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revision 1.724 by heimbach, Wed Sep 6 18:31:32 2006 UTC revision 1.1063 by jmc, Tue Feb 10 22:23:28 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/shelfice: fix bug with SHELFICEconserve flag, prepare for
8      real fresh water flux (not yet)
9    o pkg/mdsio & rw:
10     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
11     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
12    o pkg/flt:
13     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
14       init_fixed & ini_varia.
15     - clean-up & simplify linear interpolation S/R:
16       move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
17     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
18     - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
19     - add vert. coordinate & horiz. indices to output files.
20     - change vertical position in initial condition, from index to depth [m].
21     - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
22       (easier to get to a curvilinear grid) ; delX,delY no longer used.
23    o pkg/ggl90: a few modifications:
24     - fix bottom boundary condition, and interpolation of KappaE
25       near top and bottom
26     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
27     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
28     - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
29    o rename thetaMin,phiMin -> xgOrigin,ygOrigin
30      (maintain temporary backward compatibility, until next checkpoint)
31    
32    checkpoint61h
33    o pkg/diagnostics with "periodic averaging diagnostics":
34      fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
35    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
36    o pkg/obcs: fix loop ranges for balancing code
37    o pkg/flt:
38     - improve criteria for finding which tile owns a float.
39     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
40    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
41      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
42      with ocean biogeo)
43    o pkg/flt:
44     - do some cleaning and fix the restart ;
45     - add output.txt in flt_example/results to get this pkg tested.
46    o genmake2: add an EXTENDED_SRC option and flag.
47       for now, cannot be turned on on command line (only through genmake_local)
48    o pkg/mdsio: read/write vector:
49     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
50     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
51       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
52     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
53      (drop to 4 digits matching for grad). But this test does not look very
54      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
55    
56    checkpoint61g
57    o pkg/flt:
58      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
59       + make OPTIONS file more standard.
60      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
61      - fix _BYTESWAPIO CPP-Flag
62      - standard reading of file-parameter "data.flt"
63      - fix argument list of S/R FLT_RESTART
64      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
65    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
66    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
67      a still unfixed compiler/optimization bug
68    
69    checkpoint61f
70    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
71      update results of global_ocean.cs32x15.icedyn test.
72    o move getcon.F from model/src to pkg/fizhi.
73    o pkg/exf: add parameter for extrapolation of temp up to the surface
74       and option to prevent negative evap (in bulk_largeyeager04 only).
75    o Prather Advection scheme: fix tracer conservation for divergent flow
76      (e.g., when using NonLin Free-Surface).
77    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
78    o gmredi (Visbeck-variable-K):
79     - add more parameters to Visbeck-variable-K.
80     - use a 5 points average for dSigmaR in Visbeck-K calculation
81       (more "homogenous": same stencil and same weights as in dSigmaH)
82     - update output of ideal_2D_oce experiment.
83    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
84      (#undef REAL4_IS_SLOW)
85     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
86       coordinate variable
87     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
88       (surface forcing fields), removes some of the functionality
89     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
90     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
91       probably not all: copy _RS surface flux fields to RL field before
92       calling DIAGNOSTICS_FILL
93     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
94       real*4 (CALL EXCH_*_RS) versions.
95     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
96       (generate new output).
97    
98    checkpoint61e
99    o gmredi (Visbeck-variable-K):
100      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
101      - change computation of Visbeck-K where Slope > Smax :        
102        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
103        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
104    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
105      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
106    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
107    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
108      does not become too large (to avoid precision problems in implicit-diffusion
109      solver); update ideal_2D_oce output.
110    o pkg ggl90:
111      - in ggl90_cal.F: compute only one set of visc/diff, used to
112        step forward TKE/T/S/momentum
113      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
114        have Prandlt =1)
115    o gmredi (fm07):
116      - add lower limit on Transition layer thickness + lower limit on 1/lambda
117      - allow to set few more params from data.gmredi
118    o pkg ggl90:
119          - add missing sqrt(2) factor in computation of mixing length
120            scale in ggl90_calc.F
121            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
122    
123    checkpoint61d
124    o adjoint modifs
125      - adapt to new field rhoInSitu
126      - allow to revert from StoreDynVars2D, StoreDynVars3D
127        to individual fields
128        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
129    o store 3-D (in-situ) density in commom block (DYNVARS.h)
130     - save 1 rho computation.
131     - no longer modify T & S inland when using down_slope pkg.
132    o gad_som : allow to switch to SOM advection for T & S without corresponding
133      pickup files (using new S/R: MDS_CHECK4FILE).
134    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
135      (for useSingleCpuIO to work in multi-threaded)
136    o pkg/shelfice:
137     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
138       with SHELFICEtopoFile in data.shelfice
139     - move code for reading ice shelf topography and modifying hFacC into separate
140       subroutines of the shelfice package
141     - separate initialisation of "fixed" and "variable" variables
142     - kTopC is not (yet) replaced by kSurfC, although this is possible
143    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
144    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
145      and rename:
146      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
147      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
148    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
149    
150    checkpoint61c
151    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
152      to add mass source/sink of fluid in the interior (3-D generalisation
153      of oceanic real-fresh water flux).
154    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
155    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
156    o new pkg: down_slope
157      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
158      - presently, modify T & S inland (dwnslp_calc_rho.F).
159        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
160      - implementation for ocean in P-coords not tested.
161      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
162    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
163      (to facilitate conversion of oceanic pkg to p-coordinate).
164    o change FIND_RHO to FIND_RHO_2D :
165      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
166    o new pkg: cheapaml
167    
168    checkpoint61b
169    o exch2:
170      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
171      - no longer depend on the order sequence (N,S,E,W).
172      - 3rd exchange no longer needed (tested with 24 tiles).
173      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
174      - exch_UV_A-grid readily available (but not yet tested).
175      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
176      (both are no longer needed) in exch_uv: no effect in forward run; but
177       get truncation error differences with adjoint exch.
178    o exch2:
179     - change index-bounds storage (moved from target to local tile,
180       more intuitive this way) ; rename/remove some variables.
181     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
182    
183    checkpoint61a
184    o exch2/matlab-topology-generator:
185      fix bug in index bounds for N-S internal exchange (hard to tell if this
186      had any effect on the solution).
187    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
188      is exceeded
189    o testreport: modify syntax of awk, so that it works also with
190      awk, and not only with nawk and gawk
191    
192    checkpoint61
193    o autodiff
194      Change default for TAF usage by removing argument '-nonew_arg'
195      This changes TAF subroutine argument list (ordering of active var.)
196      Omission of this flag leads to incompatibility w.r.t. TAMC
197      To restore TAMC-compatibility, need following modifs:
198      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
199      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
200      Tested TAF version is 1.9.22
201      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
202    
203    checkpoint60
204    --->>> This is the last checkpoint for which generating the adjoint
205    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
206    --->>> by default.
207    --->>> Future checkpoints will ommit this flag by default.
208    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
209    o pkg/grdchk: Add gradient check to etan0 perturbations.
210    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
211    o pkg/autodiff: more flexibility in zeroadj.
212      model/src: modifying do_oceanic_phys.F accordingly.
213    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
214    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
215      special setup of gmredi for which the adjoint is stable
216      enough for parameter optimization.
217    o bridging the gap between eddy stress and GM.
218      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
219          along with a change in CPP option (now ALLOW_EDDYPSI).
220      -> when using GM w/ GM_AdvForm:
221          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
222          is applied either in the tracer Eq. or in momentum Eq.
223          depending on data.gmredi (intro. GM_InMomAsStress).
224      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
225      The key modifications are in model/src/taueddy_external_forcing.F
226      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
227    
228    checkpoint59r
229    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
230      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
231      fix option to read coriolis(@ cell-corner) from files with CS-grid.
232    o pkg/mnc: add some attributes to standard 1D-coordinate variables
233    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
234      mass points, when using mnc for output
235      - add runtime parameter (missing_value, missing_value_int) to override
236        default (which is the value of getcon('UNDEF'))
237    o pkg/mnc: prepare mnc for the actual use of missing values with the
238      diagnostics package: small fix in mnc_cw_readwrite.template and more
239      initialisation of never used fields
240      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
241      versions
242    o pkg/thsice/thsice_ini_vars.F added default initial values so that
243      thermodynamics sea ice solver does not blow up when some initial fields
244      are missing.
245    o move from external_forcing_surf.F to ini_forcing.F
246      the p-coord. hack consisting in using pLoad to set phi0surf ;
247      update output of tutorial_global_oce_in_p (affected @ truncation level).
248    o Freshen up a bit hs94.1x64x5, notably:
249      remove rotationPeriod and tRef=5*0. (adjoint only), and add
250      exactConserv=.TRUE.
251    o pkg/generic_advdiff:
252      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
253      applies to files where Temperature & Salinity 2nd Order moments are used.
254    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
255      this uses a dynamically allocated internal state data structure
256      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
257      and requires a fortran 90 compiler
258    
259    checkpoint59q
260    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
261       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
262    o Refresh tutorial_global_oce_biogeo, notably:
263      - change bathymetry (put back seamounts in ACC, use hFacs)
264      - change EOS (POLY3 --> JMD95Z)
265      - use Bryan-Lewis vertical diffusivity
266      - use multidimensional advection
267      - remove old virtual virtual in dic pkg, now done through ptracer pkg
268      - change a couple of parameters in dic pkg
269    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
270    o pkg/obcs: change default to OBCSfixTopo = .true.,
271      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
272      - replace "debugMode" with "debugLevel .GE. debLevB"
273    o implementation of TAF directives for gchem,cfc,dic
274    o remove "exp5" (replaced by tutorial_deep_convection).
275    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
276      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
277      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
278      --> changes results in exp4, seaice_obcs
279    o tutorial_deep_convection :
280      update the set-up and increase resolution and domain size ; start
281      from pseudo initial conditions = output at t=120mn in order to see
282      something happening when running testreport.
283    o pkg/seaice: add os7mp as an advection scheme
284                  add check for advection schemes
285                  add a flag for restoring T and S underneath sea ice
286    o pkg/my82: add netcdf-support and diagnostics
287    o thsice pkg:
288      - Now hsMax limits snow height by turning it into ice following
289        flooding scheme (and now conserving energy)
290      - Slight rewriting of the formula in thsice_calc_thick.F
291      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
292      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
293    
294    checkpoint59p
295    o gchem / dic / cfc :
296      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
297      - add new parameter files: "data.dic" & "data.cfc" ;
298      - various re-arrangement in initialisation & header file ;
299      - fix tutorial_global_oce_biogeo for multi-threaded test.
300    o pkg/dic: test for "pickup_dic" file when restarting ;
301      if no pickup-file, can restart with a re-initialised pH (same as it did
302      before) providing pickupStrictlyMatch is set to False.
303    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
304      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
305    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
306      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
307    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
308     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
309       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
310    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
311       scheme to use for vorticty-term ;
312     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
313       (with default selectVortScheme, return to original discretisation)
314     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
315    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
316    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
317      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
318      also fix diagnostics VISCAHW & VISCA4W.
319    
320    checkpoint59o
321    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
322    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
323      move a few statemens out the main loop into separate loops
324    o pkg/shelfice:
325      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
326        (kg/m^2/s), does not break tests, because in verification/isomip,
327        rhoConstFresh=rhoConst (by accident)
328      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
329      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
330        new file model/src/seawater.F, so that they are available for all pkgs.
331      - convert potential temperature into in-situ temperature. This changes the
332        isomip tests => update tests
333    o add a flag writePickupAtEnd (default=true) to be able to suppress
334      writing a pickup at the last timestep
335    o tools/mpack-1.6 :
336      - disable automake (not working) and autoconf (not needed).
337      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
338        also cleaner with much less compilation warnings.
339    o pkg/profiles:
340      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
341      (for "less than 32 characters name" compiler requirement)
342    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
343      conditions that have a different sampling frequency than S/T/U/V obcs
344    o pkg/diagnostics (stats-diags):
345      - fix global Min/Max in case 1 processor get only empty tiles
346    o genmake2: replace (4 times)
347         make genmake_tc_1.o >> genmake_warnings 2>&1
348      with
349         COMM="$CC $CFLAGS -c genmake_tc_1.c"
350         echo $COMM >> genmake_warnings
351         $COMM >> genmake_warnings 2>&1
352      to make genmake2 always see the value of CC as specified in the optfile.
353    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
354      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
355      - modify verification advect_cs test to test SOM-advection on CS-grid.
356    o pkg/ctrl:
357      - Rewrite of ctrl_map_ini_ecco.F,
358        introducing a generic routine (ctrl_map_ini_gen.F).
359      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
360    
361    checkpoint59n
362    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
363      number in dedicate array "hdiag":
364      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
365        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
366      - many small changes (integer format) for large number of diagnostics
367      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
368        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
369    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
370      usingSphericalGrid, this allows to define the rotated grid coordinates
371      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
372      geographical coordinates according to the inverse of the rotation defined
373      by the Euler angles, so that Coriolis parameter and online-interpolation by
374      exf works with the geographical coordinates on XC/YC/XG/YG.
375      Naturally, this feature does not work with all packages, so some
376      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
377      profiles), because there the coordinates are assumed to be regular
378      spherical grid coordinates.
379    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
380      - introduce isopycnal diffusion coefficient control.
381    o tools/adjoint_options:
382      - additional control vector components.
383    o pkg/mnc: have mnc create marginally meaning full coordinate variables
384      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
385    o pkg/mypackage:
386      - add example of read/write pickup for state-var ;
387      - add entry points to the main code for state-vars diags & write-pickup.
388    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
389      transitions for useExfYearlyFields
390      - add new subroutine that determines the file to read from for
391        use*YearlyFields = .TRUE. and .FALSE.
392      - add a verification experiment to global_with_exf that tests
393        useExfYearlyFields with USE_EXF_INTERPOLATION defined
394    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
395      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
396      subroutines (which could be generated from a template, because they are
397      almost identical), for now they are included in obcs_prescribe_read.F for
398      simplicity
399    o pkg/exf:
400      - add a little more diagnostic to exf_interp_read (in analogy to
401        mds_read_field, can be turned off with debugLevel < debugLevA=1)
402      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
403        ugly but fast by unrolling short inner loops, inserting a unroll=8
404        directive in routine lagran, and splitting a loop and making do while the
405        outermost loop (the latter requires the intoduction of index arrays)
406    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
407    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
408      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
409    o verification/seaice_obcs: updated for restart test and latest options
410    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
411      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
412      for now this is only available for the C-grid code and also within
413      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
414    
415    checkpoint59m
416    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
417      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
418    o gad_som : fix flux output (& diagnostics) to have same units as other  
419      advection scheme fluxes (was previously multiplied by deltaT).  
420    o added verification/seaice_obcs both to test seaice open boundaries
421      and to provide an example matlab scrpt for generating them
422    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
423    o pkg/salt_plume: clean up salt_plume_frac.F to
424      remove redundancy in PlumeMethod 1 and 4
425    o pkg/kpp: added saltplume diagnostics
426    o pkg/obcs and pkg/seaice:
427      - do not set uice and vice to zero when OB*icefile are unspecified
428      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
429      - moved seaice tracer obcs after call to seaice_growth
430    o pkg/salt_plume: added various options for salt plume depth
431      criterion and for vertical distribution of the salt
432    
433    checkpoint59l
434    o pkg/ptracers: new version of ptracers pickup:
435      read meta file and write only fields which are needed to restart.
436      ( same logic as main pickup file ; also using pickupStrictlyMatch )
437    o pkg/seaice:
438      - add timescale for melting due to warm mixed layer as a means of
439        setting SEAICE_availHeatFrac more conveniently
440      - add a CPP-flag/runtime parameter check for flooding algorithm
441      - reformulated availHeat in seaice_growth.F to be independent of AREA
442    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
443      unit changes
444    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
445    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
446      SX vector computer.
447    o pkg/seaice:
448      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
449        seaice forcing fields can now be read only through pkg/exf
450      - removed some unused halos
451    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
452    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
453      or U/VICE from U/VWIND before computing U/VSTRESS
454    
455    checkpoint59k
456    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
457      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
458    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
459      all experiments pass when compile with un-initialised var. checking option.
460    o added pkg/salt_plume
461    o script to test restart (for now, in MITgcm_contrib/jmc_script)
462    o pkg/seaice: new read/write pickup version.
463      read meta file and write only fields which are needed to restart.
464      ( same logic as main pickup file ; also using pickupStrictlyMatch )
465    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
466    o lab_sea.hb87: modify the domain & update output.hb87.txt :
467      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
468      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
469      process. Fixed here by closing the domain at the Northern boundary.
470    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
471    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
472      a set of consecutive levels in/from a 3-D array.
473    o pkg/ptracers:
474      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
475      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
476    
477    checkpoint59j
478    o in pkgs: dic, obcs, offline, rbcs:
479      standard way to compute coeff. for time interpolation between 2 time reccords
480      which retains full precision (& make results less dependent on compiler).
481      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
482    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
483      packages instead of reading ice cover and wind speed separately
484    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
485     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
486      to allow to compile customized code before the update)
487    o cleaning-up:
488      - fix CPP instruction syntax in pkg/obcs
489      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
490        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
491      - fix some threads issue in IO parts.
492    o pkg/dic:
493      - add tons of "_d 0" (--> much better testreports !)
494       and then update outputs of tutorial_global_oce_biogeo
495    o pkg/mom_fluxform:
496      add a special version of momentum advection intended to conserve momentum
497      next to a bathymetry step or a coastline edge. (default = off = #undef)
498    o new read/write pickup version:
499      - for now, only implemented for main (mdsio) pickup file.
500      - write out only what is needed to restart; merge pickup_nh , pickup_ph
501        and main pickup together.
502      - read meta file; read only what is needed to restart; stop if a field
503        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
504        if it make sense (even if the restart is not perfect).
505      - if no meta file, assume that pickup to read corresponds exactly to
506        a pickup that would currently be written.
507      - read pickup written in the old format (until checkpoint59i) if it
508        recognizes an old meta file (no field-list).
509      - add a meta file in exp. which starts from a pickup: 2 cases:
510        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
511         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
512        b) a meta file describing the content of the associated pickup file
513         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
514    o pkg/mdsio & pkg/rw:
515      - new routine to read a meta file ; new set of routine to read
516        Multiple-fields file (with meta file).
517    o added open boundary conditions capability for seaice
518        HSNOW, HSALT, UICE, and VICE
519    
520    checkpoint59i
521    o adjoint:
522      * fix multiDimAdvection adjoint
523        (partial recomputation problem by TAF for fVerT(:,:,kDown)
524        and comlev1 size definition (maxpass vs. max. number of tracers)
525      * verification/global_ocean.90x45x15 adjoint now tests
526        NLFS and multiDimAdvection using DST3 (=30)
527      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
528    o pkg/kpp: add "_d 0" to real constant (if missing);
529      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
530      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
531    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
532      for internal parameters related to restart process (formerly from PARAMS.h)
533      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
534    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
535      as argument. (only atm2d & obcs write_pickup have not yet been updated)
536    o pkg/monitor:
537      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
538      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
539      - account for deep Atmosphere factor and density factor (anelastic)
540    o added open boundary conditions capability for seaice HEFF and AREA
541    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
542      thermodynamics
543      - requires a little reorganization, which affects the testreport results
544        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
545        so that now the conservative form is tested
546      - add a few comments
547    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
548    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
549    o add new diagnostics to seaice: advective, diffusive fluxes (only for
550      multidim-advection, for scheme 2 they are not filled) and transports,
551      thermodynamic growth rates
552    o change units of EmPmR (inside the code, + within coupling interface)
553      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
554      Affects results @ truncation level (cg2d match) and update output of
555       experiments: lab_sea(6), global_ocean.90x40x15(10),
556      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
557      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
558      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
559      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
560    
561    checkpoint59h
562    o pkg/exf:
563      - improve vectorization by moving if-statement out of loops in
564        exf_mapfields, exf_radiation
565      - exf_bulkformulae.F: introduce 2D fields and vectorize code
566    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
567    o testreport:
568      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
569        monitor & update offline_exf_seaice exp. output.
570      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
571    o pkg/seaice:
572      - bug fix in the evp solver: boundary conditions were affected be
573        masking of zMax/zMin (changes results)
574      - minor bug fix in boundary conditions in seaice_calc_strainrates
575        (changes results for no_slip)
576      - seaice_lsr.F: make interpolation of eta dependent on boundaries
577      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
578      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
579        stress formulation and no-slip boundary conditions
580    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
581      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
582    o pkg/seaice: a first HSALT time stepping equation has been checked in
583    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
584      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
585      without requiring DO-IF statements
586    o pkg/thsice:
587      use continuous power-law function for partition of energy between lateral
588      melting/freezing and thinning/thickening ; old code using step function
589      still available with #undef THSICE_FRACEN_POWERLAW
590      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
591    o testreport: change AD testing : check against results/output_adm.txt
592      using same scripts as for forward test.
593    
594    checkpoint59g
595    o adjoint testing: in preparation for changing testreport:
596      - output format: cost and grad written on separated lines
597      - ad output results in directory "results" (instead of "results_ad")
598    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
599    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
600    o pkg/ecco: allow user defined cost function contributions
601    o testreport:
602      Allow to choose (per experiment) the list of tested output variables
603       and the main variable (used to issue a pass/FAIL ) ;
604      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
605      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
606      Also modify printing of summary:
607       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
608       b) echo the list of tested variables in the individual summary.txt of
609          each experiment.
610    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
611      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
612      (but still depend on the tile decompostion of the domain).
613    o pkg/seaice: change a discretization detail to make the B-grid code
614      "more symmetric". This change is likely to remove all "ridges/leads" that
615      where quasi-aligned with the grid in B-grid solutions. It may also be
616      the solution to the stress coupling issues with the B-grid.
617    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
618      remove .cvsignore from input dir. (since testreport no longer run here).
619    o pkg/thsice:
620     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
621     - fix reshaping of sea-ice just after advection:
622       melt all the ice only if ice-volume is too small.
623     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
624       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
625     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
626    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
627      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
628    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
629      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
630      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
631      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
632      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
633      -> update output.txt
634    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
635     this affects truncation error: -> update output.txt of exp:
636      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
637      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
638    
639    checkpoint59f
640    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
641    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
642      a bounded range (in forward mode)
643    o pkg/ecco, ctrl, autodiff and mom_common:
644     internal parameter controls, completements of implementations
645    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
646    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
647      (not seem any difference in testing results).
648    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
649       at face corners.
650    o pkg/generic_advdiff:
651     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
652      loop range indices for computing vertical advection tendency
653      and do the calculation in the interior only (no overlap) ;
654      for now, only implemented for SOM advection (to save CPU time).
655     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
656    o exch2 adjoint
657      First set of changes:
658      - add exch2 hand-written adjoint templates
659      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
660        This will require cleanup in pkg/autodiff/*.F
661        (changed routines currently kept separate in verif. code/)
662      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
663        that used to hide exch2 or cubed-sphere specific code
664        (commented via 'cph-exch2')
665    o pkg/seaice
666      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
667    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
668       output of global_ocean.cs32x15.thsice .
669    
670    checkpoint59e
671    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
672      for B-grid vector (not yet tested) and C-grid vector (<- only used
673      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
674    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
675      (#ifdef ALLOW_SALT_PLUME)
676    o gather_2d/scatter_2d: removed halo regions
677    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
678      scheme and the corresponding test case (under front_relax dir). For now,
679      only available with Skew-flux form and not yet tested in realistic set-up.
680      adjoint: store directives updated, but gradient checks deteriorated,
681      so maybe GM/Redi adjoint is now broken.
682    o seaice adjoint
683      * add AREA, HEFF, HSNOW as control variable
684        (should not change lab_sea results)
685      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
686    o pkg/seaice:
687      * added computation of saltFlux in seaice_growth;
688        For time being, sea ice salinity is assumed constant
689        contribution of snow flooding to freshening of sea ice is neglected.
690        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
691        defaults to 0.0 in order to maintain backward compatibility.
692        Typical values for SEAICE_salinity are 4 to 10 g/kg.
693      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
694      * added SEAICE_availHeatFrac, which specifies fraction of surface level
695        heat content used to melt or grow ice
696      * commented out cap of HICE: it helps keep ice thinner
697      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
698      * applied OBCS T/S mask to HEFFM sea ice mask
699    
700    checkpoint59d
701    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
702     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
703     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
704    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
705     and change default value of parameter "GM_Small_Number";
706     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
707       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
708       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
709    o pkg/ecco: cost function when applying pkg/smooth to controls
710    o pkg/ctrl: add forcingPrecond run time parameter
711    o pkg/seaice:
712     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
713     - fix bug in metric terms of u-equation in LSR solver (implicit part),
714       changes verification/lab_sea
715     - rearrange implicit part of u-equation in LSR solver to make it easier to
716       read, understand, and debug. This causes changes at the truncation level.
717     - fix (serious) bug in the boundary conditions (sign error in the implicit
718       part) of the LSR solver. Changes all LSR results.
719     - fixed problem with HSNOW initialization to avoid thick snow when AREA
720       is initilized with small values - does not change lab_sea results.
721     - added HsnowFile initialization capability
722    o pkg/smooth: addition to model/src and pkg/ctrl so allow
723     initialization of pkg/smooth and application to control vector
724    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
725    o dependencies: pkg/profiles requires pkg/cal
726    o pkg/profiles:
727     - added option ALLOW_PROFILES_GENERICGRID
728         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
729         that interpolation information (grid points and coefficients) is provided
730         within the netcdf input files.
731         -> sample matlab scripts can be found in MITgcm_contrib/gael
732         that allow you to prepare netcdf input files.
733     - also modified: cleaner include statements, cleaner error print statements,
734       cleaner stops when error, and more tests of the netcdf input files consistency.
735    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
736    o pkg/seaice:
737     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
738       requires a new routine: seaice_diagnostics_fill.F
739     - make sure that seaice does not move if not forced (pressure replacement
740       method, Hibler and Ip, 1995), changes results
741     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
742     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
743       It is turned off by default (=-1.), because it changes the results.
744     - make it possible to read AREA from a file, too.
745    
746    checkpoint59c
747    o add S/R and diagnostics for oceanic mixed-layer depth
748    o move GMRedi call after all vertical mixing schemes (including KPP)
749    o pkg/thsice:
750     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
751      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
752    o pkg/obcs:
753     - bug fix for balance code
754    o pkg/seaice:
755      - allow values of SEAICE_elasticParm > 1
756      - add new parameter SEAICE_evpTauRelax as an alternative
757        to SEAICE_elasticParm
758      - make lsr boundary conditions free slip (by default), changes result
759      - add code for no slip boundary conditions for lsr
760      - set minimum of zeta to zero (and not 4e8) (changes results)
761      - add a cap on AREA after advecting AREA if seaice_growth is not called
762    o change calculation of Visbeck K:
763      - no longer depend on tapering scheme; instead, compute slope (limited
764        by GM_maxSlope). this is equivalent to what was comuted before with
765        clipping or linear tappering.
766      - fix vertical averaging (wrong by 1/2 level)
767      - leave the old version (but will not be maintained) within
768        #ifdef OLD_VISBECK_CALC / #endif
769      - update output of exp. ideal_2D_oce
770    o change error catch in calc_r_star to improve vectorization
771    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
772      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
773    o adjoint:
774      Re-organized adjoint checkpointing according to Matt Mazloff
775      (but with modifs/completions/cleanups)
776      Storing is now bundled into large arrays to optimized I/O
777      (and second step in cleanup of the_main_loop)
778    
779    checkpoint59b
780    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
781      - export/import (between ocean & coupler) fields needed for ocean DIC.
782    o pkg/seaice:
783      - get rid of three more exchanges seaice_calc_viscosities (required
784        different loop boundaries in seaice_lsr and seaice_ocean_stress)
785      - bug fix in seaice_ocean_stress (update of lab_sea required)
786      - reduce loop boundaries to necessary minimum also in seaice_evp
787      - go back to the old way of computing deltaC/Z as the adjoint likes that
788        better
789    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
790      passive tracer to an Age Tracer) + update output.txt
791    o pkg/exf:
792      - implement A-grid / C-grid selection for wind-stress input files.
793      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
794      for now, in exf_bulk_largeyeager04.F only :
795      - change implementation for case where windspeed + 2. components wind-stress
796        are read-in. AND use rhoConstFresh to convert evap.
797    o pkg/seaice:
798      - use correct EXCH_UV for wind-forcing (on A-grid).
799      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
800        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
801    o pkg/exf:
802      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
803      EXF_INTERPOLATION:
804      - merge global_with_exf/code version of exf_interp_read.F
805        to the main code ;
806      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
807        reading the file ; Important: This options needs to be defined to recover
808        previous code.
809        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
810      - no longer loose real*8 precision along the way when using exf_iprec=64.
811    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
812      - change discretisation of evp-solver in order to avoid another exchange
813        (changes lab_sea) and clean up a little
814      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
815        help the adjoint (this also changes the results slightly)
816      - add a few "_d 0" where they had been missing in seaice_evp.F
817      - cleaning up: remove unused seaice_calc_rhs.F
818    o pkg/exf: some cleaning-up:
819      - change various "constants" into runtime parameters
820      - cleaned-up Large&Yeager04 routine which should eventually
821        replace exf_bulkformulae.F (changed names of S/R and CPP)
822        and merged various ALLOW_ATM_WIND options
823     only used with thsice pkg (in thsice_get_exf.F):
824      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
825        which are used when useStabilityFct_overIce=TRUE (= the default)
826      - change default values of ice & snow emissivity and scale downward LW
827        by ice & snow emissivity.
828    o pkg/thsice:
829     fix few little problems, in thsice_calc_thickn.F:
830      - growth vertically (and not laterally) if iceFrac == iceMaskMax
831      - melt only laterally if hIce < hThinIce (as the comments say)
832      and in thsice_extend.F:
833      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
834      - start to form ice as soon as the minimum ice-volume is reachable.
835     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
836      and cpl_aim+ocn
837    o pkg/kpp
838     - move computation of surface related input fields to KPP into a new
839       subroutine kpp_forcing_surf.F
840     - remove wrong (within bi,bj loops) EXCH calls.
841     - little cleaning (add argument myThid in last position, cvs header ...)
842     - for now, fix conservation problem by exchanging KPPviscAz (may not
843       be the best fix)
844    o pkg/seaice
845     - check for inconsistent evp parameter/cpp-flag combination
846     - remove leftover errIO flat for obsolete name list error handling
847    o OpenAD
848     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
849    
850    checkpoint59a
851    o pkg/seaice: some parameter clarifications and a little bit of clean up
852    o pkg/thsice: rename run-time parameters:
853       himin       -> hIceMin
854       himin0      -> hThinIce
855       hihig       -> hThickIce
856       i0          -> i0swFrac
857       transCoef   -> bMeltCoef
858       frac_energy -> fracMelting
859      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
860       with default values (for now) that do not change the results.
861      remove old version of thsice vars advection in pkg/seaice.
862    o in FFIELDS.h:
863      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
864      - make pLoad & sIceLoad always available (but still only used if
865         ATMOSPHERIC_LOADING is #define).
866    o pkg/kpp: replaced _KPP_RL with _RL
867    o bug fixes for vertical diffusivity computations when both KPP and
868        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
869        are no longer updating the vertical diffusivity array
870        (passed as argument) but are (re-) setting those arrays.
871    o pkg/seaice: fix bug in evp solver, while doing that
872      - change (improve?) discretization of stress computations for both
873        cgrid-lsr and evp solver
874      - add a new routine to compute strain rates
875      - the above changes lab_sea results
876      - add no slip conditions for evp solver (off by default), lsr-version
877        may follow
878      - fix exchange for shear at Z-points (does not change lab_sea)
879      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
880        (to force the user to pick a time step since there is not "safe" way
881        of choosing it)
882      - add principal stress diagnostics
883      - rearrange fields for evp a little to avoid having to call a: too many
884        exchanges and b: exchanges for stress trensor components which we do
885        not have.
886      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
887        of evp, complete rewrite for lsr case (latter is does not yet work
888        in all cases)
889    o pkg/kpp: add code to have mixing in shelf ice caverns
890      - add myThid to all kpp routines (long overdue)
891    
892    checkpoint59
893    o pkg/exf:
894      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
895        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
896      - move exf header files from lower_case.h to UPPER_CASE.h ;
897        add missing cvs Header & Name
898      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
899      - add namelist param. selectStressGridPosition, exf_monFreq
900      - retire many _CLIM routines, and remove data.exf_clim
901        + params moved to data.exf
902        + climsst, climsss now handled by exf_set_gen, i.e.
903          climss?period=0 refers to constant field,
904          climss?period=-12 to monthly forcing
905      - split up namelists in data.exf
906    o pkg/seaice:
907      - remove seaice_exch and seaice_exch_uv
908      - remove superfluous exchange of theta
909      - add myThid to seaice_budget_ocean/ice
910      - add new interface for atmospheric wind forcing (C-grid only)
911        + new routine
912        + two new field (taux, tauy for stress over ice)
913        + removed one global field (DAIRN) for C-grid case only
914    o pkg/thsise
915      - 2nd set of modifs for thsice adjoint in conjunction with exf
916    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
917    
918    checkpoint58y_post
919    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
920      vertical diffusivity, similar to that in MOM4; turned on using
921      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
922      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
923    o Added capability for 3D specification of background vertical diffusion
924      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
925      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
926      "data" file that contains the 3D vertical diffusivity coefficients.
927    o ice dynamics (pkg/seaice) with thsice thermodynamics:
928      - add code within pkg thsice to advect & diffuse sea-ice fields
929      similar to (and will replace) what has been added in  seaice_advdiff.F,
930      but: - conserving Mass, Heat & Salt.
931           - better when using non-linear advection scheme (not yet fully tested)
932           - can also be used in atmospheric set-up (for now, only the diffusion).
933    
934    checkpoint58x_post
935    o IO option for global-file compact format:
936      - add options when generating topology (utils/exch2/matlab-topology-generator)
937      - add I/O capability (pkg/mdsio).
938      - adapt utils/matlab/rdmds.m to read this format.
939      for now long-line format not yet supported by pkg/mdsio (& exch2).
940    o shelfice: add a few diagnostics
941    
942    checkpoint58w_post
943    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
944      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
945      (and replace horiVertRatio in NH code).
946      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
947                         and tutorial_plume_on_slope (sensitive to truncation)
948    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
949      directly to drive seaice model (C-grid only)
950    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
951     - reintroduce computation of wind from stress,
952     - compute tau (in exf_bulkformulae.F) from windstress averaged to
953       mass points to avoid tau = 0
954     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
955    o rdmnc.m: make it work with "global" files created with gluemnc
956    o rdmnc.m : some improvements in dealing with singleton dimension
957      (tested on all testreport mnc output files).
958    o genmake2: disable pkg/profiles if netcdf test fails.
959    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
960    o move call to cal_readparms up to make calendar parameters/variable available
961      to all packages
962    
963    checkpoint58v_post
964    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
965      useDynP_inEos_Zc tested.
966    o pkg/exf: changes to properly interpolate/mask/scale initial fields
967    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
968      and portions thereof.  See read_cs.txt for description and examples.
969    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
970      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
971      following the great-circle arc between those 2 points.
972    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
973      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
974    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
975     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
976     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
977     - still needs work (not working with some options ; efficiency to improve)
978       and serious testing.
979     - use this scheme for temperature & salinity in 2 advection test exp.:
980       advect_xy & advect_xz, respectively.
981    
982    checkpoint58u_post
983    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
984    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
985    o testreport: add option "-skipdir" to skip some test.
986    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
987      momentum calculation.
988    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
989    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
990      remove checkpoint.F and the_correction_step.F (no longer used);
991      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
992    o add option (linFSConserveTr) to correct for tracer source/sink due to
993      Linear Free surface
994    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
995    o pkg/thsice: fix reading mnc-pickups
996    
997    checkpoint58t_post
998    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
999    o pkg/mdsio:
1000     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
1001       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
1002       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
1003     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
1004     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
1005       either MDS_READ_FIELD or MDS_WRITE_FIELD )
1006     - new S/R (to replace MDSWRITEMETA), which allows to write more
1007       informations (variable names, time ...) to meta files.
1008     - modify rdmds.m to give back the meta file content.
1009    o pkg/diagnostics: change vertical interpolation to be safer, and more
1010       flexible (define p-levels to interpolate to in data.diagnostics);
1011      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
1012       diagnostic pointer.
1013    o pkg/seaice: more cleaning up of seaice_growth, added many comments
1014    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
1015    o fix multi-category seaice:
1016     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
1017       SEAICE_MULTICATEGORY
1018     - fix short wave heat flux
1019    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
1020       and allow to use EVP solver. Change forward lab_sea: test both EVP
1021       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
1022    o Initial check-in of lab_sea adjoint
1023      (very similar to natl_box_adjoint/code_seaice)
1024      * used C-grid and EVP solver
1025      * used KPP, GM/Redi
1026      * uses inAdExact=.TRUE.
1027      * gradient checks fail for both ADM and TLM
1028        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
1029        f.d. gradients actually seem more problematic than ADM, TLM gradients;
1030        issue is related to forward mismatch between g77 an ifort
1031    o pkg/seaice: overhaul of thermodynamics
1032     - growth.F and groatb.F are replaced by new routine seaice_growth.F
1033     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
1034     - move a few global fields out of SEAICE.h into seaice_growth.F and
1035       make them 2D (FICE/QNETO/ ...)
1036     - remove FO (it is the same as QNETO)
1037     - introduce a few local fields to avoid modifying external fields such
1038       as atemp, etc.
1039    
1040    checkpoint58s_post
1041    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
1042      changed exf_set_gen.F so that
1043        genperiod=0 means input file is one time-constant field and
1044        genperiod=-12 means input file contains 12 monthly means
1045    o CG2D: use pre-computed solver main-diagonal (stored in common block);
1046      this affects truncation error ; generate new output file for exp. which
1047      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
1048        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
1049        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
1050        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
1051        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
1052        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
1053    o start implementation of deep-atmosphere and anelastic formulation
1054    o verification: remove 2nd copy of input files and use script "prepare_run"
1055      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
1056    o mom_common/vecinv/fluxform: fix a few initialisation isssues
1057    o profiles: fix for multithreaded case
1058    
1059    o diagnostics: rename few diags:
1060      s/'PRESSURE'/'RCENTER '/g
1061      s/'TICE    '/'oceFreez'/g
1062      s/'TAUX    '/'oceTAUX '/g
1063      s/'TAUY    '/'oceTAUY '/g
1064      s/'SWFLUX  '/'oceQsw  '/g
1065      s/DIFx/DFxE/g
1066      s/DIFy/DFyE/g
1067      and add few ocean-forcing diagnostics:
1068      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
1069    o modifications to pkg/seaice/growth.F and budget.F, which change results of
1070      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
1071      as actual snow thickness.  It now refers everywhere to effective snow
1072      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
1073    
1074    checkpoint58r_post
1075    o modifications to pkg/seaice/growth.F, which change results of
1076      lab_sea experiment: fixes pertain to melting snow over open water, to
1077      masking EVAP under sea ice, and to using the correct AREA variable for
1078      computations of EVAP, PRECIP, HSNOW, and GHEFF
1079    o add ability to read bathy, salt, and theta using MNC (off by def)
1080    o add flooding algorithm and advection of HSNOW for pkg/seaice;
1081      both are turned off by default and do no change any results
1082    o seaice advection with pkg/thsice: a step toward the use of non-linear
1083      advection scheme, but #ifdef or commented out for now (requires more EXCH).
1084    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
1085      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
1086      in natl_box (affects results @ truncation level: update output.txt)
1087    o multi-threading and IO:
1088      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
1089      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
1090        (needed to work with SingleCpuIO): tested in all verif. exp.
1091    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
1092      affects the results (but none of the verification test uses this scheme).
1093    o Adding some pkg/diagnostics capability to pkg/seaice
1094      (will certainly be subject to changes)
1095    o ctrl: adding new control variables:
1096      lwflux, lwdown, evap, snowprecip, apressure, runoff
1097    
1098    checkpoint58q_post
1099    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
1100      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
1101      high_res_cube configuration by 4% on Columbia.
1102    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
1103      add (in global_with_exf/code) a version of EXF_INTERP_READ without
1104      dynamical allocation (seems to work in multi-threaded).
1105    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
1106      single CPU io) so that TAF does not have to see EESUPPORT.h
1107    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
1108    
1109    checkpoint58p_post
1110    o obcs: stop if obcs is used with useCDscheme = .true.
1111  o shelfice:  o shelfice:
1112   - fix a sign error so that no slip at shelfice interface works   - fix a sign error so that no slip at shelfice interface works
1113   - remove stop for combination non-hydrostatic code and shelfice. That does   - remove stop for combination non-hydrostatic code and shelfice. That does
Legend:
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