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revision 1.740 by heimbach, Fri Oct 27 05:19:42 2006 UTC revision 1.1072 by jmc, Fri Feb 27 03:22:34 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/ctrl:
8      fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
9    o non-hydrostatic (calc_gw.F):
10      fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
11      update output of exp. global_ocean.cs32x15.viscA4
12    o remove backward compatibility for thetaMin,phiMin
13      (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
14    o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
15      interpolated wind field not only for curvilineargrid=.true., but also
16      for a rotated grid (rotateGrid=.true.)
17    o pkg/exf: add capability to bypass interpolation for runoff
18      by setting yet another CPP-flag
19    o eesupp/src, B-grid exchange:
20      add simple (6 tiles, non MPI) CS exch + standard interface S/R.
21    o autodiff
22      new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
23      allows to switch to single-prec common blocks;
24      corresponding switch occurs in tamc.h, integer isbyte
25      TAF store directivs "byte" and "kind" seem equivalent;
26      Most tamc.h have been updated correspondingly.
27    
28    checkpoint61i
29    o autodiff:
30      fix autodiff_sore/_restore indices for obcs
31      (spotted by I. Hoteit, M. Mazloff)
32    o pkg/autodiff, pkg/ctrl:
33      Add flag to reduce all tapelev I/O to single-prec.
34      In data.ctrl set
35        doSinglePrecTapelev = .TRUE.
36    o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
37      check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
38    o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
39      real fresh water flux (not yet)
40    o pkg/mdsio & rw:
41     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
42     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
43    o pkg/flt:
44     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
45       init_fixed & ini_varia.
46     - clean-up & simplify linear interpolation S/R:
47       move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
48     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
49     - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
50     - add vert. coordinate & horiz. indices to output files.
51     - change vertical position in initial condition, from index to depth [m].
52     - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
53       (easier to get to a curvilinear grid) ; delX,delY no longer used.
54    o pkg/ggl90: a few modifications:
55     - fix bottom boundary condition, and interpolation of KappaE
56       near top and bottom
57     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
58     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
59     - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
60    o rename thetaMin,phiMin -> xgOrigin,ygOrigin
61      (maintain temporary backward compatibility, until next checkpoint)
62    
63    checkpoint61h
64    o pkg/diagnostics with "periodic averaging diagnostics":
65      fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
66    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
67    o pkg/obcs: fix loop ranges for balancing code
68    o pkg/flt:
69     - improve criteria for finding which tile owns a float.
70     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
71    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
72      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
73      with ocean biogeo)
74    o pkg/flt:
75     - do some cleaning and fix the restart ;
76     - add output.txt in flt_example/results to get this pkg tested.
77    o genmake2: add an EXTENDED_SRC option and flag.
78       for now, cannot be turned on on command line (only through genmake_local)
79    o pkg/mdsio: read/write vector:
80     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
81     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
82       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
83     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
84      (drop to 4 digits matching for grad). But this test does not look very
85      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
86    
87    checkpoint61g
88    o pkg/flt:
89      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
90       + make OPTIONS file more standard.
91      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
92      - fix _BYTESWAPIO CPP-Flag
93      - standard reading of file-parameter "data.flt"
94      - fix argument list of S/R FLT_RESTART
95      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
96    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
97    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
98      a still unfixed compiler/optimization bug
99    
100    checkpoint61f
101    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
102      update results of global_ocean.cs32x15.icedyn test.
103    o move getcon.F from model/src to pkg/fizhi.
104    o pkg/exf: add parameter for extrapolation of temp up to the surface
105       and option to prevent negative evap (in bulk_largeyeager04 only).
106    o Prather Advection scheme: fix tracer conservation for divergent flow
107      (e.g., when using NonLin Free-Surface).
108    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
109    o gmredi (Visbeck-variable-K):
110     - add more parameters to Visbeck-variable-K.
111     - use a 5 points average for dSigmaR in Visbeck-K calculation
112       (more "homogenous": same stencil and same weights as in dSigmaH)
113     - update output of ideal_2D_oce experiment.
114    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
115      (#undef REAL4_IS_SLOW)
116     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
117       coordinate variable
118     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
119       (surface forcing fields), removes some of the functionality
120     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
121     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
122       probably not all: copy _RS surface flux fields to RL field before
123       calling DIAGNOSTICS_FILL
124     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
125       real*4 (CALL EXCH_*_RS) versions.
126     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
127       (generate new output).
128    
129    checkpoint61e
130    o gmredi (Visbeck-variable-K):
131      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
132      - change computation of Visbeck-K where Slope > Smax :        
133        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
134        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
135    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
136      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
137    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
138    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
139      does not become too large (to avoid precision problems in implicit-diffusion
140      solver); update ideal_2D_oce output.
141    o pkg ggl90:
142      - in ggl90_cal.F: compute only one set of visc/diff, used to
143        step forward TKE/T/S/momentum
144      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
145        have Prandlt =1)
146    o gmredi (fm07):
147      - add lower limit on Transition layer thickness + lower limit on 1/lambda
148      - allow to set few more params from data.gmredi
149    o pkg ggl90:
150          - add missing sqrt(2) factor in computation of mixing length
151            scale in ggl90_calc.F
152            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
153    
154    checkpoint61d
155    o adjoint modifs
156      - adapt to new field rhoInSitu
157      - allow to revert from StoreDynVars2D, StoreDynVars3D
158        to individual fields
159        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
160    o store 3-D (in-situ) density in commom block (DYNVARS.h)
161     - save 1 rho computation.
162     - no longer modify T & S inland when using down_slope pkg.
163    o gad_som : allow to switch to SOM advection for T & S without corresponding
164      pickup files (using new S/R: MDS_CHECK4FILE).
165    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
166      (for useSingleCpuIO to work in multi-threaded)
167    o pkg/shelfice:
168     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
169       with SHELFICEtopoFile in data.shelfice
170     - move code for reading ice shelf topography and modifying hFacC into separate
171       subroutines of the shelfice package
172     - separate initialisation of "fixed" and "variable" variables
173     - kTopC is not (yet) replaced by kSurfC, although this is possible
174    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
175    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
176      and rename:
177      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
178      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
179    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
180    
181    checkpoint61c
182    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
183      to add mass source/sink of fluid in the interior (3-D generalisation
184      of oceanic real-fresh water flux).
185    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
186    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
187    o new pkg: down_slope
188      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
189      - presently, modify T & S inland (dwnslp_calc_rho.F).
190        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
191      - implementation for ocean in P-coords not tested.
192      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
193    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
194      (to facilitate conversion of oceanic pkg to p-coordinate).
195    o change FIND_RHO to FIND_RHO_2D :
196      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
197    o new pkg: cheapaml
198    
199    checkpoint61b
200    o exch2:
201      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
202      - no longer depend on the order sequence (N,S,E,W).
203      - 3rd exchange no longer needed (tested with 24 tiles).
204      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
205      - exch_UV_A-grid readily available (but not yet tested).
206      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
207      (both are no longer needed) in exch_uv: no effect in forward run; but
208       get truncation error differences with adjoint exch.
209    o exch2:
210     - change index-bounds storage (moved from target to local tile,
211       more intuitive this way) ; rename/remove some variables.
212     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
213    
214    checkpoint61a
215    o exch2/matlab-topology-generator:
216      fix bug in index bounds for N-S internal exchange (hard to tell if this
217      had any effect on the solution).
218    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
219      is exceeded
220    o testreport: modify syntax of awk, so that it works also with
221      awk, and not only with nawk and gawk
222    
223    checkpoint61
224    o autodiff
225      Change default for TAF usage by removing argument '-nonew_arg'
226      This changes TAF subroutine argument list (ordering of active var.)
227      Omission of this flag leads to incompatibility w.r.t. TAMC
228      To restore TAMC-compatibility, need following modifs:
229      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
230      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
231      Tested TAF version is 1.9.22
232      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
233    
234    checkpoint60
235    --->>> This is the last checkpoint for which generating the adjoint
236    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
237    --->>> by default.
238    --->>> Future checkpoints will ommit this flag by default.
239    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
240    o pkg/grdchk: Add gradient check to etan0 perturbations.
241    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
242    o pkg/autodiff: more flexibility in zeroadj.
243      model/src: modifying do_oceanic_phys.F accordingly.
244    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
245    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
246      special setup of gmredi for which the adjoint is stable
247      enough for parameter optimization.
248    o bridging the gap between eddy stress and GM.
249      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
250          along with a change in CPP option (now ALLOW_EDDYPSI).
251      -> when using GM w/ GM_AdvForm:
252          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
253          is applied either in the tracer Eq. or in momentum Eq.
254          depending on data.gmredi (intro. GM_InMomAsStress).
255      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
256      The key modifications are in model/src/taueddy_external_forcing.F
257      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
258    
259    checkpoint59r
260    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
261      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
262      fix option to read coriolis(@ cell-corner) from files with CS-grid.
263    o pkg/mnc: add some attributes to standard 1D-coordinate variables
264    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
265      mass points, when using mnc for output
266      - add runtime parameter (missing_value, missing_value_int) to override
267        default (which is the value of getcon('UNDEF'))
268    o pkg/mnc: prepare mnc for the actual use of missing values with the
269      diagnostics package: small fix in mnc_cw_readwrite.template and more
270      initialisation of never used fields
271      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
272      versions
273    o pkg/thsice/thsice_ini_vars.F added default initial values so that
274      thermodynamics sea ice solver does not blow up when some initial fields
275      are missing.
276    o move from external_forcing_surf.F to ini_forcing.F
277      the p-coord. hack consisting in using pLoad to set phi0surf ;
278      update output of tutorial_global_oce_in_p (affected @ truncation level).
279    o Freshen up a bit hs94.1x64x5, notably:
280      remove rotationPeriod and tRef=5*0. (adjoint only), and add
281      exactConserv=.TRUE.
282    o pkg/generic_advdiff:
283      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
284      applies to files where Temperature & Salinity 2nd Order moments are used.
285    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
286      this uses a dynamically allocated internal state data structure
287      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
288      and requires a fortran 90 compiler
289    
290    checkpoint59q
291    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
292       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
293    o Refresh tutorial_global_oce_biogeo, notably:
294      - change bathymetry (put back seamounts in ACC, use hFacs)
295      - change EOS (POLY3 --> JMD95Z)
296      - use Bryan-Lewis vertical diffusivity
297      - use multidimensional advection
298      - remove old virtual virtual in dic pkg, now done through ptracer pkg
299      - change a couple of parameters in dic pkg
300    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
301    o pkg/obcs: change default to OBCSfixTopo = .true.,
302      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
303      - replace "debugMode" with "debugLevel .GE. debLevB"
304    o implementation of TAF directives for gchem,cfc,dic
305    o remove "exp5" (replaced by tutorial_deep_convection).
306    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
307      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
308      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
309      --> changes results in exp4, seaice_obcs
310    o tutorial_deep_convection :
311      update the set-up and increase resolution and domain size ; start
312      from pseudo initial conditions = output at t=120mn in order to see
313      something happening when running testreport.
314    o pkg/seaice: add os7mp as an advection scheme
315                  add check for advection schemes
316                  add a flag for restoring T and S underneath sea ice
317    o pkg/my82: add netcdf-support and diagnostics
318    o thsice pkg:
319      - Now hsMax limits snow height by turning it into ice following
320        flooding scheme (and now conserving energy)
321      - Slight rewriting of the formula in thsice_calc_thick.F
322      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
323      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
324    
325    checkpoint59p
326    o gchem / dic / cfc :
327      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
328      - add new parameter files: "data.dic" & "data.cfc" ;
329      - various re-arrangement in initialisation & header file ;
330      - fix tutorial_global_oce_biogeo for multi-threaded test.
331    o pkg/dic: test for "pickup_dic" file when restarting ;
332      if no pickup-file, can restart with a re-initialised pH (same as it did
333      before) providing pickupStrictlyMatch is set to False.
334    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
335      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
336    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
337      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
338    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
339     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
340       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
341    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
342       scheme to use for vorticty-term ;
343     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
344       (with default selectVortScheme, return to original discretisation)
345     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
346    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
347    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
348      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
349      also fix diagnostics VISCAHW & VISCA4W.
350    
351    checkpoint59o
352    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
353    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
354      move a few statemens out the main loop into separate loops
355    o pkg/shelfice:
356      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
357        (kg/m^2/s), does not break tests, because in verification/isomip,
358        rhoConstFresh=rhoConst (by accident)
359      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
360      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
361        new file model/src/seawater.F, so that they are available for all pkgs.
362      - convert potential temperature into in-situ temperature. This changes the
363        isomip tests => update tests
364    o add a flag writePickupAtEnd (default=true) to be able to suppress
365      writing a pickup at the last timestep
366    o tools/mpack-1.6 :
367      - disable automake (not working) and autoconf (not needed).
368      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
369        also cleaner with much less compilation warnings.
370    o pkg/profiles:
371      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
372      (for "less than 32 characters name" compiler requirement)
373    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
374      conditions that have a different sampling frequency than S/T/U/V obcs
375    o pkg/diagnostics (stats-diags):
376      - fix global Min/Max in case 1 processor get only empty tiles
377    o genmake2: replace (4 times)
378         make genmake_tc_1.o >> genmake_warnings 2>&1
379      with
380         COMM="$CC $CFLAGS -c genmake_tc_1.c"
381         echo $COMM >> genmake_warnings
382         $COMM >> genmake_warnings 2>&1
383      to make genmake2 always see the value of CC as specified in the optfile.
384    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
385      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
386      - modify verification advect_cs test to test SOM-advection on CS-grid.
387    o pkg/ctrl:
388      - Rewrite of ctrl_map_ini_ecco.F,
389        introducing a generic routine (ctrl_map_ini_gen.F).
390      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
391    
392    checkpoint59n
393    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
394      number in dedicate array "hdiag":
395      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
396        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
397      - many small changes (integer format) for large number of diagnostics
398      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
399        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
400    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
401      usingSphericalGrid, this allows to define the rotated grid coordinates
402      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
403      geographical coordinates according to the inverse of the rotation defined
404      by the Euler angles, so that Coriolis parameter and online-interpolation by
405      exf works with the geographical coordinates on XC/YC/XG/YG.
406      Naturally, this feature does not work with all packages, so some
407      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
408      profiles), because there the coordinates are assumed to be regular
409      spherical grid coordinates.
410    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
411      - introduce isopycnal diffusion coefficient control.
412    o tools/adjoint_options:
413      - additional control vector components.
414    o pkg/mnc: have mnc create marginally meaning full coordinate variables
415      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
416    o pkg/mypackage:
417      - add example of read/write pickup for state-var ;
418      - add entry points to the main code for state-vars diags & write-pickup.
419    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
420      transitions for useExfYearlyFields
421      - add new subroutine that determines the file to read from for
422        use*YearlyFields = .TRUE. and .FALSE.
423      - add a verification experiment to global_with_exf that tests
424        useExfYearlyFields with USE_EXF_INTERPOLATION defined
425    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
426      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
427      subroutines (which could be generated from a template, because they are
428      almost identical), for now they are included in obcs_prescribe_read.F for
429      simplicity
430    o pkg/exf:
431      - add a little more diagnostic to exf_interp_read (in analogy to
432        mds_read_field, can be turned off with debugLevel < debugLevA=1)
433      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
434        ugly but fast by unrolling short inner loops, inserting a unroll=8
435        directive in routine lagran, and splitting a loop and making do while the
436        outermost loop (the latter requires the intoduction of index arrays)
437    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
438    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
439      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
440    o verification/seaice_obcs: updated for restart test and latest options
441    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
442      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
443      for now this is only available for the C-grid code and also within
444      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
445    
446    checkpoint59m
447    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
448      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
449    o gad_som : fix flux output (& diagnostics) to have same units as other  
450      advection scheme fluxes (was previously multiplied by deltaT).  
451    o added verification/seaice_obcs both to test seaice open boundaries
452      and to provide an example matlab scrpt for generating them
453    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
454    o pkg/salt_plume: clean up salt_plume_frac.F to
455      remove redundancy in PlumeMethod 1 and 4
456    o pkg/kpp: added saltplume diagnostics
457    o pkg/obcs and pkg/seaice:
458      - do not set uice and vice to zero when OB*icefile are unspecified
459      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
460      - moved seaice tracer obcs after call to seaice_growth
461    o pkg/salt_plume: added various options for salt plume depth
462      criterion and for vertical distribution of the salt
463    
464    checkpoint59l
465    o pkg/ptracers: new version of ptracers pickup:
466      read meta file and write only fields which are needed to restart.
467      ( same logic as main pickup file ; also using pickupStrictlyMatch )
468    o pkg/seaice:
469      - add timescale for melting due to warm mixed layer as a means of
470        setting SEAICE_availHeatFrac more conveniently
471      - add a CPP-flag/runtime parameter check for flooding algorithm
472      - reformulated availHeat in seaice_growth.F to be independent of AREA
473    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
474      unit changes
475    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
476    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
477      SX vector computer.
478    o pkg/seaice:
479      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
480        seaice forcing fields can now be read only through pkg/exf
481      - removed some unused halos
482    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
483    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
484      or U/VICE from U/VWIND before computing U/VSTRESS
485    
486    checkpoint59k
487    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
488      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
489    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
490      all experiments pass when compile with un-initialised var. checking option.
491    o added pkg/salt_plume
492    o script to test restart (for now, in MITgcm_contrib/jmc_script)
493    o pkg/seaice: new read/write pickup version.
494      read meta file and write only fields which are needed to restart.
495      ( same logic as main pickup file ; also using pickupStrictlyMatch )
496    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
497    o lab_sea.hb87: modify the domain & update output.hb87.txt :
498      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
499      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
500      process. Fixed here by closing the domain at the Northern boundary.
501    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
502    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
503      a set of consecutive levels in/from a 3-D array.
504    o pkg/ptracers:
505      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
506      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
507    
508    checkpoint59j
509    o in pkgs: dic, obcs, offline, rbcs:
510      standard way to compute coeff. for time interpolation between 2 time reccords
511      which retains full precision (& make results less dependent on compiler).
512      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
513    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
514      packages instead of reading ice cover and wind speed separately
515    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
516     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
517      to allow to compile customized code before the update)
518    o cleaning-up:
519      - fix CPP instruction syntax in pkg/obcs
520      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
521        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
522      - fix some threads issue in IO parts.
523    o pkg/dic:
524      - add tons of "_d 0" (--> much better testreports !)
525       and then update outputs of tutorial_global_oce_biogeo
526    o pkg/mom_fluxform:
527      add a special version of momentum advection intended to conserve momentum
528      next to a bathymetry step or a coastline edge. (default = off = #undef)
529    o new read/write pickup version:
530      - for now, only implemented for main (mdsio) pickup file.
531      - write out only what is needed to restart; merge pickup_nh , pickup_ph
532        and main pickup together.
533      - read meta file; read only what is needed to restart; stop if a field
534        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
535        if it make sense (even if the restart is not perfect).
536      - if no meta file, assume that pickup to read corresponds exactly to
537        a pickup that would currently be written.
538      - read pickup written in the old format (until checkpoint59i) if it
539        recognizes an old meta file (no field-list).
540      - add a meta file in exp. which starts from a pickup: 2 cases:
541        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
542         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
543        b) a meta file describing the content of the associated pickup file
544         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
545    o pkg/mdsio & pkg/rw:
546      - new routine to read a meta file ; new set of routine to read
547        Multiple-fields file (with meta file).
548    o added open boundary conditions capability for seaice
549        HSNOW, HSALT, UICE, and VICE
550    
551    checkpoint59i
552    o adjoint:
553      * fix multiDimAdvection adjoint
554        (partial recomputation problem by TAF for fVerT(:,:,kDown)
555        and comlev1 size definition (maxpass vs. max. number of tracers)
556      * verification/global_ocean.90x45x15 adjoint now tests
557        NLFS and multiDimAdvection using DST3 (=30)
558      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
559    o pkg/kpp: add "_d 0" to real constant (if missing);
560      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
561      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
562    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
563      for internal parameters related to restart process (formerly from PARAMS.h)
564      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
565    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
566      as argument. (only atm2d & obcs write_pickup have not yet been updated)
567    o pkg/monitor:
568      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
569      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
570      - account for deep Atmosphere factor and density factor (anelastic)
571    o added open boundary conditions capability for seaice HEFF and AREA
572    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
573      thermodynamics
574      - requires a little reorganization, which affects the testreport results
575        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
576        so that now the conservative form is tested
577      - add a few comments
578    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
579    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
580    o add new diagnostics to seaice: advective, diffusive fluxes (only for
581      multidim-advection, for scheme 2 they are not filled) and transports,
582      thermodynamic growth rates
583    o change units of EmPmR (inside the code, + within coupling interface)
584      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
585      Affects results @ truncation level (cg2d match) and update output of
586       experiments: lab_sea(6), global_ocean.90x40x15(10),
587      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
588      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
589      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
590      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
591    
592    checkpoint59h
593    o pkg/exf:
594      - improve vectorization by moving if-statement out of loops in
595        exf_mapfields, exf_radiation
596      - exf_bulkformulae.F: introduce 2D fields and vectorize code
597    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
598    o testreport:
599      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
600        monitor & update offline_exf_seaice exp. output.
601      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
602    o pkg/seaice:
603      - bug fix in the evp solver: boundary conditions were affected be
604        masking of zMax/zMin (changes results)
605      - minor bug fix in boundary conditions in seaice_calc_strainrates
606        (changes results for no_slip)
607      - seaice_lsr.F: make interpolation of eta dependent on boundaries
608      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
609      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
610        stress formulation and no-slip boundary conditions
611    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
612      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
613    o pkg/seaice: a first HSALT time stepping equation has been checked in
614    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
615      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
616      without requiring DO-IF statements
617    o pkg/thsice:
618      use continuous power-law function for partition of energy between lateral
619      melting/freezing and thinning/thickening ; old code using step function
620      still available with #undef THSICE_FRACEN_POWERLAW
621      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
622    o testreport: change AD testing : check against results/output_adm.txt
623      using same scripts as for forward test.
624    
625    checkpoint59g
626    o adjoint testing: in preparation for changing testreport:
627      - output format: cost and grad written on separated lines
628      - ad output results in directory "results" (instead of "results_ad")
629    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
630    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
631    o pkg/ecco: allow user defined cost function contributions
632    o testreport:
633      Allow to choose (per experiment) the list of tested output variables
634       and the main variable (used to issue a pass/FAIL ) ;
635      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
636      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
637      Also modify printing of summary:
638       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
639       b) echo the list of tested variables in the individual summary.txt of
640          each experiment.
641    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
642      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
643      (but still depend on the tile decompostion of the domain).
644    o pkg/seaice: change a discretization detail to make the B-grid code
645      "more symmetric". This change is likely to remove all "ridges/leads" that
646      where quasi-aligned with the grid in B-grid solutions. It may also be
647      the solution to the stress coupling issues with the B-grid.
648    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
649      remove .cvsignore from input dir. (since testreport no longer run here).
650    o pkg/thsice:
651     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
652     - fix reshaping of sea-ice just after advection:
653       melt all the ice only if ice-volume is too small.
654     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
655       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
656     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
657    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
658      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
659    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
660      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
661      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
662      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
663      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
664      -> update output.txt
665    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
666     this affects truncation error: -> update output.txt of exp:
667      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
668      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
669    
670    checkpoint59f
671    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
672    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
673      a bounded range (in forward mode)
674    o pkg/ecco, ctrl, autodiff and mom_common:
675     internal parameter controls, completements of implementations
676    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
677    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
678      (not seem any difference in testing results).
679    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
680       at face corners.
681    o pkg/generic_advdiff:
682     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
683      loop range indices for computing vertical advection tendency
684      and do the calculation in the interior only (no overlap) ;
685      for now, only implemented for SOM advection (to save CPU time).
686     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
687    o exch2 adjoint
688      First set of changes:
689      - add exch2 hand-written adjoint templates
690      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
691        This will require cleanup in pkg/autodiff/*.F
692        (changed routines currently kept separate in verif. code/)
693      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
694        that used to hide exch2 or cubed-sphere specific code
695        (commented via 'cph-exch2')
696    o pkg/seaice
697      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
698    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
699       output of global_ocean.cs32x15.thsice .
700    
701    checkpoint59e
702    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
703      for B-grid vector (not yet tested) and C-grid vector (<- only used
704      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
705    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
706      (#ifdef ALLOW_SALT_PLUME)
707    o gather_2d/scatter_2d: removed halo regions
708    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
709      scheme and the corresponding test case (under front_relax dir). For now,
710      only available with Skew-flux form and not yet tested in realistic set-up.
711      adjoint: store directives updated, but gradient checks deteriorated,
712      so maybe GM/Redi adjoint is now broken.
713    o seaice adjoint
714      * add AREA, HEFF, HSNOW as control variable
715        (should not change lab_sea results)
716      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
717    o pkg/seaice:
718      * added computation of saltFlux in seaice_growth;
719        For time being, sea ice salinity is assumed constant
720        contribution of snow flooding to freshening of sea ice is neglected.
721        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
722        defaults to 0.0 in order to maintain backward compatibility.
723        Typical values for SEAICE_salinity are 4 to 10 g/kg.
724      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
725      * added SEAICE_availHeatFrac, which specifies fraction of surface level
726        heat content used to melt or grow ice
727      * commented out cap of HICE: it helps keep ice thinner
728      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
729      * applied OBCS T/S mask to HEFFM sea ice mask
730    
731    checkpoint59d
732    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
733     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
734     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
735    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
736     and change default value of parameter "GM_Small_Number";
737     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
738       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
739       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
740    o pkg/ecco: cost function when applying pkg/smooth to controls
741    o pkg/ctrl: add forcingPrecond run time parameter
742    o pkg/seaice:
743     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
744     - fix bug in metric terms of u-equation in LSR solver (implicit part),
745       changes verification/lab_sea
746     - rearrange implicit part of u-equation in LSR solver to make it easier to
747       read, understand, and debug. This causes changes at the truncation level.
748     - fix (serious) bug in the boundary conditions (sign error in the implicit
749       part) of the LSR solver. Changes all LSR results.
750     - fixed problem with HSNOW initialization to avoid thick snow when AREA
751       is initilized with small values - does not change lab_sea results.
752     - added HsnowFile initialization capability
753    o pkg/smooth: addition to model/src and pkg/ctrl so allow
754     initialization of pkg/smooth and application to control vector
755    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
756    o dependencies: pkg/profiles requires pkg/cal
757    o pkg/profiles:
758     - added option ALLOW_PROFILES_GENERICGRID
759         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
760         that interpolation information (grid points and coefficients) is provided
761         within the netcdf input files.
762         -> sample matlab scripts can be found in MITgcm_contrib/gael
763         that allow you to prepare netcdf input files.
764     - also modified: cleaner include statements, cleaner error print statements,
765       cleaner stops when error, and more tests of the netcdf input files consistency.
766    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
767    o pkg/seaice:
768     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
769       requires a new routine: seaice_diagnostics_fill.F
770     - make sure that seaice does not move if not forced (pressure replacement
771       method, Hibler and Ip, 1995), changes results
772     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
773     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
774       It is turned off by default (=-1.), because it changes the results.
775     - make it possible to read AREA from a file, too.
776    
777    checkpoint59c
778    o add S/R and diagnostics for oceanic mixed-layer depth
779    o move GMRedi call after all vertical mixing schemes (including KPP)
780    o pkg/thsice:
781     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
782      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
783    o pkg/obcs:
784     - bug fix for balance code
785    o pkg/seaice:
786      - allow values of SEAICE_elasticParm > 1
787      - add new parameter SEAICE_evpTauRelax as an alternative
788        to SEAICE_elasticParm
789      - make lsr boundary conditions free slip (by default), changes result
790      - add code for no slip boundary conditions for lsr
791      - set minimum of zeta to zero (and not 4e8) (changes results)
792      - add a cap on AREA after advecting AREA if seaice_growth is not called
793    o change calculation of Visbeck K:
794      - no longer depend on tapering scheme; instead, compute slope (limited
795        by GM_maxSlope). this is equivalent to what was comuted before with
796        clipping or linear tappering.
797      - fix vertical averaging (wrong by 1/2 level)
798      - leave the old version (but will not be maintained) within
799        #ifdef OLD_VISBECK_CALC / #endif
800      - update output of exp. ideal_2D_oce
801    o change error catch in calc_r_star to improve vectorization
802    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
803      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
804    o adjoint:
805      Re-organized adjoint checkpointing according to Matt Mazloff
806      (but with modifs/completions/cleanups)
807      Storing is now bundled into large arrays to optimized I/O
808      (and second step in cleanup of the_main_loop)
809    
810    checkpoint59b
811    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
812      - export/import (between ocean & coupler) fields needed for ocean DIC.
813    o pkg/seaice:
814      - get rid of three more exchanges seaice_calc_viscosities (required
815        different loop boundaries in seaice_lsr and seaice_ocean_stress)
816      - bug fix in seaice_ocean_stress (update of lab_sea required)
817      - reduce loop boundaries to necessary minimum also in seaice_evp
818      - go back to the old way of computing deltaC/Z as the adjoint likes that
819        better
820    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
821      passive tracer to an Age Tracer) + update output.txt
822    o pkg/exf:
823      - implement A-grid / C-grid selection for wind-stress input files.
824      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
825      for now, in exf_bulk_largeyeager04.F only :
826      - change implementation for case where windspeed + 2. components wind-stress
827        are read-in. AND use rhoConstFresh to convert evap.
828    o pkg/seaice:
829      - use correct EXCH_UV for wind-forcing (on A-grid).
830      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
831        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
832    o pkg/exf:
833      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
834      EXF_INTERPOLATION:
835      - merge global_with_exf/code version of exf_interp_read.F
836        to the main code ;
837      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
838        reading the file ; Important: This options needs to be defined to recover
839        previous code.
840        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
841      - no longer loose real*8 precision along the way when using exf_iprec=64.
842    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
843      - change discretisation of evp-solver in order to avoid another exchange
844        (changes lab_sea) and clean up a little
845      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
846        help the adjoint (this also changes the results slightly)
847      - add a few "_d 0" where they had been missing in seaice_evp.F
848      - cleaning up: remove unused seaice_calc_rhs.F
849    o pkg/exf: some cleaning-up:
850      - change various "constants" into runtime parameters
851      - cleaned-up Large&Yeager04 routine which should eventually
852        replace exf_bulkformulae.F (changed names of S/R and CPP)
853        and merged various ALLOW_ATM_WIND options
854     only used with thsice pkg (in thsice_get_exf.F):
855      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
856        which are used when useStabilityFct_overIce=TRUE (= the default)
857      - change default values of ice & snow emissivity and scale downward LW
858        by ice & snow emissivity.
859    o pkg/thsice:
860     fix few little problems, in thsice_calc_thickn.F:
861      - growth vertically (and not laterally) if iceFrac == iceMaskMax
862      - melt only laterally if hIce < hThinIce (as the comments say)
863      and in thsice_extend.F:
864      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
865      - start to form ice as soon as the minimum ice-volume is reachable.
866     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
867      and cpl_aim+ocn
868    o pkg/kpp
869     - move computation of surface related input fields to KPP into a new
870       subroutine kpp_forcing_surf.F
871     - remove wrong (within bi,bj loops) EXCH calls.
872     - little cleaning (add argument myThid in last position, cvs header ...)
873     - for now, fix conservation problem by exchanging KPPviscAz (may not
874       be the best fix)
875    o pkg/seaice
876     - check for inconsistent evp parameter/cpp-flag combination
877     - remove leftover errIO flat for obsolete name list error handling
878    o OpenAD
879     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
880    
881    checkpoint59a
882    o pkg/seaice: some parameter clarifications and a little bit of clean up
883    o pkg/thsice: rename run-time parameters:
884       himin       -> hIceMin
885       himin0      -> hThinIce
886       hihig       -> hThickIce
887       i0          -> i0swFrac
888       transCoef   -> bMeltCoef
889       frac_energy -> fracMelting
890      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
891       with default values (for now) that do not change the results.
892      remove old version of thsice vars advection in pkg/seaice.
893    o in FFIELDS.h:
894      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
895      - make pLoad & sIceLoad always available (but still only used if
896         ATMOSPHERIC_LOADING is #define).
897    o pkg/kpp: replaced _KPP_RL with _RL
898    o bug fixes for vertical diffusivity computations when both KPP and
899        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
900        are no longer updating the vertical diffusivity array
901        (passed as argument) but are (re-) setting those arrays.
902    o pkg/seaice: fix bug in evp solver, while doing that
903      - change (improve?) discretization of stress computations for both
904        cgrid-lsr and evp solver
905      - add a new routine to compute strain rates
906      - the above changes lab_sea results
907      - add no slip conditions for evp solver (off by default), lsr-version
908        may follow
909      - fix exchange for shear at Z-points (does not change lab_sea)
910      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
911        (to force the user to pick a time step since there is not "safe" way
912        of choosing it)
913      - add principal stress diagnostics
914      - rearrange fields for evp a little to avoid having to call a: too many
915        exchanges and b: exchanges for stress trensor components which we do
916        not have.
917      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
918        of evp, complete rewrite for lsr case (latter is does not yet work
919        in all cases)
920    o pkg/kpp: add code to have mixing in shelf ice caverns
921      - add myThid to all kpp routines (long overdue)
922    
923    checkpoint59
924    o pkg/exf:
925      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
926        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
927      - move exf header files from lower_case.h to UPPER_CASE.h ;
928        add missing cvs Header & Name
929      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
930      - add namelist param. selectStressGridPosition, exf_monFreq
931      - retire many _CLIM routines, and remove data.exf_clim
932        + params moved to data.exf
933        + climsst, climsss now handled by exf_set_gen, i.e.
934          climss?period=0 refers to constant field,
935          climss?period=-12 to monthly forcing
936      - split up namelists in data.exf
937    o pkg/seaice:
938      - remove seaice_exch and seaice_exch_uv
939      - remove superfluous exchange of theta
940      - add myThid to seaice_budget_ocean/ice
941      - add new interface for atmospheric wind forcing (C-grid only)
942        + new routine
943        + two new field (taux, tauy for stress over ice)
944        + removed one global field (DAIRN) for C-grid case only
945    o pkg/thsise
946      - 2nd set of modifs for thsice adjoint in conjunction with exf
947    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
948    
949    checkpoint58y_post
950    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
951      vertical diffusivity, similar to that in MOM4; turned on using
952      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
953      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
954    o Added capability for 3D specification of background vertical diffusion
955      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
956      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
957      "data" file that contains the 3D vertical diffusivity coefficients.
958    o ice dynamics (pkg/seaice) with thsice thermodynamics:
959      - add code within pkg thsice to advect & diffuse sea-ice fields
960      similar to (and will replace) what has been added in  seaice_advdiff.F,
961      but: - conserving Mass, Heat & Salt.
962           - better when using non-linear advection scheme (not yet fully tested)
963           - can also be used in atmospheric set-up (for now, only the diffusion).
964    
965    checkpoint58x_post
966    o IO option for global-file compact format:
967      - add options when generating topology (utils/exch2/matlab-topology-generator)
968      - add I/O capability (pkg/mdsio).
969      - adapt utils/matlab/rdmds.m to read this format.
970      for now long-line format not yet supported by pkg/mdsio (& exch2).
971    o shelfice: add a few diagnostics
972    
973    checkpoint58w_post
974    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
975      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
976      (and replace horiVertRatio in NH code).
977      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
978                         and tutorial_plume_on_slope (sensitive to truncation)
979    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
980      directly to drive seaice model (C-grid only)
981    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
982     - reintroduce computation of wind from stress,
983     - compute tau (in exf_bulkformulae.F) from windstress averaged to
984       mass points to avoid tau = 0
985     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
986    o rdmnc.m: make it work with "global" files created with gluemnc
987    o rdmnc.m : some improvements in dealing with singleton dimension
988      (tested on all testreport mnc output files).
989    o genmake2: disable pkg/profiles if netcdf test fails.
990    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
991    o move call to cal_readparms up to make calendar parameters/variable available
992      to all packages
993    
994    checkpoint58v_post
995    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
996      useDynP_inEos_Zc tested.
997    o pkg/exf: changes to properly interpolate/mask/scale initial fields
998    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
999      and portions thereof.  See read_cs.txt for description and examples.
1000    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
1001      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
1002      following the great-circle arc between those 2 points.
1003    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
1004      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
1005    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
1006     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
1007     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
1008     - still needs work (not working with some options ; efficiency to improve)
1009       and serious testing.
1010     - use this scheme for temperature & salinity in 2 advection test exp.:
1011       advect_xy & advect_xz, respectively.
1012    
1013    checkpoint58u_post
1014    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
1015    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
1016    o testreport: add option "-skipdir" to skip some test.
1017    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
1018      momentum calculation.
1019    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
1020    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
1021      remove checkpoint.F and the_correction_step.F (no longer used);
1022      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
1023    o add option (linFSConserveTr) to correct for tracer source/sink due to
1024      Linear Free surface
1025    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
1026    o pkg/thsice: fix reading mnc-pickups
1027    
1028    checkpoint58t_post
1029    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
1030    o pkg/mdsio:
1031     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
1032       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
1033       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
1034     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
1035     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
1036       either MDS_READ_FIELD or MDS_WRITE_FIELD )
1037     - new S/R (to replace MDSWRITEMETA), which allows to write more
1038       informations (variable names, time ...) to meta files.
1039     - modify rdmds.m to give back the meta file content.
1040    o pkg/diagnostics: change vertical interpolation to be safer, and more
1041       flexible (define p-levels to interpolate to in data.diagnostics);
1042      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
1043       diagnostic pointer.
1044    o pkg/seaice: more cleaning up of seaice_growth, added many comments
1045    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
1046    o fix multi-category seaice:
1047     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
1048       SEAICE_MULTICATEGORY
1049     - fix short wave heat flux
1050    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
1051       and allow to use EVP solver. Change forward lab_sea: test both EVP
1052       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
1053    o Initial check-in of lab_sea adjoint
1054      (very similar to natl_box_adjoint/code_seaice)
1055      * used C-grid and EVP solver
1056      * used KPP, GM/Redi
1057      * uses inAdExact=.TRUE.
1058      * gradient checks fail for both ADM and TLM
1059        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
1060        f.d. gradients actually seem more problematic than ADM, TLM gradients;
1061        issue is related to forward mismatch between g77 an ifort
1062    o pkg/seaice: overhaul of thermodynamics
1063     - growth.F and groatb.F are replaced by new routine seaice_growth.F
1064     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
1065     - move a few global fields out of SEAICE.h into seaice_growth.F and
1066       make them 2D (FICE/QNETO/ ...)
1067     - remove FO (it is the same as QNETO)
1068     - introduce a few local fields to avoid modifying external fields such
1069       as atemp, etc.
1070    
1071    checkpoint58s_post
1072    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
1073      changed exf_set_gen.F so that
1074        genperiod=0 means input file is one time-constant field and
1075        genperiod=-12 means input file contains 12 monthly means
1076    o CG2D: use pre-computed solver main-diagonal (stored in common block);
1077      this affects truncation error ; generate new output file for exp. which
1078      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
1079        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
1080        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
1081        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
1082        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
1083        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
1084    o start implementation of deep-atmosphere and anelastic formulation
1085    o verification: remove 2nd copy of input files and use script "prepare_run"
1086      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
1087    o mom_common/vecinv/fluxform: fix a few initialisation isssues
1088    o profiles: fix for multithreaded case
1089    
1090    o diagnostics: rename few diags:
1091      s/'PRESSURE'/'RCENTER '/g
1092      s/'TICE    '/'oceFreez'/g
1093      s/'TAUX    '/'oceTAUX '/g
1094      s/'TAUY    '/'oceTAUY '/g
1095      s/'SWFLUX  '/'oceQsw  '/g
1096      s/DIFx/DFxE/g
1097      s/DIFy/DFyE/g
1098      and add few ocean-forcing diagnostics:
1099      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
1100    o modifications to pkg/seaice/growth.F and budget.F, which change results of
1101      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
1102      as actual snow thickness.  It now refers everywhere to effective snow
1103      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
1104    
1105    checkpoint58r_post
1106    o modifications to pkg/seaice/growth.F, which change results of
1107      lab_sea experiment: fixes pertain to melting snow over open water, to
1108      masking EVAP under sea ice, and to using the correct AREA variable for
1109      computations of EVAP, PRECIP, HSNOW, and GHEFF
1110    o add ability to read bathy, salt, and theta using MNC (off by def)
1111    o add flooding algorithm and advection of HSNOW for pkg/seaice;
1112      both are turned off by default and do no change any results
1113    o seaice advection with pkg/thsice: a step toward the use of non-linear
1114      advection scheme, but #ifdef or commented out for now (requires more EXCH).
1115  o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens  o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
1116    (identical results) and the standard version of EXTERNAL_FIELDS_LOAD    (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
1117    in natl_box (affects results @ truncation level: update output.txt)    in natl_box (affects results @ truncation level: update output.txt)
# Line 1272  o add two new packages Line 2380  o add two new packages
2380    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
2381    - these scheme operate in a similar manner as KPP (without ghat, of    - these scheme operate in a similar manner as KPP (without ghat, of
2382      course), however there is only one diffusivity that is used for both      course), however there is only one diffusivity that is used for both
2383      temperature and salinity (and passive tracers)ç      temperature and salinity (and passive tracers)
2384  o add offline package  o add offline package
2385  o add "verification/dic_example" which contains a dic-gchem-ptracer setup  o add "verification/dic_example" which contains a dic-gchem-ptracer setup
2386    provided by Stephanie Dutkiewicz    provided by Stephanie Dutkiewicz
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