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revision 1.728 by jmc, Fri Oct 6 19:39:03 2006 UTC revision 1.1074 by mlosch, Tue Mar 3 10:01:40 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/mnc: fix the coordinate variables for multi-tile curvi-linear grids
8      that are not cubed-sphere grids
9    o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
10    o pkg/ctrl:
11      fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
12    o non-hydrostatic (calc_gw.F):
13      fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
14      update output of exp. global_ocean.cs32x15.viscA4
15    o remove backward compatibility for thetaMin,phiMin
16      (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
17    o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
18      interpolated wind field not only for curvilineargrid=.true., but also
19      for a rotated grid (rotateGrid=.true.)
20    o pkg/exf: add capability to bypass interpolation for runoff
21      by setting yet another CPP-flag
22    o eesupp/src, B-grid exchange:
23      add simple (6 tiles, non MPI) CS exch + standard interface S/R.
24    o autodiff
25      new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
26      allows to switch to single-prec common blocks;
27      corresponding switch occurs in tamc.h, integer isbyte
28      TAF store directivs "byte" and "kind" seem equivalent;
29      Most tamc.h have been updated correspondingly.
30    
31    checkpoint61i
32    o autodiff:
33      fix autodiff_sore/_restore indices for obcs
34      (spotted by I. Hoteit, M. Mazloff)
35    o pkg/autodiff, pkg/ctrl:
36      Add flag to reduce all tapelev I/O to single-prec.
37      In data.ctrl set
38        doSinglePrecTapelev = .TRUE.
39    o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
40      check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
41    o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
42      real fresh water flux (not yet)
43    o pkg/mdsio & rw:
44     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
45     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
46    o pkg/flt:
47     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
48       init_fixed & ini_varia.
49     - clean-up & simplify linear interpolation S/R:
50       move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
51     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
52     - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
53     - add vert. coordinate & horiz. indices to output files.
54     - change vertical position in initial condition, from index to depth [m].
55     - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
56       (easier to get to a curvilinear grid) ; delX,delY no longer used.
57    o pkg/ggl90: a few modifications:
58     - fix bottom boundary condition, and interpolation of KappaE
59       near top and bottom
60     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
61     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
62     - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
63    o rename thetaMin,phiMin -> xgOrigin,ygOrigin
64      (maintain temporary backward compatibility, until next checkpoint)
65    
66    checkpoint61h
67    o pkg/diagnostics with "periodic averaging diagnostics":
68      fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
69    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
70    o pkg/obcs: fix loop ranges for balancing code
71    o pkg/flt:
72     - improve criteria for finding which tile owns a float.
73     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
74    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
75      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
76      with ocean biogeo)
77    o pkg/flt:
78     - do some cleaning and fix the restart ;
79     - add output.txt in flt_example/results to get this pkg tested.
80    o genmake2: add an EXTENDED_SRC option and flag.
81       for now, cannot be turned on on command line (only through genmake_local)
82    o pkg/mdsio: read/write vector:
83     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
84     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
85       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
86     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
87      (drop to 4 digits matching for grad). But this test does not look very
88      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
89    
90    checkpoint61g
91    o pkg/flt:
92      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
93       + make OPTIONS file more standard.
94      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
95      - fix _BYTESWAPIO CPP-Flag
96      - standard reading of file-parameter "data.flt"
97      - fix argument list of S/R FLT_RESTART
98      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
99    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
100    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
101      a still unfixed compiler/optimization bug
102    
103    checkpoint61f
104    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
105      update results of global_ocean.cs32x15.icedyn test.
106    o move getcon.F from model/src to pkg/fizhi.
107    o pkg/exf: add parameter for extrapolation of temp up to the surface
108       and option to prevent negative evap (in bulk_largeyeager04 only).
109    o Prather Advection scheme: fix tracer conservation for divergent flow
110      (e.g., when using NonLin Free-Surface).
111    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
112    o gmredi (Visbeck-variable-K):
113     - add more parameters to Visbeck-variable-K.
114     - use a 5 points average for dSigmaR in Visbeck-K calculation
115       (more "homogenous": same stencil and same weights as in dSigmaH)
116     - update output of ideal_2D_oce experiment.
117    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
118      (#undef REAL4_IS_SLOW)
119     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
120       coordinate variable
121     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
122       (surface forcing fields), removes some of the functionality
123     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
124     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
125       probably not all: copy _RS surface flux fields to RL field before
126       calling DIAGNOSTICS_FILL
127     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
128       real*4 (CALL EXCH_*_RS) versions.
129     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
130       (generate new output).
131    
132    checkpoint61e
133    o gmredi (Visbeck-variable-K):
134      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
135      - change computation of Visbeck-K where Slope > Smax :        
136        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
137        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
138    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
139      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
140    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
141    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
142      does not become too large (to avoid precision problems in implicit-diffusion
143      solver); update ideal_2D_oce output.
144    o pkg ggl90:
145      - in ggl90_cal.F: compute only one set of visc/diff, used to
146        step forward TKE/T/S/momentum
147      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
148        have Prandlt =1)
149    o gmredi (fm07):
150      - add lower limit on Transition layer thickness + lower limit on 1/lambda
151      - allow to set few more params from data.gmredi
152    o pkg ggl90:
153          - add missing sqrt(2) factor in computation of mixing length
154            scale in ggl90_calc.F
155            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
156    
157    checkpoint61d
158    o adjoint modifs
159      - adapt to new field rhoInSitu
160      - allow to revert from StoreDynVars2D, StoreDynVars3D
161        to individual fields
162        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
163    o store 3-D (in-situ) density in commom block (DYNVARS.h)
164     - save 1 rho computation.
165     - no longer modify T & S inland when using down_slope pkg.
166    o gad_som : allow to switch to SOM advection for T & S without corresponding
167      pickup files (using new S/R: MDS_CHECK4FILE).
168    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
169      (for useSingleCpuIO to work in multi-threaded)
170    o pkg/shelfice:
171     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
172       with SHELFICEtopoFile in data.shelfice
173     - move code for reading ice shelf topography and modifying hFacC into separate
174       subroutines of the shelfice package
175     - separate initialisation of "fixed" and "variable" variables
176     - kTopC is not (yet) replaced by kSurfC, although this is possible
177    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
178    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
179      and rename:
180      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
181      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
182    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
183    
184    checkpoint61c
185    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
186      to add mass source/sink of fluid in the interior (3-D generalisation
187      of oceanic real-fresh water flux).
188    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
189    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
190    o new pkg: down_slope
191      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
192      - presently, modify T & S inland (dwnslp_calc_rho.F).
193        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
194      - implementation for ocean in P-coords not tested.
195      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
196    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
197      (to facilitate conversion of oceanic pkg to p-coordinate).
198    o change FIND_RHO to FIND_RHO_2D :
199      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
200    o new pkg: cheapaml
201    
202    checkpoint61b
203    o exch2:
204      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
205      - no longer depend on the order sequence (N,S,E,W).
206      - 3rd exchange no longer needed (tested with 24 tiles).
207      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
208      - exch_UV_A-grid readily available (but not yet tested).
209      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
210      (both are no longer needed) in exch_uv: no effect in forward run; but
211       get truncation error differences with adjoint exch.
212    o exch2:
213     - change index-bounds storage (moved from target to local tile,
214       more intuitive this way) ; rename/remove some variables.
215     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
216    
217    checkpoint61a
218    o exch2/matlab-topology-generator:
219      fix bug in index bounds for N-S internal exchange (hard to tell if this
220      had any effect on the solution).
221    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
222      is exceeded
223    o testreport: modify syntax of awk, so that it works also with
224      awk, and not only with nawk and gawk
225    
226    checkpoint61
227    o autodiff
228      Change default for TAF usage by removing argument '-nonew_arg'
229      This changes TAF subroutine argument list (ordering of active var.)
230      Omission of this flag leads to incompatibility w.r.t. TAMC
231      To restore TAMC-compatibility, need following modifs:
232      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
233      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
234      Tested TAF version is 1.9.22
235      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
236    
237    checkpoint60
238    --->>> This is the last checkpoint for which generating the adjoint
239    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
240    --->>> by default.
241    --->>> Future checkpoints will ommit this flag by default.
242    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
243    o pkg/grdchk: Add gradient check to etan0 perturbations.
244    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
245    o pkg/autodiff: more flexibility in zeroadj.
246      model/src: modifying do_oceanic_phys.F accordingly.
247    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
248    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
249      special setup of gmredi for which the adjoint is stable
250      enough for parameter optimization.
251    o bridging the gap between eddy stress and GM.
252      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
253          along with a change in CPP option (now ALLOW_EDDYPSI).
254      -> when using GM w/ GM_AdvForm:
255          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
256          is applied either in the tracer Eq. or in momentum Eq.
257          depending on data.gmredi (intro. GM_InMomAsStress).
258      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
259      The key modifications are in model/src/taueddy_external_forcing.F
260      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
261    
262    checkpoint59r
263    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
264      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
265      fix option to read coriolis(@ cell-corner) from files with CS-grid.
266    o pkg/mnc: add some attributes to standard 1D-coordinate variables
267    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
268      mass points, when using mnc for output
269      - add runtime parameter (missing_value, missing_value_int) to override
270        default (which is the value of getcon('UNDEF'))
271    o pkg/mnc: prepare mnc for the actual use of missing values with the
272      diagnostics package: small fix in mnc_cw_readwrite.template and more
273      initialisation of never used fields
274      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
275      versions
276    o pkg/thsice/thsice_ini_vars.F added default initial values so that
277      thermodynamics sea ice solver does not blow up when some initial fields
278      are missing.
279    o move from external_forcing_surf.F to ini_forcing.F
280      the p-coord. hack consisting in using pLoad to set phi0surf ;
281      update output of tutorial_global_oce_in_p (affected @ truncation level).
282    o Freshen up a bit hs94.1x64x5, notably:
283      remove rotationPeriod and tRef=5*0. (adjoint only), and add
284      exactConserv=.TRUE.
285    o pkg/generic_advdiff:
286      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
287      applies to files where Temperature & Salinity 2nd Order moments are used.
288    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
289      this uses a dynamically allocated internal state data structure
290      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
291      and requires a fortran 90 compiler
292    
293    checkpoint59q
294    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
295       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
296    o Refresh tutorial_global_oce_biogeo, notably:
297      - change bathymetry (put back seamounts in ACC, use hFacs)
298      - change EOS (POLY3 --> JMD95Z)
299      - use Bryan-Lewis vertical diffusivity
300      - use multidimensional advection
301      - remove old virtual virtual in dic pkg, now done through ptracer pkg
302      - change a couple of parameters in dic pkg
303    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
304    o pkg/obcs: change default to OBCSfixTopo = .true.,
305      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
306      - replace "debugMode" with "debugLevel .GE. debLevB"
307    o implementation of TAF directives for gchem,cfc,dic
308    o remove "exp5" (replaced by tutorial_deep_convection).
309    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
310      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
311      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
312      --> changes results in exp4, seaice_obcs
313    o tutorial_deep_convection :
314      update the set-up and increase resolution and domain size ; start
315      from pseudo initial conditions = output at t=120mn in order to see
316      something happening when running testreport.
317    o pkg/seaice: add os7mp as an advection scheme
318                  add check for advection schemes
319                  add a flag for restoring T and S underneath sea ice
320    o pkg/my82: add netcdf-support and diagnostics
321    o thsice pkg:
322      - Now hsMax limits snow height by turning it into ice following
323        flooding scheme (and now conserving energy)
324      - Slight rewriting of the formula in thsice_calc_thick.F
325      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
326      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
327    
328    checkpoint59p
329    o gchem / dic / cfc :
330      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
331      - add new parameter files: "data.dic" & "data.cfc" ;
332      - various re-arrangement in initialisation & header file ;
333      - fix tutorial_global_oce_biogeo for multi-threaded test.
334    o pkg/dic: test for "pickup_dic" file when restarting ;
335      if no pickup-file, can restart with a re-initialised pH (same as it did
336      before) providing pickupStrictlyMatch is set to False.
337    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
338      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
339    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
340      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
341    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
342     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
343       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
344    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
345       scheme to use for vorticty-term ;
346     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
347       (with default selectVortScheme, return to original discretisation)
348     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
349    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
350    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
351      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
352      also fix diagnostics VISCAHW & VISCA4W.
353    
354    checkpoint59o
355    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
356    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
357      move a few statemens out the main loop into separate loops
358    o pkg/shelfice:
359      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
360        (kg/m^2/s), does not break tests, because in verification/isomip,
361        rhoConstFresh=rhoConst (by accident)
362      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
363      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
364        new file model/src/seawater.F, so that they are available for all pkgs.
365      - convert potential temperature into in-situ temperature. This changes the
366        isomip tests => update tests
367    o add a flag writePickupAtEnd (default=true) to be able to suppress
368      writing a pickup at the last timestep
369    o tools/mpack-1.6 :
370      - disable automake (not working) and autoconf (not needed).
371      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
372        also cleaner with much less compilation warnings.
373    o pkg/profiles:
374      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
375      (for "less than 32 characters name" compiler requirement)
376    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
377      conditions that have a different sampling frequency than S/T/U/V obcs
378    o pkg/diagnostics (stats-diags):
379      - fix global Min/Max in case 1 processor get only empty tiles
380    o genmake2: replace (4 times)
381         make genmake_tc_1.o >> genmake_warnings 2>&1
382      with
383         COMM="$CC $CFLAGS -c genmake_tc_1.c"
384         echo $COMM >> genmake_warnings
385         $COMM >> genmake_warnings 2>&1
386      to make genmake2 always see the value of CC as specified in the optfile.
387    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
388      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
389      - modify verification advect_cs test to test SOM-advection on CS-grid.
390    o pkg/ctrl:
391      - Rewrite of ctrl_map_ini_ecco.F,
392        introducing a generic routine (ctrl_map_ini_gen.F).
393      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
394    
395    checkpoint59n
396    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
397      number in dedicate array "hdiag":
398      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
399        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
400      - many small changes (integer format) for large number of diagnostics
401      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
402        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
403    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
404      usingSphericalGrid, this allows to define the rotated grid coordinates
405      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
406      geographical coordinates according to the inverse of the rotation defined
407      by the Euler angles, so that Coriolis parameter and online-interpolation by
408      exf works with the geographical coordinates on XC/YC/XG/YG.
409      Naturally, this feature does not work with all packages, so some
410      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
411      profiles), because there the coordinates are assumed to be regular
412      spherical grid coordinates.
413    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
414      - introduce isopycnal diffusion coefficient control.
415    o tools/adjoint_options:
416      - additional control vector components.
417    o pkg/mnc: have mnc create marginally meaning full coordinate variables
418      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
419    o pkg/mypackage:
420      - add example of read/write pickup for state-var ;
421      - add entry points to the main code for state-vars diags & write-pickup.
422    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
423      transitions for useExfYearlyFields
424      - add new subroutine that determines the file to read from for
425        use*YearlyFields = .TRUE. and .FALSE.
426      - add a verification experiment to global_with_exf that tests
427        useExfYearlyFields with USE_EXF_INTERPOLATION defined
428    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
429      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
430      subroutines (which could be generated from a template, because they are
431      almost identical), for now they are included in obcs_prescribe_read.F for
432      simplicity
433    o pkg/exf:
434      - add a little more diagnostic to exf_interp_read (in analogy to
435        mds_read_field, can be turned off with debugLevel < debugLevA=1)
436      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
437        ugly but fast by unrolling short inner loops, inserting a unroll=8
438        directive in routine lagran, and splitting a loop and making do while the
439        outermost loop (the latter requires the intoduction of index arrays)
440    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
441    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
442      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
443    o verification/seaice_obcs: updated for restart test and latest options
444    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
445      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
446      for now this is only available for the C-grid code and also within
447      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
448    
449    checkpoint59m
450    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
451      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
452    o gad_som : fix flux output (& diagnostics) to have same units as other  
453      advection scheme fluxes (was previously multiplied by deltaT).  
454    o added verification/seaice_obcs both to test seaice open boundaries
455      and to provide an example matlab scrpt for generating them
456    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
457    o pkg/salt_plume: clean up salt_plume_frac.F to
458      remove redundancy in PlumeMethod 1 and 4
459    o pkg/kpp: added saltplume diagnostics
460    o pkg/obcs and pkg/seaice:
461      - do not set uice and vice to zero when OB*icefile are unspecified
462      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
463      - moved seaice tracer obcs after call to seaice_growth
464    o pkg/salt_plume: added various options for salt plume depth
465      criterion and for vertical distribution of the salt
466    
467    checkpoint59l
468    o pkg/ptracers: new version of ptracers pickup:
469      read meta file and write only fields which are needed to restart.
470      ( same logic as main pickup file ; also using pickupStrictlyMatch )
471    o pkg/seaice:
472      - add timescale for melting due to warm mixed layer as a means of
473        setting SEAICE_availHeatFrac more conveniently
474      - add a CPP-flag/runtime parameter check for flooding algorithm
475      - reformulated availHeat in seaice_growth.F to be independent of AREA
476    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
477      unit changes
478    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
479    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
480      SX vector computer.
481    o pkg/seaice:
482      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
483        seaice forcing fields can now be read only through pkg/exf
484      - removed some unused halos
485    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
486    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
487      or U/VICE from U/VWIND before computing U/VSTRESS
488    
489    checkpoint59k
490    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
491      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
492    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
493      all experiments pass when compile with un-initialised var. checking option.
494    o added pkg/salt_plume
495    o script to test restart (for now, in MITgcm_contrib/jmc_script)
496    o pkg/seaice: new read/write pickup version.
497      read meta file and write only fields which are needed to restart.
498      ( same logic as main pickup file ; also using pickupStrictlyMatch )
499    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
500    o lab_sea.hb87: modify the domain & update output.hb87.txt :
501      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
502      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
503      process. Fixed here by closing the domain at the Northern boundary.
504    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
505    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
506      a set of consecutive levels in/from a 3-D array.
507    o pkg/ptracers:
508      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
509      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
510    
511    checkpoint59j
512    o in pkgs: dic, obcs, offline, rbcs:
513      standard way to compute coeff. for time interpolation between 2 time reccords
514      which retains full precision (& make results less dependent on compiler).
515      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
516    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
517      packages instead of reading ice cover and wind speed separately
518    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
519     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
520      to allow to compile customized code before the update)
521    o cleaning-up:
522      - fix CPP instruction syntax in pkg/obcs
523      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
524        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
525      - fix some threads issue in IO parts.
526    o pkg/dic:
527      - add tons of "_d 0" (--> much better testreports !)
528       and then update outputs of tutorial_global_oce_biogeo
529    o pkg/mom_fluxform:
530      add a special version of momentum advection intended to conserve momentum
531      next to a bathymetry step or a coastline edge. (default = off = #undef)
532    o new read/write pickup version:
533      - for now, only implemented for main (mdsio) pickup file.
534      - write out only what is needed to restart; merge pickup_nh , pickup_ph
535        and main pickup together.
536      - read meta file; read only what is needed to restart; stop if a field
537        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
538        if it make sense (even if the restart is not perfect).
539      - if no meta file, assume that pickup to read corresponds exactly to
540        a pickup that would currently be written.
541      - read pickup written in the old format (until checkpoint59i) if it
542        recognizes an old meta file (no field-list).
543      - add a meta file in exp. which starts from a pickup: 2 cases:
544        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
545         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
546        b) a meta file describing the content of the associated pickup file
547         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
548    o pkg/mdsio & pkg/rw:
549      - new routine to read a meta file ; new set of routine to read
550        Multiple-fields file (with meta file).
551    o added open boundary conditions capability for seaice
552        HSNOW, HSALT, UICE, and VICE
553    
554    checkpoint59i
555    o adjoint:
556      * fix multiDimAdvection adjoint
557        (partial recomputation problem by TAF for fVerT(:,:,kDown)
558        and comlev1 size definition (maxpass vs. max. number of tracers)
559      * verification/global_ocean.90x45x15 adjoint now tests
560        NLFS and multiDimAdvection using DST3 (=30)
561      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
562    o pkg/kpp: add "_d 0" to real constant (if missing);
563      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
564      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
565    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
566      for internal parameters related to restart process (formerly from PARAMS.h)
567      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
568    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
569      as argument. (only atm2d & obcs write_pickup have not yet been updated)
570    o pkg/monitor:
571      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
572      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
573      - account for deep Atmosphere factor and density factor (anelastic)
574    o added open boundary conditions capability for seaice HEFF and AREA
575    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
576      thermodynamics
577      - requires a little reorganization, which affects the testreport results
578        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
579        so that now the conservative form is tested
580      - add a few comments
581    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
582    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
583    o add new diagnostics to seaice: advective, diffusive fluxes (only for
584      multidim-advection, for scheme 2 they are not filled) and transports,
585      thermodynamic growth rates
586    o change units of EmPmR (inside the code, + within coupling interface)
587      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
588      Affects results @ truncation level (cg2d match) and update output of
589       experiments: lab_sea(6), global_ocean.90x40x15(10),
590      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
591      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
592      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
593      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
594    
595    checkpoint59h
596    o pkg/exf:
597      - improve vectorization by moving if-statement out of loops in
598        exf_mapfields, exf_radiation
599      - exf_bulkformulae.F: introduce 2D fields and vectorize code
600    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
601    o testreport:
602      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
603        monitor & update offline_exf_seaice exp. output.
604      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
605    o pkg/seaice:
606      - bug fix in the evp solver: boundary conditions were affected be
607        masking of zMax/zMin (changes results)
608      - minor bug fix in boundary conditions in seaice_calc_strainrates
609        (changes results for no_slip)
610      - seaice_lsr.F: make interpolation of eta dependent on boundaries
611      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
612      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
613        stress formulation and no-slip boundary conditions
614    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
615      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
616    o pkg/seaice: a first HSALT time stepping equation has been checked in
617    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
618      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
619      without requiring DO-IF statements
620    o pkg/thsice:
621      use continuous power-law function for partition of energy between lateral
622      melting/freezing and thinning/thickening ; old code using step function
623      still available with #undef THSICE_FRACEN_POWERLAW
624      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
625    o testreport: change AD testing : check against results/output_adm.txt
626      using same scripts as for forward test.
627    
628    checkpoint59g
629    o adjoint testing: in preparation for changing testreport:
630      - output format: cost and grad written on separated lines
631      - ad output results in directory "results" (instead of "results_ad")
632    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
633    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
634    o pkg/ecco: allow user defined cost function contributions
635    o testreport:
636      Allow to choose (per experiment) the list of tested output variables
637       and the main variable (used to issue a pass/FAIL ) ;
638      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
639      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
640      Also modify printing of summary:
641       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
642       b) echo the list of tested variables in the individual summary.txt of
643          each experiment.
644    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
645      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
646      (but still depend on the tile decompostion of the domain).
647    o pkg/seaice: change a discretization detail to make the B-grid code
648      "more symmetric". This change is likely to remove all "ridges/leads" that
649      where quasi-aligned with the grid in B-grid solutions. It may also be
650      the solution to the stress coupling issues with the B-grid.
651    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
652      remove .cvsignore from input dir. (since testreport no longer run here).
653    o pkg/thsice:
654     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
655     - fix reshaping of sea-ice just after advection:
656       melt all the ice only if ice-volume is too small.
657     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
658       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
659     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
660    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
661      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
662    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
663      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
664      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
665      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
666      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
667      -> update output.txt
668    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
669     this affects truncation error: -> update output.txt of exp:
670      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
671      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
672    
673    checkpoint59f
674    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
675    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
676      a bounded range (in forward mode)
677    o pkg/ecco, ctrl, autodiff and mom_common:
678     internal parameter controls, completements of implementations
679    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
680    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
681      (not seem any difference in testing results).
682    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
683       at face corners.
684    o pkg/generic_advdiff:
685     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
686      loop range indices for computing vertical advection tendency
687      and do the calculation in the interior only (no overlap) ;
688      for now, only implemented for SOM advection (to save CPU time).
689     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
690    o exch2 adjoint
691      First set of changes:
692      - add exch2 hand-written adjoint templates
693      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
694        This will require cleanup in pkg/autodiff/*.F
695        (changed routines currently kept separate in verif. code/)
696      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
697        that used to hide exch2 or cubed-sphere specific code
698        (commented via 'cph-exch2')
699    o pkg/seaice
700      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
701    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
702       output of global_ocean.cs32x15.thsice .
703    
704    checkpoint59e
705    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
706      for B-grid vector (not yet tested) and C-grid vector (<- only used
707      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
708    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
709      (#ifdef ALLOW_SALT_PLUME)
710    o gather_2d/scatter_2d: removed halo regions
711    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
712      scheme and the corresponding test case (under front_relax dir). For now,
713      only available with Skew-flux form and not yet tested in realistic set-up.
714      adjoint: store directives updated, but gradient checks deteriorated,
715      so maybe GM/Redi adjoint is now broken.
716    o seaice adjoint
717      * add AREA, HEFF, HSNOW as control variable
718        (should not change lab_sea results)
719      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
720    o pkg/seaice:
721      * added computation of saltFlux in seaice_growth;
722        For time being, sea ice salinity is assumed constant
723        contribution of snow flooding to freshening of sea ice is neglected.
724        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
725        defaults to 0.0 in order to maintain backward compatibility.
726        Typical values for SEAICE_salinity are 4 to 10 g/kg.
727      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
728      * added SEAICE_availHeatFrac, which specifies fraction of surface level
729        heat content used to melt or grow ice
730      * commented out cap of HICE: it helps keep ice thinner
731      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
732      * applied OBCS T/S mask to HEFFM sea ice mask
733    
734    checkpoint59d
735    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
736     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
737     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
738    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
739     and change default value of parameter "GM_Small_Number";
740     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
741       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
742       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
743    o pkg/ecco: cost function when applying pkg/smooth to controls
744    o pkg/ctrl: add forcingPrecond run time parameter
745    o pkg/seaice:
746     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
747     - fix bug in metric terms of u-equation in LSR solver (implicit part),
748       changes verification/lab_sea
749     - rearrange implicit part of u-equation in LSR solver to make it easier to
750       read, understand, and debug. This causes changes at the truncation level.
751     - fix (serious) bug in the boundary conditions (sign error in the implicit
752       part) of the LSR solver. Changes all LSR results.
753     - fixed problem with HSNOW initialization to avoid thick snow when AREA
754       is initilized with small values - does not change lab_sea results.
755     - added HsnowFile initialization capability
756    o pkg/smooth: addition to model/src and pkg/ctrl so allow
757     initialization of pkg/smooth and application to control vector
758    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
759    o dependencies: pkg/profiles requires pkg/cal
760    o pkg/profiles:
761     - added option ALLOW_PROFILES_GENERICGRID
762         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
763         that interpolation information (grid points and coefficients) is provided
764         within the netcdf input files.
765         -> sample matlab scripts can be found in MITgcm_contrib/gael
766         that allow you to prepare netcdf input files.
767     - also modified: cleaner include statements, cleaner error print statements,
768       cleaner stops when error, and more tests of the netcdf input files consistency.
769    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
770    o pkg/seaice:
771     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
772       requires a new routine: seaice_diagnostics_fill.F
773     - make sure that seaice does not move if not forced (pressure replacement
774       method, Hibler and Ip, 1995), changes results
775     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
776     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
777       It is turned off by default (=-1.), because it changes the results.
778     - make it possible to read AREA from a file, too.
779    
780    checkpoint59c
781    o add S/R and diagnostics for oceanic mixed-layer depth
782    o move GMRedi call after all vertical mixing schemes (including KPP)
783    o pkg/thsice:
784     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
785      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
786    o pkg/obcs:
787     - bug fix for balance code
788    o pkg/seaice:
789      - allow values of SEAICE_elasticParm > 1
790      - add new parameter SEAICE_evpTauRelax as an alternative
791        to SEAICE_elasticParm
792      - make lsr boundary conditions free slip (by default), changes result
793      - add code for no slip boundary conditions for lsr
794      - set minimum of zeta to zero (and not 4e8) (changes results)
795      - add a cap on AREA after advecting AREA if seaice_growth is not called
796    o change calculation of Visbeck K:
797      - no longer depend on tapering scheme; instead, compute slope (limited
798        by GM_maxSlope). this is equivalent to what was comuted before with
799        clipping or linear tappering.
800      - fix vertical averaging (wrong by 1/2 level)
801      - leave the old version (but will not be maintained) within
802        #ifdef OLD_VISBECK_CALC / #endif
803      - update output of exp. ideal_2D_oce
804    o change error catch in calc_r_star to improve vectorization
805    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
806      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
807    o adjoint:
808      Re-organized adjoint checkpointing according to Matt Mazloff
809      (but with modifs/completions/cleanups)
810      Storing is now bundled into large arrays to optimized I/O
811      (and second step in cleanup of the_main_loop)
812    
813    checkpoint59b
814    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
815      - export/import (between ocean & coupler) fields needed for ocean DIC.
816    o pkg/seaice:
817      - get rid of three more exchanges seaice_calc_viscosities (required
818        different loop boundaries in seaice_lsr and seaice_ocean_stress)
819      - bug fix in seaice_ocean_stress (update of lab_sea required)
820      - reduce loop boundaries to necessary minimum also in seaice_evp
821      - go back to the old way of computing deltaC/Z as the adjoint likes that
822        better
823    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
824      passive tracer to an Age Tracer) + update output.txt
825    o pkg/exf:
826      - implement A-grid / C-grid selection for wind-stress input files.
827      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
828      for now, in exf_bulk_largeyeager04.F only :
829      - change implementation for case where windspeed + 2. components wind-stress
830        are read-in. AND use rhoConstFresh to convert evap.
831    o pkg/seaice:
832      - use correct EXCH_UV for wind-forcing (on A-grid).
833      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
834        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
835    o pkg/exf:
836      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
837      EXF_INTERPOLATION:
838      - merge global_with_exf/code version of exf_interp_read.F
839        to the main code ;
840      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
841        reading the file ; Important: This options needs to be defined to recover
842        previous code.
843        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
844      - no longer loose real*8 precision along the way when using exf_iprec=64.
845    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
846      - change discretisation of evp-solver in order to avoid another exchange
847        (changes lab_sea) and clean up a little
848      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
849        help the adjoint (this also changes the results slightly)
850      - add a few "_d 0" where they had been missing in seaice_evp.F
851      - cleaning up: remove unused seaice_calc_rhs.F
852    o pkg/exf: some cleaning-up:
853      - change various "constants" into runtime parameters
854      - cleaned-up Large&Yeager04 routine which should eventually
855        replace exf_bulkformulae.F (changed names of S/R and CPP)
856        and merged various ALLOW_ATM_WIND options
857     only used with thsice pkg (in thsice_get_exf.F):
858      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
859        which are used when useStabilityFct_overIce=TRUE (= the default)
860      - change default values of ice & snow emissivity and scale downward LW
861        by ice & snow emissivity.
862    o pkg/thsice:
863     fix few little problems, in thsice_calc_thickn.F:
864      - growth vertically (and not laterally) if iceFrac == iceMaskMax
865      - melt only laterally if hIce < hThinIce (as the comments say)
866      and in thsice_extend.F:
867      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
868      - start to form ice as soon as the minimum ice-volume is reachable.
869     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
870      and cpl_aim+ocn
871    o pkg/kpp
872     - move computation of surface related input fields to KPP into a new
873       subroutine kpp_forcing_surf.F
874     - remove wrong (within bi,bj loops) EXCH calls.
875     - little cleaning (add argument myThid in last position, cvs header ...)
876     - for now, fix conservation problem by exchanging KPPviscAz (may not
877       be the best fix)
878    o pkg/seaice
879     - check for inconsistent evp parameter/cpp-flag combination
880     - remove leftover errIO flat for obsolete name list error handling
881    o OpenAD
882     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
883    
884    checkpoint59a
885    o pkg/seaice: some parameter clarifications and a little bit of clean up
886    o pkg/thsice: rename run-time parameters:
887       himin       -> hIceMin
888       himin0      -> hThinIce
889       hihig       -> hThickIce
890       i0          -> i0swFrac
891       transCoef   -> bMeltCoef
892       frac_energy -> fracMelting
893      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
894       with default values (for now) that do not change the results.
895      remove old version of thsice vars advection in pkg/seaice.
896    o in FFIELDS.h:
897      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
898      - make pLoad & sIceLoad always available (but still only used if
899         ATMOSPHERIC_LOADING is #define).
900    o pkg/kpp: replaced _KPP_RL with _RL
901    o bug fixes for vertical diffusivity computations when both KPP and
902        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
903        are no longer updating the vertical diffusivity array
904        (passed as argument) but are (re-) setting those arrays.
905    o pkg/seaice: fix bug in evp solver, while doing that
906      - change (improve?) discretization of stress computations for both
907        cgrid-lsr and evp solver
908      - add a new routine to compute strain rates
909      - the above changes lab_sea results
910      - add no slip conditions for evp solver (off by default), lsr-version
911        may follow
912      - fix exchange for shear at Z-points (does not change lab_sea)
913      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
914        (to force the user to pick a time step since there is not "safe" way
915        of choosing it)
916      - add principal stress diagnostics
917      - rearrange fields for evp a little to avoid having to call a: too many
918        exchanges and b: exchanges for stress trensor components which we do
919        not have.
920      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
921        of evp, complete rewrite for lsr case (latter is does not yet work
922        in all cases)
923    o pkg/kpp: add code to have mixing in shelf ice caverns
924      - add myThid to all kpp routines (long overdue)
925    
926    checkpoint59
927    o pkg/exf:
928      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
929        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
930      - move exf header files from lower_case.h to UPPER_CASE.h ;
931        add missing cvs Header & Name
932      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
933      - add namelist param. selectStressGridPosition, exf_monFreq
934      - retire many _CLIM routines, and remove data.exf_clim
935        + params moved to data.exf
936        + climsst, climsss now handled by exf_set_gen, i.e.
937          climss?period=0 refers to constant field,
938          climss?period=-12 to monthly forcing
939      - split up namelists in data.exf
940    o pkg/seaice:
941      - remove seaice_exch and seaice_exch_uv
942      - remove superfluous exchange of theta
943      - add myThid to seaice_budget_ocean/ice
944      - add new interface for atmospheric wind forcing (C-grid only)
945        + new routine
946        + two new field (taux, tauy for stress over ice)
947        + removed one global field (DAIRN) for C-grid case only
948    o pkg/thsise
949      - 2nd set of modifs for thsice adjoint in conjunction with exf
950    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
951    
952    checkpoint58y_post
953    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
954      vertical diffusivity, similar to that in MOM4; turned on using
955      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
956      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
957    o Added capability for 3D specification of background vertical diffusion
958      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
959      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
960      "data" file that contains the 3D vertical diffusivity coefficients.
961    o ice dynamics (pkg/seaice) with thsice thermodynamics:
962      - add code within pkg thsice to advect & diffuse sea-ice fields
963      similar to (and will replace) what has been added in  seaice_advdiff.F,
964      but: - conserving Mass, Heat & Salt.
965           - better when using non-linear advection scheme (not yet fully tested)
966           - can also be used in atmospheric set-up (for now, only the diffusion).
967    
968    checkpoint58x_post
969    o IO option for global-file compact format:
970      - add options when generating topology (utils/exch2/matlab-topology-generator)
971      - add I/O capability (pkg/mdsio).
972      - adapt utils/matlab/rdmds.m to read this format.
973      for now long-line format not yet supported by pkg/mdsio (& exch2).
974    o shelfice: add a few diagnostics
975    
976    checkpoint58w_post
977    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
978      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
979      (and replace horiVertRatio in NH code).
980      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
981                         and tutorial_plume_on_slope (sensitive to truncation)
982    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
983      directly to drive seaice model (C-grid only)
984    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
985     - reintroduce computation of wind from stress,
986     - compute tau (in exf_bulkformulae.F) from windstress averaged to
987       mass points to avoid tau = 0
988     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
989    o rdmnc.m: make it work with "global" files created with gluemnc
990    o rdmnc.m : some improvements in dealing with singleton dimension
991      (tested on all testreport mnc output files).
992    o genmake2: disable pkg/profiles if netcdf test fails.
993    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
994    o move call to cal_readparms up to make calendar parameters/variable available
995      to all packages
996    
997    checkpoint58v_post
998    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
999      useDynP_inEos_Zc tested.
1000    o pkg/exf: changes to properly interpolate/mask/scale initial fields
1001    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
1002      and portions thereof.  See read_cs.txt for description and examples.
1003    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
1004      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
1005      following the great-circle arc between those 2 points.
1006    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
1007      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
1008    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
1009     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
1010     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
1011     - still needs work (not working with some options ; efficiency to improve)
1012       and serious testing.
1013     - use this scheme for temperature & salinity in 2 advection test exp.:
1014       advect_xy & advect_xz, respectively.
1015    
1016    checkpoint58u_post
1017    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
1018    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
1019    o testreport: add option "-skipdir" to skip some test.
1020    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
1021      momentum calculation.
1022    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
1023    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
1024      remove checkpoint.F and the_correction_step.F (no longer used);
1025      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
1026    o add option (linFSConserveTr) to correct for tracer source/sink due to
1027      Linear Free surface
1028    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
1029    o pkg/thsice: fix reading mnc-pickups
1030    
1031    checkpoint58t_post
1032    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
1033    o pkg/mdsio:
1034     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
1035       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
1036       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
1037     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
1038     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
1039       either MDS_READ_FIELD or MDS_WRITE_FIELD )
1040     - new S/R (to replace MDSWRITEMETA), which allows to write more
1041       informations (variable names, time ...) to meta files.
1042     - modify rdmds.m to give back the meta file content.
1043    o pkg/diagnostics: change vertical interpolation to be safer, and more
1044       flexible (define p-levels to interpolate to in data.diagnostics);
1045      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
1046       diagnostic pointer.
1047    o pkg/seaice: more cleaning up of seaice_growth, added many comments
1048    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
1049    o fix multi-category seaice:
1050     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
1051       SEAICE_MULTICATEGORY
1052     - fix short wave heat flux
1053    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
1054       and allow to use EVP solver. Change forward lab_sea: test both EVP
1055       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
1056    o Initial check-in of lab_sea adjoint
1057      (very similar to natl_box_adjoint/code_seaice)
1058      * used C-grid and EVP solver
1059      * used KPP, GM/Redi
1060      * uses inAdExact=.TRUE.
1061      * gradient checks fail for both ADM and TLM
1062        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
1063        f.d. gradients actually seem more problematic than ADM, TLM gradients;
1064        issue is related to forward mismatch between g77 an ifort
1065    o pkg/seaice: overhaul of thermodynamics
1066     - growth.F and groatb.F are replaced by new routine seaice_growth.F
1067     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
1068     - move a few global fields out of SEAICE.h into seaice_growth.F and
1069       make them 2D (FICE/QNETO/ ...)
1070     - remove FO (it is the same as QNETO)
1071     - introduce a few local fields to avoid modifying external fields such
1072       as atemp, etc.
1073    
1074    checkpoint58s_post
1075    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
1076      changed exf_set_gen.F so that
1077        genperiod=0 means input file is one time-constant field and
1078        genperiod=-12 means input file contains 12 monthly means
1079    o CG2D: use pre-computed solver main-diagonal (stored in common block);
1080      this affects truncation error ; generate new output file for exp. which
1081      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
1082        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
1083        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
1084        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
1085        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
1086        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
1087    o start implementation of deep-atmosphere and anelastic formulation
1088    o verification: remove 2nd copy of input files and use script "prepare_run"
1089      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
1090    o mom_common/vecinv/fluxform: fix a few initialisation isssues
1091    o profiles: fix for multithreaded case
1092    
1093    o diagnostics: rename few diags:
1094      s/'PRESSURE'/'RCENTER '/g
1095      s/'TICE    '/'oceFreez'/g
1096      s/'TAUX    '/'oceTAUX '/g
1097      s/'TAUY    '/'oceTAUY '/g
1098      s/'SWFLUX  '/'oceQsw  '/g
1099      s/DIFx/DFxE/g
1100      s/DIFy/DFyE/g
1101      and add few ocean-forcing diagnostics:
1102      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
1103    o modifications to pkg/seaice/growth.F and budget.F, which change results of
1104      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
1105      as actual snow thickness.  It now refers everywhere to effective snow
1106      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
1107    
1108    checkpoint58r_post
1109    o modifications to pkg/seaice/growth.F, which change results of
1110      lab_sea experiment: fixes pertain to melting snow over open water, to
1111      masking EVAP under sea ice, and to using the correct AREA variable for
1112      computations of EVAP, PRECIP, HSNOW, and GHEFF
1113    o add ability to read bathy, salt, and theta using MNC (off by def)
1114    o add flooding algorithm and advection of HSNOW for pkg/seaice;
1115      both are turned off by default and do no change any results
1116    o seaice advection with pkg/thsice: a step toward the use of non-linear
1117      advection scheme, but #ifdef or commented out for now (requires more EXCH).
1118    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
1119      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
1120      in natl_box (affects results @ truncation level: update output.txt)
1121    o multi-threading and IO:
1122      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
1123      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
1124        (needed to work with SingleCpuIO): tested in all verif. exp.
1125    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
1126      affects the results (but none of the verification test uses this scheme).
1127    o Adding some pkg/diagnostics capability to pkg/seaice
1128      (will certainly be subject to changes)
1129    o ctrl: adding new control variables:
1130      lwflux, lwdown, evap, snowprecip, apressure, runoff
1131    
1132    checkpoint58q_post
1133    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
1134      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
1135      high_res_cube configuration by 4% on Columbia.
1136    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
1137      add (in global_with_exf/code) a version of EXF_INTERP_READ without
1138      dynamical allocation (seems to work in multi-threaded).
1139    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
1140      single CPU io) so that TAF does not have to see EESUPPORT.h
1141  o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)  o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
1142    
1143  checkpoint58p_post  checkpoint58p_post
# Line 1250  o add two new packages Line 2383  o add two new packages
2383    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
2384    - these scheme operate in a similar manner as KPP (without ghat, of    - these scheme operate in a similar manner as KPP (without ghat, of
2385      course), however there is only one diffusivity that is used for both      course), however there is only one diffusivity that is used for both
2386      temperature and salinity (and passive tracers)ç      temperature and salinity (and passive tracers)
2387  o add offline package  o add offline package
2388  o add "verification/dic_example" which contains a dic-gchem-ptracer setup  o add "verification/dic_example" which contains a dic-gchem-ptracer setup
2389    provided by Stephanie Dutkiewicz    provided by Stephanie Dutkiewicz
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