolling short inner loops, inserting a unroll=8
413        directive in routine lagran, and splitting a loop and making do while the
414        outermost loop (the latter requires the intoduction of index arrays)
415    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
416    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
417      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
418    o verification/seaice_obcs: updated for restart test and latest options
419    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
420      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
421      for now this is only available for the C-grid code and also within
422      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
423    
424    checkpoint59m
425    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
426      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
427    o gad_som : fix flux output (& diagnostics) to have same units as other  
428      advection scheme fluxes (was previously multiplied by deltaT).  
429    o added verification/seaice_obcs both to test seaice open boundaries
430      and to provide an example matlab scrpt for generating them
431    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
432    o pkg/salt_plume: clean up salt_plume_frac.F to
433      remove redundancy in PlumeMethod 1 and 4
434    o pkg/kpp: added saltplume diagnostics
435    o pkg/obcs and pkg/seaice:
436      - do not set uice and vice to zero when OB*icefile are unspecified
437      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
438      - moved seaice tracer obcs after call to seaice_growth
439    o pkg/salt_plume: added various options for salt plume depth
440      criterion and for vertical distribution of the salt
441    
442    checkpoint59l
443    o pkg/ptracers: new version of ptracers pickup:
444      read meta file and write only fields which are needed to restart.
445      ( same logic as main pickup file ; also using pickupStrictlyMatch )
446    o pkg/seaice:
447      - add timescale for melting due to warm mixed layer as a means of
448        setting SEAICE_availHeatFrac more conveniently
449      - add a CPP-flag/runtime parameter check for flooding algorithm
450      - reformulated availHeat in seaice_growth.F to be independent of AREA
451    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
452      unit changes
453    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
454    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
455      SX vector computer.
456    o pkg/seaice:
457      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
458        seaice forcing fields can now be read only through pkg/exf
459      - removed some unused halos
460    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
461    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
462      or U/VICE from U/VWIND before computing U/VSTRESS
463    
464    checkpoint59k
465    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
466      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
467    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
468      all experiments pass when compile with un-initialised var. checking option.
469    o added pkg/salt_plume
470    o script to test restart (for now, in MITgcm_contrib/jmc_script)
471    o pkg/seaice: new read/write pickup version.
472      read meta file and write only fields which are needed to restart.
473      ( same logic as main pickup file ; also using pickupStrictlyMatch )
474    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
475    o lab_sea.hb87: modify the domain & update output.hb87.txt :
476      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
477      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
478      process. Fixed here by closing the domain at the Northern boundary.
479    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
480    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
481      a set of consecutive levels in/from a 3-D array.
482    o pkg/ptracers:
483      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
484      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
485    
486    checkpoint59j
487    o in pkgs: dic, obcs, offline, rbcs:
488      standard way to compute coeff. for time interpolation between 2 time reccords
489      which retains full precision (& make results less dependent on compiler).
490      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
491    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
492      packages instead of reading ice cover and wind speed separately
493    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
494     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
495      to allow to compile customized code before the update)
496    o cleaning-up:
497      - fix CPP instruction syntax in pkg/obcs
498      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
499        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
500      - fix some threads issue in IO parts.
501    o pkg/dic:
502      - add tons of "_d 0" (--> much better testreports !)
503       and then update outputs of tutorial_global_oce_biogeo
504    o pkg/mom_fluxform:
505      add a special version of momentum advection intended to conserve momentum
506      next to a bathymetry step or a coastline edge. (default = off = #undef)
507    o new read/write pickup version:
508      - for now, only implemented for main (mdsio) pickup file.
509      - write out only what is needed to restart; merge pickup_nh , pickup_ph
510        and main pickup together.
511      - read meta file; read only what is needed to restart; stop if a field
512        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
513        if it make sense (even if the restart is not perfect).
514      - if no meta file, assume that pickup to read corresponds exactly to
515        a pickup that would currently be written.
516      - read pickup written in the old format (until checkpoint59i) if it
517        recognizes an old meta file (no field-list).
518      - add a meta file in exp. which starts from a pickup: 2 cases:
519        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
520         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
521        b) a meta file describing the content of the associated pickup file
522         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
523    o pkg/mdsio & pkg/rw:
524      - new routine to read a meta file ; new set of routine to read
525        Multiple-fields file (with meta file).
526    o added open boundary conditions capability for seaice
527        HSNOW, HSALT, UICE, and VICE
528    
529    checkpoint59i
530    o adjoint:
531      * fix multiDimAdvection adjoint
532        (partial recomputation problem by TAF for fVerT(:,:,kDown)
533        and comlev1 size definition (maxpass vs. max. number of tracers)
534      * verification/global_ocean.90x45x15 adjoint now tests
535        NLFS and multiDimAdvection using DST3 (=30)
536      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
537    o pkg/kpp: add "_d 0" to real constant (if missing);
538      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
539      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
540    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
541      for internal parameters related to restart process (formerly from PARAMS.h)
542      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
543    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
544      as argument. (only atm2d & obcs write_pickup have not yet been updated)
545    o pkg/monitor:
546      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
547      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
548      - account for deep Atmosphere factor and density factor (anelastic)
549    o added open boundary conditions capability for seaice HEFF and AREA
550    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
551      thermodynamics
552      - requires a little reorganization, which affects the testreport results
553        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
554        so that now the conservative form is tested
555      - add a few comments
556    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
557    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
558    o add new diagnostics to seaice: advective, diffusive fluxes (only for
559      multidim-advection, for scheme 2 they are not filled) and transports,
560      thermodynamic growth rates
561    o change units of EmPmR (inside the code, + within coupling interface)
562      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
563      Affects results @ truncation level (cg2d match) and update output of
564       experiments: lab_sea(6), global_ocean.90x40x15(10),
565      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
566      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
567      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
568      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
569    
570    checkpoint59h
571    o pkg/exf:
572      - improve vectorization by moving if-statement out of loops in
573        exf_mapfields, exf_radiation
574      - exf_bulkformulae.F: introduce 2D fields and vectorize code
575    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
576    o testreport:
577      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
578        monitor & update offline_exf_seaice exp. output.
579      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
580    o pkg/seaice:
581      - bug fix in the evp solver: boundary conditions were affected be
582        masking of zMax/zMin (changes results)
583      - minor bug fix in boundary conditions in seaice_calc_strainrates
584        (changes results for no_slip)
585      - seaice_lsr.F: make interpolation of eta dependent on boundaries
586      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
587      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
588        stress formulation and no-slip boundary conditions
589    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
590      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
591    o pkg/seaice: a first HSALT time stepping equation has been checked in
592    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
593      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
594      without requiring DO-IF statements
595    o pkg/thsice:
596      use continuous power-law function for partition of energy between lateral
597      melting/freezing and thinning/thickening ; old code using step function
598      still available with #undef THSICE_FRACEN_POWERLAW
599      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
600    o testreport: change AD testing : check against results/output_adm.txt
601      using same scripts as for forward test.
602    
603    checkpoint59g
604    o adjoint testing: in preparation for changing testreport:
605      - output format: cost and grad written on separated lines
606      - ad output results in directory "results" (instead of "results_ad")
607    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
608    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
609    o pkg/ecco: allow user defined cost function contributions
610    o testreport:
611      Allow to choose (per experiment) the list of tested output variables
612       and the main variable (used to issue a pass/FAIL ) ;
613      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
614      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
615      Also modify printing of summary:
616       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
617       b) echo the list of tested variables in the individual summary.txt of
618          each experiment.
619    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
620      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
621      (but still depend on the tile decompostion of the domain).
622    o pkg/seaice: change a discretization detail to make the B-grid code
623      "more symmetric". This change is likely to remove all "ridges/leads" that
624      where quasi-aligned with the grid in B-grid solutions. It may also be
625      the solution to the stress coupling issues with the B-grid.
626    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
627      remove .cvsignore from input dir. (since testreport no longer run here).
628    o pkg/thsice:
629     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
630     - fix reshaping of sea-ice just after advection:
631       melt all the ice only if ice-volume is too small.
632     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
633       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
634     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
635    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
636      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
637    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
638      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
639      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
640      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
641      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
642      -> update output.txt
643    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
644     this affects truncation error: -> update output.txt of exp:
645      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
646      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
647    
648    checkpoint59f
649    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
650    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
651      a bounded range (in forward mode)
652    o pkg/ecco, ctrl, autodiff and mom_common:
653     internal parameter controls, completements of implementations
654  o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.  o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
655    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
656      (not seem any difference in testing results).
657  o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains  o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
658     at face corners.     at face corners.
659  o pkg/generic_advdiff:  o pkg/generic_advdiff:
# Line 225  o in FFIELDS.h: Line 874  o in FFIELDS.h:
874       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
875  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
876  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
877      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
878        are no longer updating the vertical diffusivity array
879        (passed as argument) but are (re-) setting those arrays.
880  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
881    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
882      cgrid-lsr and evp solver      cgrid-lsr and evp solver

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