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revision 1.703 by gforget, Fri Jul 14 22:14:28 2006 UTC revision 1.1057 by dfer, Fri Jan 30 14:31:18 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/ggl90: a few modifications:
8     - fix bottom boundary condition, and interpolation of KappaE
9       near top and bottom
10     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
11     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
12     - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
13    o rename thetaMin,phiMin -> xgOrigin,ygOrigin
14      (maintain temporary backward compatibility, until next checkpoint)
15    
16    checkpoint61h
17    o pkg/diagnostics with "periodic averaging diagnostics":
18      fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
19    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
20    o pkg/obcs: fix loop ranges for balancing code
21    o pkg/flt:
22     - improve criteria for finding which tile owns a float.
23     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
24    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
25      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
26      with ocean biogeo)
27    o pkg/flt:
28     - do some cleaning and fix the restart ;
29     - add output.txt in flt_example/results to get this pkg tested.
30    o genmake2: add an EXTENDED_SRC option and flag.
31       for now, cannot be turned on on command line (only through genmake_local)
32    o pkg/mdsio: read/write vector:
33     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
34     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
35       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
36     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
37      (drop to 4 digits matching for grad). But this test does not look very
38      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
39    
40    checkpoint61g
41    o pkg/flt:
42      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
43       + make OPTIONS file more standard.
44      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
45      - fix _BYTESWAPIO CPP-Flag
46      - standard reading of file-parameter "data.flt"
47      - fix argument list of S/R FLT_RESTART
48      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
49    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
50    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
51      a still unfixed compiler/optimization bug
52    
53    checkpoint61f
54    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
55      update results of global_ocean.cs32x15.icedyn test.
56    o move getcon.F from model/src to pkg/fizhi.
57    o pkg/exf: add parameter for extrapolation of temp up to the surface
58       and option to prevent negative evap (in bulk_largeyeager04 only).
59    o Prather Advection scheme: fix tracer conservation for divergent flow
60      (e.g., when using NonLin Free-Surface).
61    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
62    o gmredi (Visbeck-variable-K):
63     - add more parameters to Visbeck-variable-K.
64     - use a 5 points average for dSigmaR in Visbeck-K calculation
65       (more "homogenous": same stencil and same weights as in dSigmaH)
66     - update output of ideal_2D_oce experiment.
67    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
68      (#undef REAL4_IS_SLOW)
69     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
70       coordinate variable
71     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
72       (surface forcing fields), removes some of the functionality
73     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
74     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
75       probably not all: copy _RS surface flux fields to RL field before
76       calling DIAGNOSTICS_FILL
77     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
78       real*4 (CALL EXCH_*_RS) versions.
79     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
80       (generate new output).
81    
82    checkpoint61e
83    o gmredi (Visbeck-variable-K):
84      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
85      - change computation of Visbeck-K where Slope > Smax :        
86        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
87        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
88    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
89      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
90    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
91    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
92      does not become too large (to avoid precision problems in implicit-diffusion
93      solver); update ideal_2D_oce output.
94    o pkg ggl90:
95      - in ggl90_cal.F: compute only one set of visc/diff, used to
96        step forward TKE/T/S/momentum
97      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
98        have Prandlt =1)
99    o gmredi (fm07):
100      - add lower limit on Transition layer thickness + lower limit on 1/lambda
101      - allow to set few more params from data.gmredi
102    o pkg ggl90:
103          - add missing sqrt(2) factor in computation of mixing length
104            scale in ggl90_calc.F
105            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
106    
107    checkpoint61d
108    o adjoint modifs
109      - adapt to new field rhoInSitu
110      - allow to revert from StoreDynVars2D, StoreDynVars3D
111        to individual fields
112        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
113    o store 3-D (in-situ) density in commom block (DYNVARS.h)
114     - save 1 rho computation.
115     - no longer modify T & S inland when using down_slope pkg.
116    o gad_som : allow to switch to SOM advection for T & S without corresponding
117      pickup files (using new S/R: MDS_CHECK4FILE).
118    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
119      (for useSingleCpuIO to work in multi-threaded)
120    o pkg/shelfice:
121     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
122       with SHELFICEtopoFile in data.shelfice
123     - move code for reading ice shelf topography and modifying hFacC into separate
124       subroutines of the shelfice package
125     - separate initialisation of "fixed" and "variable" variables
126     - kTopC is not (yet) replaced by kSurfC, although this is possible
127    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
128    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
129      and rename:
130      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
131      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
132    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
133    
134    checkpoint61c
135    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
136      to add mass source/sink of fluid in the interior (3-D generalisation
137      of oceanic real-fresh water flux).
138    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
139    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
140    o new pkg: down_slope
141      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
142      - presently, modify T & S inland (dwnslp_calc_rho.F).
143        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
144      - implementation for ocean in P-coords not tested.
145      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
146    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
147      (to facilitate conversion of oceanic pkg to p-coordinate).
148    o change FIND_RHO to FIND_RHO_2D :
149      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
150    o new pkg: cheapaml
151    
152    checkpoint61b
153    o exch2:
154      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
155      - no longer depend on the order sequence (N,S,E,W).
156      - 3rd exchange no longer needed (tested with 24 tiles).
157      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
158      - exch_UV_A-grid readily available (but not yet tested).
159      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
160      (both are no longer needed) in exch_uv: no effect in forward run; but
161       get truncation error differences with adjoint exch.
162    o exch2:
163     - change index-bounds storage (moved from target to local tile,
164       more intuitive this way) ; rename/remove some variables.
165     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
166    
167    checkpoint61a
168    o exch2/matlab-topology-generator:
169      fix bug in index bounds for N-S internal exchange (hard to tell if this
170      had any effect on the solution).
171    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
172      is exceeded
173    o testreport: modify syntax of awk, so that it works also with
174      awk, and not only with nawk and gawk
175    
176    checkpoint61
177    o autodiff
178      Change default for TAF usage by removing argument '-nonew_arg'
179      This changes TAF subroutine argument list (ordering of active var.)
180      Omission of this flag leads to incompatibility w.r.t. TAMC
181      To restore TAMC-compatibility, need following modifs:
182      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
183      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
184      Tested TAF version is 1.9.22
185      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
186    
187    checkpoint60
188    --->>> This is the last checkpoint for which generating the adjoint
189    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
190    --->>> by default.
191    --->>> Future checkpoints will ommit this flag by default.
192    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
193    o pkg/grdchk: Add gradient check to etan0 perturbations.
194    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
195    o pkg/autodiff: more flexibility in zeroadj.
196      model/src: modifying do_oceanic_phys.F accordingly.
197    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
198    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
199      special setup of gmredi for which the adjoint is stable
200      enough for parameter optimization.
201    o bridging the gap between eddy stress and GM.
202      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
203          along with a change in CPP option (now ALLOW_EDDYPSI).
204      -> when using GM w/ GM_AdvForm:
205          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
206          is applied either in the tracer Eq. or in momentum Eq.
207          depending on data.gmredi (intro. GM_InMomAsStress).
208      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
209      The key modifications are in model/src/taueddy_external_forcing.F
210      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
211    
212    checkpoint59r
213    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
214      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
215      fix option to read coriolis(@ cell-corner) from files with CS-grid.
216    o pkg/mnc: add some attributes to standard 1D-coordinate variables
217    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
218      mass points, when using mnc for output
219      - add runtime parameter (missing_value, missing_value_int) to override
220        default (which is the value of getcon('UNDEF'))
221    o pkg/mnc: prepare mnc for the actual use of missing values with the
222      diagnostics package: small fix in mnc_cw_readwrite.template and more
223      initialisation of never used fields
224      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
225      versions
226    o pkg/thsice/thsice_ini_vars.F added default initial values so that
227      thermodynamics sea ice solver does not blow up when some initial fields
228      are missing.
229    o move from external_forcing_surf.F to ini_forcing.F
230      the p-coord. hack consisting in using pLoad to set phi0surf ;
231      update output of tutorial_global_oce_in_p (affected @ truncation level).
232    o Freshen up a bit hs94.1x64x5, notably:
233      remove rotationPeriod and tRef=5*0. (adjoint only), and add
234      exactConserv=.TRUE.
235    o pkg/generic_advdiff:
236      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
237      applies to files where Temperature & Salinity 2nd Order moments are used.
238    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
239      this uses a dynamically allocated internal state data structure
240      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
241      and requires a fortran 90 compiler
242    
243    checkpoint59q
244    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
245       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
246    o Refresh tutorial_global_oce_biogeo, notably:
247      - change bathymetry (put back seamounts in ACC, use hFacs)
248      - change EOS (POLY3 --> JMD95Z)
249      - use Bryan-Lewis vertical diffusivity
250      - use multidimensional advection
251      - remove old virtual virtual in dic pkg, now done through ptracer pkg
252      - change a couple of parameters in dic pkg
253    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
254    o pkg/obcs: change default to OBCSfixTopo = .true.,
255      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
256      - replace "debugMode" with "debugLevel .GE. debLevB"
257    o implementation of TAF directives for gchem,cfc,dic
258    o remove "exp5" (replaced by tutorial_deep_convection).
259    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
260      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
261      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
262      --> changes results in exp4, seaice_obcs
263    o tutorial_deep_convection :
264      update the set-up and increase resolution and domain size ; start
265      from pseudo initial conditions = output at t=120mn in order to see
266      something happening when running testreport.
267    o pkg/seaice: add os7mp as an advection scheme
268                  add check for advection schemes
269                  add a flag for restoring T and S underneath sea ice
270    o pkg/my82: add netcdf-support and diagnostics
271    o thsice pkg:
272      - Now hsMax limits snow height by turning it into ice following
273        flooding scheme (and now conserving energy)
274      - Slight rewriting of the formula in thsice_calc_thick.F
275      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
276      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
277    
278    checkpoint59p
279    o gchem / dic / cfc :
280      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
281      - add new parameter files: "data.dic" & "data.cfc" ;
282      - various re-arrangement in initialisation & header file ;
283      - fix tutorial_global_oce_biogeo for multi-threaded test.
284    o pkg/dic: test for "pickup_dic" file when restarting ;
285      if no pickup-file, can restart with a re-initialised pH (same as it did
286      before) providing pickupStrictlyMatch is set to False.
287    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
288      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
289    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
290      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
291    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
292     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
293       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
294    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
295       scheme to use for vorticty-term ;
296     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
297       (with default selectVortScheme, return to original discretisation)
298     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
299    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
300    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
301      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
302      also fix diagnostics VISCAHW & VISCA4W.
303    
304    checkpoint59o
305    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
306    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
307      move a few statemens out the main loop into separate loops
308    o pkg/shelfice:
309      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
310        (kg/m^2/s), does not break tests, because in verification/isomip,
311        rhoConstFresh=rhoConst (by accident)
312      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
313      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
314        new file model/src/seawater.F, so that they are available for all pkgs.
315      - convert potential temperature into in-situ temperature. This changes the
316        isomip tests => update tests
317    o add a flag writePickupAtEnd (default=true) to be able to suppress
318      writing a pickup at the last timestep
319    o tools/mpack-1.6 :
320      - disable automake (not working) and autoconf (not needed).
321      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
322        also cleaner with much less compilation warnings.
323    o pkg/profiles:
324      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
325      (for "less than 32 characters name" compiler requirement)
326    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
327      conditions that have a different sampling frequency than S/T/U/V obcs
328    o pkg/diagnostics (stats-diags):
329      - fix global Min/Max in case 1 processor get only empty tiles
330    o genmake2: replace (4 times)
331         make genmake_tc_1.o >> genmake_warnings 2>&1
332      with
333         COMM="$CC $CFLAGS -c genmake_tc_1.c"
334         echo $COMM >> genmake_warnings
335         $COMM >> genmake_warnings 2>&1
336      to make genmake2 always see the value of CC as specified in the optfile.
337    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
338      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
339      - modify verification advect_cs test to test SOM-advection on CS-grid.
340    o pkg/ctrl:
341      - Rewrite of ctrl_map_ini_ecco.F,
342        introducing a generic routine (ctrl_map_ini_gen.F).
343      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
344    
345    checkpoint59n
346    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
347      number in dedicate array "hdiag":
348      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
349        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
350      - many small changes (integer format) for large number of diagnostics
351      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
352        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
353    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
354      usingSphericalGrid, this allows to define the rotated grid coordinates
355      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
356      geographical coordinates according to the inverse of the rotation defined
357      by the Euler angles, so that Coriolis parameter and online-interpolation by
358      exf works with the geographical coordinates on XC/YC/XG/YG.
359      Naturally, this feature does not work with all packages, so some
360      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
361      profiles), because there the coordinates are assumed to be regular
362      spherical grid coordinates.
363    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
364      - introduce isopycnal diffusion coefficient control.
365    o tools/adjoint_options:
366      - additional control vector components.
367    o pkg/mnc: have mnc create marginally meaning full coordinate variables
368      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
369    o pkg/mypackage:
370      - add example of read/write pickup for state-var ;
371      - add entry points to the main code for state-vars diags & write-pickup.
372    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
373      transitions for useExfYearlyFields
374      - add new subroutine that determines the file to read from for
375        use*YearlyFields = .TRUE. and .FALSE.
376      - add a verification experiment to global_with_exf that tests
377        useExfYearlyFields with USE_EXF_INTERPOLATION defined
378    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
379      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
380      subroutines (which could be generated from a template, because they are
381      almost identical), for now they are included in obcs_prescribe_read.F for
382      simplicity
383    o pkg/exf:
384      - add a little more diagnostic to exf_interp_read (in analogy to
385        mds_read_field, can be turned off with debugLevel < debugLevA=1)
386      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
387        ugly but fast by unrolling short inner loops, inserting a unroll=8
388        directive in routine lagran, and splitting a loop and making do while the
389        outermost loop (the latter requires the intoduction of index arrays)
390    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
391    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
392      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
393    o verification/seaice_obcs: updated for restart test and latest options
394    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
395      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
396      for now this is only available for the C-grid code and also within
397      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
398    
399    checkpoint59m
400    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
401      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
402    o gad_som : fix flux output (& diagnostics) to have same units as other  
403      advection scheme fluxes (was previously multiplied by deltaT).  
404    o added verification/seaice_obcs both to test seaice open boundaries
405      and to provide an example matlab scrpt for generating them
406    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
407    o pkg/salt_plume: clean up salt_plume_frac.F to
408      remove redundancy in PlumeMethod 1 and 4
409    o pkg/kpp: added saltplume diagnostics
410    o pkg/obcs and pkg/seaice:
411      - do not set uice and vice to zero when OB*icefile are unspecified
412      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
413      - moved seaice tracer obcs after call to seaice_growth
414    o pkg/salt_plume: added various options for salt plume depth
415      criterion and for vertical distribution of the salt
416    
417    checkpoint59l
418    o pkg/ptracers: new version of ptracers pickup:
419      read meta file and write only fields which are needed to restart.
420      ( same logic as main pickup file ; also using pickupStrictlyMatch )
421    o pkg/seaice:
422      - add timescale for melting due to warm mixed layer as a means of
423        setting SEAICE_availHeatFrac more conveniently
424      - add a CPP-flag/runtime parameter check for flooding algorithm
425      - reformulated availHeat in seaice_growth.F to be independent of AREA
426    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
427      unit changes
428    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
429    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
430      SX vector computer.
431    o pkg/seaice:
432      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
433        seaice forcing fields can now be read only through pkg/exf
434      - removed some unused halos
435    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
436    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
437      or U/VICE from U/VWIND before computing U/VSTRESS
438    
439    checkpoint59k
440    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
441      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
442    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
443      all experiments pass when compile with un-initialised var. checking option.
444    o added pkg/salt_plume
445    o script to test restart (for now, in MITgcm_contrib/jmc_script)
446    o pkg/seaice: new read/write pickup version.
447      read meta file and write only fields which are needed to restart.
448      ( same logic as main pickup file ; also using pickupStrictlyMatch )
449    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
450    o lab_sea.hb87: modify the domain & update output.hb87.txt :
451      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
452      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
453      process. Fixed here by closing the domain at the Northern boundary.
454    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
455    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
456      a set of consecutive levels in/from a 3-D array.
457    o pkg/ptracers:
458      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
459      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
460    
461    checkpoint59j
462    o in pkgs: dic, obcs, offline, rbcs:
463      standard way to compute coeff. for time interpolation between 2 time reccords
464      which retains full precision (& make results less dependent on compiler).
465      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
466    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
467      packages instead of reading ice cover and wind speed separately
468    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
469     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
470      to allow to compile customized code before the update)
471    o cleaning-up:
472      - fix CPP instruction syntax in pkg/obcs
473      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
474        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
475      - fix some threads issue in IO parts.
476    o pkg/dic:
477      - add tons of "_d 0" (--> much better testreports !)
478       and then update outputs of tutorial_global_oce_biogeo
479    o pkg/mom_fluxform:
480      add a special version of momentum advection intended to conserve momentum
481      next to a bathymetry step or a coastline edge. (default = off = #undef)
482    o new read/write pickup version:
483      - for now, only implemented for main (mdsio) pickup file.
484      - write out only what is needed to restart; merge pickup_nh , pickup_ph
485        and main pickup together.
486      - read meta file; read only what is needed to restart; stop if a field
487        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
488        if it make sense (even if the restart is not perfect).
489      - if no meta file, assume that pickup to read corresponds exactly to
490        a pickup that would currently be written.
491      - read pickup written in the old format (until checkpoint59i) if it
492        recognizes an old meta file (no field-list).
493      - add a meta file in exp. which starts from a pickup: 2 cases:
494        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
495         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
496        b) a meta file describing the content of the associated pickup file
497         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
498    o pkg/mdsio & pkg/rw:
499      - new routine to read a meta file ; new set of routine to read
500        Multiple-fields file (with meta file).
501    o added open boundary conditions capability for seaice
502        HSNOW, HSALT, UICE, and VICE
503    
504    checkpoint59i
505    o adjoint:
506      * fix multiDimAdvection adjoint
507        (partial recomputation problem by TAF for fVerT(:,:,kDown)
508        and comlev1 size definition (maxpass vs. max. number of tracers)
509      * verification/global_ocean.90x45x15 adjoint now tests
510        NLFS and multiDimAdvection using DST3 (=30)
511      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
512    o pkg/kpp: add "_d 0" to real constant (if missing);
513      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
514      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
515    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
516      for internal parameters related to restart process (formerly from PARAMS.h)
517      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
518    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
519      as argument. (only atm2d & obcs write_pickup have not yet been updated)
520    o pkg/monitor:
521      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
522      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
523      - account for deep Atmosphere factor and density factor (anelastic)
524    o added open boundary conditions capability for seaice HEFF and AREA
525    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
526      thermodynamics
527      - requires a little reorganization, which affects the testreport results
528        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
529        so that now the conservative form is tested
530      - add a few comments
531    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
532    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
533    o add new diagnostics to seaice: advective, diffusive fluxes (only for
534      multidim-advection, for scheme 2 they are not filled) and transports,
535      thermodynamic growth rates
536    o change units of EmPmR (inside the code, + within coupling interface)
537      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
538      Affects results @ truncation level (cg2d match) and update output of
539       experiments: lab_sea(6), global_ocean.90x40x15(10),
540      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
541      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
542      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
543      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
544    
545    checkpoint59h
546    o pkg/exf:
547      - improve vectorization by moving if-statement out of loops in
548        exf_mapfields, exf_radiation
549      - exf_bulkformulae.F: introduce 2D fields and vectorize code
550    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
551    o testreport:
552      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
553        monitor & update offline_exf_seaice exp. output.
554      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
555    o pkg/seaice:
556      - bug fix in the evp solver: boundary conditions were affected be
557        masking of zMax/zMin (changes results)
558      - minor bug fix in boundary conditions in seaice_calc_strainrates
559        (changes results for no_slip)
560      - seaice_lsr.F: make interpolation of eta dependent on boundaries
561      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
562      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
563        stress formulation and no-slip boundary conditions
564    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
565      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
566    o pkg/seaice: a first HSALT time stepping equation has been checked in
567    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
568      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
569      without requiring DO-IF statements
570    o pkg/thsice:
571      use continuous power-law function for partition of energy between lateral
572      melting/freezing and thinning/thickening ; old code using step function
573      still available with #undef THSICE_FRACEN_POWERLAW
574      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
575    o testreport: change AD testing : check against results/output_adm.txt
576      using same scripts as for forward test.
577    
578    checkpoint59g
579    o adjoint testing: in preparation for changing testreport:
580      - output format: cost and grad written on separated lines
581      - ad output results in directory "results" (instead of "results_ad")
582    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
583    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
584    o pkg/ecco: allow user defined cost function contributions
585    o testreport:
586      Allow to choose (per experiment) the list of tested output variables
587       and the main variable (used to issue a pass/FAIL ) ;
588      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
589      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
590      Also modify printing of summary:
591       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
592       b) echo the list of tested variables in the individual summary.txt of
593          each experiment.
594    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
595      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
596      (but still depend on the tile decompostion of the domain).
597    o pkg/seaice: change a discretization detail to make the B-grid code
598      "more symmetric". This change is likely to remove all "ridges/leads" that
599      where quasi-aligned with the grid in B-grid solutions. It may also be
600      the solution to the stress coupling issues with the B-grid.
601    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
602      remove .cvsignore from input dir. (since testreport no longer run here).
603    o pkg/thsice:
604     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
605     - fix reshaping of sea-ice just after advection:
606       melt all the ice only if ice-volume is too small.
607     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
608       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
609     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
610    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
611      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
612    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
613      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
614      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
615      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
616      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
617      -> update output.txt
618    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
619     this affects truncation error: -> update output.txt of exp:
620      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
621      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
622    
623    checkpoint59f
624    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
625    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
626      a bounded range (in forward mode)
627    o pkg/ecco, ctrl, autodiff and mom_common:
628     internal parameter controls, completements of implementations
629    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
630    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
631      (not seem any difference in testing results).
632    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
633       at face corners.
634    o pkg/generic_advdiff:
635     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
636      loop range indices for computing vertical advection tendency
637      and do the calculation in the interior only (no overlap) ;
638      for now, only implemented for SOM advection (to save CPU time).
639     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
640    o exch2 adjoint
641      First set of changes:
642      - add exch2 hand-written adjoint templates
643      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
644        This will require cleanup in pkg/autodiff/*.F
645        (changed routines currently kept separate in verif. code/)
646      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
647        that used to hide exch2 or cubed-sphere specific code
648        (commented via 'cph-exch2')
649    o pkg/seaice
650      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
651    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
652       output of global_ocean.cs32x15.thsice .
653    
654    checkpoint59e
655    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
656      for B-grid vector (not yet tested) and C-grid vector (<- only used
657      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
658    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
659      (#ifdef ALLOW_SALT_PLUME)
660    o gather_2d/scatter_2d: removed halo regions
661    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
662      scheme and the corresponding test case (under front_relax dir). For now,
663      only available with Skew-flux form and not yet tested in realistic set-up.
664      adjoint: store directives updated, but gradient checks deteriorated,
665      so maybe GM/Redi adjoint is now broken.
666    o seaice adjoint
667      * add AREA, HEFF, HSNOW as control variable
668        (should not change lab_sea results)
669      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
670    o pkg/seaice:
671      * added computation of saltFlux in seaice_growth;
672        For time being, sea ice salinity is assumed constant
673        contribution of snow flooding to freshening of sea ice is neglected.
674        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
675        defaults to 0.0 in order to maintain backward compatibility.
676        Typical values for SEAICE_salinity are 4 to 10 g/kg.
677      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
678      * added SEAICE_availHeatFrac, which specifies fraction of surface level
679        heat content used to melt or grow ice
680      * commented out cap of HICE: it helps keep ice thinner
681      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
682      * applied OBCS T/S mask to HEFFM sea ice mask
683    
684    checkpoint59d
685    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
686     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
687     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
688    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
689     and change default value of parameter "GM_Small_Number";
690     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
691       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
692       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
693    o pkg/ecco: cost function when applying pkg/smooth to controls
694    o pkg/ctrl: add forcingPrecond run time parameter
695    o pkg/seaice:
696     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
697     - fix bug in metric terms of u-equation in LSR solver (implicit part),
698       changes verification/lab_sea
699     - rearrange implicit part of u-equation in LSR solver to make it easier to
700       read, understand, and debug. This causes changes at the truncation level.
701     - fix (serious) bug in the boundary conditions (sign error in the implicit
702       part) of the LSR solver. Changes all LSR results.
703     - fixed problem with HSNOW initialization to avoid thick snow when AREA
704       is initilized with small values - does not change lab_sea results.
705     - added HsnowFile initialization capability
706    o pkg/smooth: addition to model/src and pkg/ctrl so allow
707     initialization of pkg/smooth and application to control vector
708    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
709    o dependencies: pkg/profiles requires pkg/cal
710    o pkg/profiles:
711     - added option ALLOW_PROFILES_GENERICGRID
712         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
713         that interpolation information (grid points and coefficients) is provided
714         within the netcdf input files.
715         -> sample matlab scripts can be found in MITgcm_contrib/gael
716         that allow you to prepare netcdf input files.
717     - also modified: cleaner include statements, cleaner error print statements,
718       cleaner stops when error, and more tests of the netcdf input files consistency.
719    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
720    o pkg/seaice:
721     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
722       requires a new routine: seaice_diagnostics_fill.F
723     - make sure that seaice does not move if not forced (pressure replacement
724       method, Hibler and Ip, 1995), changes results
725     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
726     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
727       It is turned off by default (=-1.), because it changes the results.
728     - make it possible to read AREA from a file, too.
729    
730    checkpoint59c
731    o add S/R and diagnostics for oceanic mixed-layer depth
732    o move GMRedi call after all vertical mixing schemes (including KPP)
733    o pkg/thsice:
734     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
735      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
736    o pkg/obcs:
737     - bug fix for balance code
738    o pkg/seaice:
739      - allow values of SEAICE_elasticParm > 1
740      - add new parameter SEAICE_evpTauRelax as an alternative
741        to SEAICE_elasticParm
742      - make lsr boundary conditions free slip (by default), changes result
743      - add code for no slip boundary conditions for lsr
744      - set minimum of zeta to zero (and not 4e8) (changes results)
745      - add a cap on AREA after advecting AREA if seaice_growth is not called
746    o change calculation of Visbeck K:
747      - no longer depend on tapering scheme; instead, compute slope (limited
748        by GM_maxSlope). this is equivalent to what was comuted before with
749        clipping or linear tappering.
750      - fix vertical averaging (wrong by 1/2 level)
751      - leave the old version (but will not be maintained) within
752        #ifdef OLD_VISBECK_CALC / #endif
753      - update output of exp. ideal_2D_oce
754    o change error catch in calc_r_star to improve vectorization
755    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
756      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
757    o adjoint:
758      Re-organized adjoint checkpointing according to Matt Mazloff
759      (but with modifs/completions/cleanups)
760      Storing is now bundled into large arrays to optimized I/O
761      (and second step in cleanup of the_main_loop)
762    
763    checkpoint59b
764    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
765      - export/import (between ocean & coupler) fields needed for ocean DIC.
766    o pkg/seaice:
767      - get rid of three more exchanges seaice_calc_viscosities (required
768        different loop boundaries in seaice_lsr and seaice_ocean_stress)
769      - bug fix in seaice_ocean_stress (update of lab_sea required)
770      - reduce loop boundaries to necessary minimum also in seaice_evp
771      - go back to the old way of computing deltaC/Z as the adjoint likes that
772        better
773    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
774      passive tracer to an Age Tracer) + update output.txt
775    o pkg/exf:
776      - implement A-grid / C-grid selection for wind-stress input files.
777      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
778      for now, in exf_bulk_largeyeager04.F only :
779      - change implementation for case where windspeed + 2. components wind-stress
780        are read-in. AND use rhoConstFresh to convert evap.
781    o pkg/seaice:
782      - use correct EXCH_UV for wind-forcing (on A-grid).
783      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
784        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
785    o pkg/exf:
786      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
787      EXF_INTERPOLATION:
788      - merge global_with_exf/code version of exf_interp_read.F
789        to the main code ;
790      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
791        reading the file ; Important: This options needs to be defined to recover
792        previous code.
793        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
794      - no longer loose real*8 precision along the way when using exf_iprec=64.
795    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
796      - change discretisation of evp-solver in order to avoid another exchange
797        (changes lab_sea) and clean up a little
798      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
799        help the adjoint (this also changes the results slightly)
800      - add a few "_d 0" where they had been missing in seaice_evp.F
801      - cleaning up: remove unused seaice_calc_rhs.F
802    o pkg/exf: some cleaning-up:
803      - change various "constants" into runtime parameters
804      - cleaned-up Large&Yeager04 routine which should eventually
805        replace exf_bulkformulae.F (changed names of S/R and CPP)
806        and merged various ALLOW_ATM_WIND options
807     only used with thsice pkg (in thsice_get_exf.F):
808      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
809        which are used when useStabilityFct_overIce=TRUE (= the default)
810      - change default values of ice & snow emissivity and scale downward LW
811        by ice & snow emissivity.
812    o pkg/thsice:
813     fix few little problems, in thsice_calc_thickn.F:
814      - growth vertically (and not laterally) if iceFrac == iceMaskMax
815      - melt only laterally if hIce < hThinIce (as the comments say)
816      and in thsice_extend.F:
817      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
818      - start to form ice as soon as the minimum ice-volume is reachable.
819     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
820      and cpl_aim+ocn
821    o pkg/kpp
822     - move computation of surface related input fields to KPP into a new
823       subroutine kpp_forcing_surf.F
824     - remove wrong (within bi,bj loops) EXCH calls.
825     - little cleaning (add argument myThid in last position, cvs header ...)
826     - for now, fix conservation problem by exchanging KPPviscAz (may not
827       be the best fix)
828    o pkg/seaice
829     - check for inconsistent evp parameter/cpp-flag combination
830     - remove leftover errIO flat for obsolete name list error handling
831    o OpenAD
832     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
833    
834    checkpoint59a
835    o pkg/seaice: some parameter clarifications and a little bit of clean up
836    o pkg/thsice: rename run-time parameters:
837       himin       -> hIceMin
838       himin0      -> hThinIce
839       hihig       -> hThickIce
840       i0          -> i0swFrac
841       transCoef   -> bMeltCoef
842       frac_energy -> fracMelting
843      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
844       with default values (for now) that do not change the results.
845      remove old version of thsice vars advection in pkg/seaice.
846    o in FFIELDS.h:
847      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
848      - make pLoad & sIceLoad always available (but still only used if
849         ATMOSPHERIC_LOADING is #define).
850    o pkg/kpp: replaced _KPP_RL with _RL
851    o bug fixes for vertical diffusivity computations when both KPP and
852        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
853        are no longer updating the vertical diffusivity array
854        (passed as argument) but are (re-) setting those arrays.
855    o pkg/seaice: fix bug in evp solver, while doing that
856      - change (improve?) discretization of stress computations for both
857        cgrid-lsr and evp solver
858      - add a new routine to compute strain rates
859      - the above changes lab_sea results
860      - add no slip conditions for evp solver (off by default), lsr-version
861        may follow
862      - fix exchange for shear at Z-points (does not change lab_sea)
863      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
864        (to force the user to pick a time step since there is not "safe" way
865        of choosing it)
866      - add principal stress diagnostics
867      - rearrange fields for evp a little to avoid having to call a: too many
868        exchanges and b: exchanges for stress trensor components which we do
869        not have.
870      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
871        of evp, complete rewrite for lsr case (latter is does not yet work
872        in all cases)
873    o pkg/kpp: add code to have mixing in shelf ice caverns
874      - add myThid to all kpp routines (long overdue)
875    
876    checkpoint59
877    o pkg/exf:
878      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
879        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
880      - move exf header files from lower_case.h to UPPER_CASE.h ;
881        add missing cvs Header & Name
882      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
883      - add namelist param. selectStressGridPosition, exf_monFreq
884      - retire many _CLIM routines, and remove data.exf_clim
885        + params moved to data.exf
886        + climsst, climsss now handled by exf_set_gen, i.e.
887          climss?period=0 refers to constant field,
888          climss?period=-12 to monthly forcing
889      - split up namelists in data.exf
890    o pkg/seaice:
891      - remove seaice_exch and seaice_exch_uv
892      - remove superfluous exchange of theta
893      - add myThid to seaice_budget_ocean/ice
894      - add new interface for atmospheric wind forcing (C-grid only)
895        + new routine
896        + two new field (taux, tauy for stress over ice)
897        + removed one global field (DAIRN) for C-grid case only
898    o pkg/thsise
899      - 2nd set of modifs for thsice adjoint in conjunction with exf
900    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
901    
902    checkpoint58y_post
903    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
904      vertical diffusivity, similar to that in MOM4; turned on using
905      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
906      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
907    o Added capability for 3D specification of background vertical diffusion
908      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
909      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
910      "data" file that contains the 3D vertical diffusivity coefficients.
911    o ice dynamics (pkg/seaice) with thsice thermodynamics:
912      - add code within pkg thsice to advect & diffuse sea-ice fields
913      similar to (and will replace) what has been added in  seaice_advdiff.F,
914      but: - conserving Mass, Heat & Salt.
915           - better when using non-linear advection scheme (not yet fully tested)
916           - can also be used in atmospheric set-up (for now, only the diffusion).
917    
918    checkpoint58x_post
919    o IO option for global-file compact format:
920      - add options when generating topology (utils/exch2/matlab-topology-generator)
921      - add I/O capability (pkg/mdsio).
922      - adapt utils/matlab/rdmds.m to read this format.
923      for now long-line format not yet supported by pkg/mdsio (& exch2).
924    o shelfice: add a few diagnostics
925    
926    checkpoint58w_post
927    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
928      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
929      (and replace horiVertRatio in NH code).
930      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
931                         and tutorial_plume_on_slope (sensitive to truncation)
932    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
933      directly to drive seaice model (C-grid only)
934    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
935     - reintroduce computation of wind from stress,
936     - compute tau (in exf_bulkformulae.F) from windstress averaged to
937       mass points to avoid tau = 0
938     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
939    o rdmnc.m: make it work with "global" files created with gluemnc
940    o rdmnc.m : some improvements in dealing with singleton dimension
941      (tested on all testreport mnc output files).
942    o genmake2: disable pkg/profiles if netcdf test fails.
943    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
944    o move call to cal_readparms up to make calendar parameters/variable available
945      to all packages
946    
947    checkpoint58v_post
948    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
949      useDynP_inEos_Zc tested.
950    o pkg/exf: changes to properly interpolate/mask/scale initial fields
951    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
952      and portions thereof.  See read_cs.txt for description and examples.
953    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
954      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
955      following the great-circle arc between those 2 points.
956    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
957      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
958    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
959     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
960     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
961     - still needs work (not working with some options ; efficiency to improve)
962       and serious testing.
963     - use this scheme for temperature & salinity in 2 advection test exp.:
964       advect_xy & advect_xz, respectively.
965    
966    checkpoint58u_post
967    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
968    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
969    o testreport: add option "-skipdir" to skip some test.
970    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
971      momentum calculation.
972    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
973    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
974      remove checkpoint.F and the_correction_step.F (no longer used);
975      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
976    o add option (linFSConserveTr) to correct for tracer source/sink due to
977      Linear Free surface
978    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
979    o pkg/thsice: fix reading mnc-pickups
980    
981    checkpoint58t_post
982    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
983    o pkg/mdsio:
984     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
985       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
986       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
987     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
988     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
989       either MDS_READ_FIELD or MDS_WRITE_FIELD )
990     - new S/R (to replace MDSWRITEMETA), which allows to write more
991       informations (variable names, time ...) to meta files.
992     - modify rdmds.m to give back the meta file content.
993    o pkg/diagnostics: change vertical interpolation to be safer, and more
994       flexible (define p-levels to interpolate to in data.diagnostics);
995      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
996       diagnostic pointer.
997    o pkg/seaice: more cleaning up of seaice_growth, added many comments
998    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
999    o fix multi-category seaice:
1000     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
1001       SEAICE_MULTICATEGORY
1002     - fix short wave heat flux
1003    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
1004       and allow to use EVP solver. Change forward lab_sea: test both EVP
1005       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
1006    o Initial check-in of lab_sea adjoint
1007      (very similar to natl_box_adjoint/code_seaice)
1008      * used C-grid and EVP solver
1009      * used KPP, GM/Redi
1010      * uses inAdExact=.TRUE.
1011      * gradient checks fail for both ADM and TLM
1012        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
1013        f.d. gradients actually seem more problematic than ADM, TLM gradients;
1014        issue is related to forward mismatch between g77 an ifort
1015    o pkg/seaice: overhaul of thermodynamics
1016     - growth.F and groatb.F are replaced by new routine seaice_growth.F
1017     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
1018     - move a few global fields out of SEAICE.h into seaice_growth.F and
1019       make them 2D (FICE/QNETO/ ...)
1020     - remove FO (it is the same as QNETO)
1021     - introduce a few local fields to avoid modifying external fields such
1022       as atemp, etc.
1023    
1024    checkpoint58s_post
1025    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
1026      changed exf_set_gen.F so that
1027        genperiod=0 means input file is one time-constant field and
1028        genperiod=-12 means input file contains 12 monthly means
1029    o CG2D: use pre-computed solver main-diagonal (stored in common block);
1030      this affects truncation error ; generate new output file for exp. which
1031      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
1032        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
1033        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
1034        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
1035        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
1036        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
1037    o start implementation of deep-atmosphere and anelastic formulation
1038    o verification: remove 2nd copy of input files and use script "prepare_run"
1039      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
1040    o mom_common/vecinv/fluxform: fix a few initialisation isssues
1041    o profiles: fix for multithreaded case
1042    
1043    o diagnostics: rename few diags:
1044      s/'PRESSURE'/'RCENTER '/g
1045      s/'TICE    '/'oceFreez'/g
1046      s/'TAUX    '/'oceTAUX '/g
1047      s/'TAUY    '/'oceTAUY '/g
1048      s/'SWFLUX  '/'oceQsw  '/g
1049      s/DIFx/DFxE/g
1050      s/DIFy/DFyE/g
1051      and add few ocean-forcing diagnostics:
1052      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
1053    o modifications to pkg/seaice/growth.F and budget.F, which change results of
1054      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
1055      as actual snow thickness.  It now refers everywhere to effective snow
1056      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
1057    
1058    checkpoint58r_post
1059    o modifications to pkg/seaice/growth.F, which change results of
1060      lab_sea experiment: fixes pertain to melting snow over open water, to
1061      masking EVAP under sea ice, and to using the correct AREA variable for
1062      computations of EVAP, PRECIP, HSNOW, and GHEFF
1063    o add ability to read bathy, salt, and theta using MNC (off by def)
1064    o add flooding algorithm and advection of HSNOW for pkg/seaice;
1065      both are turned off by default and do no change any results
1066    o seaice advection with pkg/thsice: a step toward the use of non-linear
1067      advection scheme, but #ifdef or commented out for now (requires more EXCH).
1068    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
1069      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
1070      in natl_box (affects results @ truncation level: update output.txt)
1071    o multi-threading and IO:
1072      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
1073      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
1074        (needed to work with SingleCpuIO): tested in all verif. exp.
1075    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
1076      affects the results (but none of the verification test uses this scheme).
1077    o Adding some pkg/diagnostics capability to pkg/seaice
1078      (will certainly be subject to changes)
1079    o ctrl: adding new control variables:
1080      lwflux, lwdown, evap, snowprecip, apressure, runoff
1081    
1082    checkpoint58q_post
1083    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
1084      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
1085      high_res_cube configuration by 4% on Columbia.
1086    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
1087      add (in global_with_exf/code) a version of EXF_INTERP_READ without
1088      dynamical allocation (seems to work in multi-threaded).
1089    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
1090      single CPU io) so that TAF does not have to see EESUPPORT.h
1091    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
1092    
1093    checkpoint58p_post
1094    o obcs: stop if obcs is used with useCDscheme = .true.
1095    o shelfice:
1096     - fix a sign error so that no slip at shelfice interface works
1097     - remove stop for combination non-hydrostatic code and shelfice. That does
1098       not mean, that the results are correct, but at least they are numerically
1099       stable
1100    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
1101    o added adjoint exch routined for all exch*3d* routines
1102      and updated flow directives
1103    
1104    checkpoint58o_post
1105    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
1106      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
1107    o change controling S/R for writing pickup file (new S/R do_write_pickup)
1108      and clean-up reading/writing of pickup files.
1109    o fix local version of read/write pickup (NH part) in rotating_tank/code
1110    o simplify EXCH interface:
1111     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
1112     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
1113    o added the regrid package
1114    o shelfice:
1115     - add a simple boundary layer scheme to reduce noise
1116     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
1117    
1118    checkpoint58n_post
1119    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
1120       local variable (not in common block).
1121    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
1122      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
1123      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
1124        to work with SingleCpuIO.
1125    o add "_d 0" to real constant of pkg/cfc subroutines ;
1126       update exp. cfc_exemple & tutorial_cfc_offline output files.
1127    o multi-threading and IO:
1128      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
1129        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
1130      - barrier before and after reading.
1131      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
1132      - avoid using MDS_WRITELOCAL for LAND pkg output.
1133      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
1134        common-block variables ; Allows multi-threading with master-thread IO.
1135    o change default MAX_NO_THREADS from 32 to 4 ;
1136      and stop cleanly when MAX_NO_THREADS is too small.
1137    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
1138    
1139    checkpoint58m_post
1140    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
1141       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
1142    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
1143       keep global_ocean.90x40x15 (for AD testing) with former secondary test
1144       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
1145    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
1146        add MITgcm_tutorials (= code + all the tutorials)
1147    o ecco, option to compute cost for total ssh (mean+anom)
1148    o consistent with addition of ptracer and ssh in pkg/profiles
1149  o profiles: adding ptracer and ssh  o profiles: adding ptracer and ssh
1150  o testreport: change multi-test output-file name  o testreport: change multi-test output-file name
1151    (from output.txt.{name} to output.{name}.txt)    (from output.txt.{name} to output.{name}.txt)
1152  o profiles: now ok for mutli-threaded case  o profiles: now ok for mutli-tiles case
1153  o seaice: add 4 parameters for different advection schemes for area,  o seaice: add 4 parameters for different advection schemes for area,
1154    (effective) seaice thickness, enthalphy, and snow height. Their default    (effective) seaice thickness, enthalphy, and snow height. Their default
1155    is the standard parameter SEAICEadvScheme    is the standard parameter SEAICEadvScheme
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