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revision 1.696 by heimbach, Sat Jul 8 00:29:20 2006 UTC revision 1.1053 by jmc, Tue Jan 20 00:34:15 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 take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V  o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
8    o pkg/obcs: fix loop ranges for balancing code
9    o pkg/flt:
10     - improve criteria for finding which tile owns a float.
11     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
12    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
13      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
14      with ocean biogeo)
15    o pkg/flt:
16     - do some cleaning and fix the restart ;
17     - add output.txt in flt_example/results to get this pkg tested.
18    o genmake2: add an EXTENDED_SRC option and flag.
19       for now, cannot be turned on on command line (only through genmake_local)
20    o pkg/mdsio: read/write vector:
21     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
22     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
23       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
24     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
25      (drop to 4 digits matching for grad). But this test does not look very
26      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
27    
28    checkpoint61g
29    o pkg/flt:
30      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
31       + make OPTIONS file more standard.
32      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
33      - fix _BYTESWAPIO CPP-Flag
34      - standard reading of file-parameter "data.flt"
35      - fix argument list of S/R FLT_RESTART
36      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
37    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
38    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
39      a still unfixed compiler/optimization bug
40    
41    checkpoint61f
42    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
43      update results of global_ocean.cs32x15.icedyn test.
44    o move getcon.F from model/src to pkg/fizhi.
45    o pkg/exf: add parameter for extrapolation of temp up to the surface
46       and option to prevent negative evap (in bulk_largeyeager04 only).
47    o Prather Advection scheme: fix tracer conservation for divergent flow
48      (e.g., when using NonLin Free-Surface).
49    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
50    o gmredi (Visbeck-variable-K):
51     - add more parameters to Visbeck-variable-K.
52     - use a 5 points average for dSigmaR in Visbeck-K calculation
53       (more "homogenous": same stencil and same weights as in dSigmaH)
54     - update output of ideal_2D_oce experiment.
55    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
56      (#undef REAL4_IS_SLOW)
57     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
58       coordinate variable
59     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
60       (surface forcing fields), removes some of the functionality
61     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
62     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
63       probably not all: copy _RS surface flux fields to RL field before
64       calling DIAGNOSTICS_FILL
65     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
66       real*4 (CALL EXCH_*_RS) versions.
67     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
68       (generate new output).
69    
70    checkpoint61e
71    o gmredi (Visbeck-variable-K):
72      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
73      - change computation of Visbeck-K where Slope > Smax :        
74        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
75        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
76    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
77      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
78    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
79    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
80      does not become too large (to avoid precision problems in implicit-diffusion
81      solver); update ideal_2D_oce output.
82    o pkg ggl90:
83      - in ggl90_cal.F: compute only one set of visc/diff, used to
84        step forward TKE/T/S/momentum
85      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
86        have Prandlt =1)
87    o gmredi (fm07):
88      - add lower limit on Transition layer thickness + lower limit on 1/lambda
89      - allow to set few more params from data.gmredi
90    o pkg ggl90:
91          - add missing sqrt(2) factor in computation of mixing length
92            scale in ggl90_calc.F
93            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
94    
95    checkpoint61d
96    o adjoint modifs
97      - adapt to new field rhoInSitu
98      - allow to revert from StoreDynVars2D, StoreDynVars3D
99        to individual fields
100        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
101    o store 3-D (in-situ) density in commom block (DYNVARS.h)
102     - save 1 rho computation.
103     - no longer modify T & S inland when using down_slope pkg.
104    o gad_som : allow to switch to SOM advection for T & S without corresponding
105      pickup files (using new S/R: MDS_CHECK4FILE).
106    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
107      (for useSingleCpuIO to work in multi-threaded)
108    o pkg/shelfice:
109     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
110       with SHELFICEtopoFile in data.shelfice
111     - move code for reading ice shelf topography and modifying hFacC into separate
112       subroutines of the shelfice package
113     - separate initialisation of "fixed" and "variable" variables
114     - kTopC is not (yet) replaced by kSurfC, although this is possible
115    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
116    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
117      and rename:
118      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
119      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
120    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
121    
122    checkpoint61c
123    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
124      to add mass source/sink of fluid in the interior (3-D generalisation
125      of oceanic real-fresh water flux).
126    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
127    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
128    o new pkg: down_slope
129      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
130      - presently, modify T & S inland (dwnslp_calc_rho.F).
131        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
132      - implementation for ocean in P-coords not tested.
133      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
134    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
135      (to facilitate conversion of oceanic pkg to p-coordinate).
136    o change FIND_RHO to FIND_RHO_2D :
137      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
138    o new pkg: cheapaml
139    
140    checkpoint61b
141    o exch2:
142      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
143      - no longer depend on the order sequence (N,S,E,W).
144      - 3rd exchange no longer needed (tested with 24 tiles).
145      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
146      - exch_UV_A-grid readily available (but not yet tested).
147      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
148      (both are no longer needed) in exch_uv: no effect in forward run; but
149       get truncation error differences with adjoint exch.
150    o exch2:
151     - change index-bounds storage (moved from target to local tile,
152       more intuitive this way) ; rename/remove some variables.
153     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
154    
155    checkpoint61a
156    o exch2/matlab-topology-generator:
157      fix bug in index bounds for N-S internal exchange (hard to tell if this
158      had any effect on the solution).
159    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
160      is exceeded
161    o testreport: modify syntax of awk, so that it works also with
162      awk, and not only with nawk and gawk
163    
164    checkpoint61
165    o autodiff
166      Change default for TAF usage by removing argument '-nonew_arg'
167      This changes TAF subroutine argument list (ordering of active var.)
168      Omission of this flag leads to incompatibility w.r.t. TAMC
169      To restore TAMC-compatibility, need following modifs:
170      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
171      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
172      Tested TAF version is 1.9.22
173      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
174    
175    checkpoint60
176    --->>> This is the last checkpoint for which generating the adjoint
177    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
178    --->>> by default.
179    --->>> Future checkpoints will ommit this flag by default.
180    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
181    o pkg/grdchk: Add gradient check to etan0 perturbations.
182    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
183    o pkg/autodiff: more flexibility in zeroadj.
184      model/src: modifying do_oceanic_phys.F accordingly.
185    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
186    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
187      special setup of gmredi for which the adjoint is stable
188      enough for parameter optimization.
189    o bridging the gap between eddy stress and GM.
190      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
191          along with a change in CPP option (now ALLOW_EDDYPSI).
192      -> when using GM w/ GM_AdvForm:
193          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
194          is applied either in the tracer Eq. or in momentum Eq.
195          depending on data.gmredi (intro. GM_InMomAsStress).
196      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
197      The key modifications are in model/src/taueddy_external_forcing.F
198      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
199    
200    checkpoint59r
201    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
202      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
203      fix option to read coriolis(@ cell-corner) from files with CS-grid.
204    o pkg/mnc: add some attributes to standard 1D-coordinate variables
205    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
206      mass points, when using mnc for output
207      - add runtime parameter (missing_value, missing_value_int) to override
208        default (which is the value of getcon('UNDEF'))
209    o pkg/mnc: prepare mnc for the actual use of missing values with the
210      diagnostics package: small fix in mnc_cw_readwrite.template and more
211      initialisation of never used fields
212      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
213      versions
214    o pkg/thsice/thsice_ini_vars.F added default initial values so that
215      thermodynamics sea ice solver does not blow up when some initial fields
216      are missing.
217    o move from external_forcing_surf.F to ini_forcing.F
218      the p-coord. hack consisting in using pLoad to set phi0surf ;
219      update output of tutorial_global_oce_in_p (affected @ truncation level).
220    o Freshen up a bit hs94.1x64x5, notably:
221      remove rotationPeriod and tRef=5*0. (adjoint only), and add
222      exactConserv=.TRUE.
223    o pkg/generic_advdiff:
224      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
225      applies to files where Temperature & Salinity 2nd Order moments are used.
226    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
227      this uses a dynamically allocated internal state data structure
228      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
229      and requires a fortran 90 compiler
230    
231    checkpoint59q
232    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
233       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
234    o Refresh tutorial_global_oce_biogeo, notably:
235      - change bathymetry (put back seamounts in ACC, use hFacs)
236      - change EOS (POLY3 --> JMD95Z)
237      - use Bryan-Lewis vertical diffusivity
238      - use multidimensional advection
239      - remove old virtual virtual in dic pkg, now done through ptracer pkg
240      - change a couple of parameters in dic pkg
241    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
242    o pkg/obcs: change default to OBCSfixTopo = .true.,
243      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
244      - replace "debugMode" with "debugLevel .GE. debLevB"
245    o implementation of TAF directives for gchem,cfc,dic
246    o remove "exp5" (replaced by tutorial_deep_convection).
247    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
248      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
249      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
250      --> changes results in exp4, seaice_obcs
251    o tutorial_deep_convection :
252      update the set-up and increase resolution and domain size ; start
253      from pseudo initial conditions = output at t=120mn in order to see
254      something happening when running testreport.
255    o pkg/seaice: add os7mp as an advection scheme
256                  add check for advection schemes
257                  add a flag for restoring T and S underneath sea ice
258    o pkg/my82: add netcdf-support and diagnostics
259    o thsice pkg:
260      - Now hsMax limits snow height by turning it into ice following
261        flooding scheme (and now conserving energy)
262      - Slight rewriting of the formula in thsice_calc_thick.F
263      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
264      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
265    
266    checkpoint59p
267    o gchem / dic / cfc :
268      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
269      - add new parameter files: "data.dic" & "data.cfc" ;
270      - various re-arrangement in initialisation & header file ;
271      - fix tutorial_global_oce_biogeo for multi-threaded test.
272    o pkg/dic: test for "pickup_dic" file when restarting ;
273      if no pickup-file, can restart with a re-initialised pH (same as it did
274      before) providing pickupStrictlyMatch is set to False.
275    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
276      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
277    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
278      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
279    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
280     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
281       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
282    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
283       scheme to use for vorticty-term ;
284     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
285       (with default selectVortScheme, return to original discretisation)
286     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
287    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
288    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
289      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
290      also fix diagnostics VISCAHW & VISCA4W.
291    
292    checkpoint59o
293    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
294    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
295      move a few statemens out the main loop into separate loops
296    o pkg/shelfice:
297      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
298        (kg/m^2/s), does not break tests, because in verification/isomip,
299        rhoConstFresh=rhoConst (by accident)
300      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
301      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
302        new file model/src/seawater.F, so that they are available for all pkgs.
303      - convert potential temperature into in-situ temperature. This changes the
304        isomip tests => update tests
305    o add a flag writePickupAtEnd (default=true) to be able to suppress
306      writing a pickup at the last timestep
307    o tools/mpack-1.6 :
308      - disable automake (not working) and autoconf (not needed).
309      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
310        also cleaner with much less compilation warnings.
311    o pkg/profiles:
312      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
313      (for "less than 32 characters name" compiler requirement)
314    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
315      conditions that have a different sampling frequency than S/T/U/V obcs
316    o pkg/diagnostics (stats-diags):
317      - fix global Min/Max in case 1 processor get only empty tiles
318    o genmake2: replace (4 times)
319         make genmake_tc_1.o >> genmake_warnings 2>&1
320      with
321         COMM="$CC $CFLAGS -c genmake_tc_1.c"
322         echo $COMM >> genmake_warnings
323         $COMM >> genmake_warnings 2>&1
324      to make genmake2 always see the value of CC as specified in the optfile.
325    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
326      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
327      - modify verification advect_cs test to test SOM-advection on CS-grid.
328    o pkg/ctrl:
329      - Rewrite of ctrl_map_ini_ecco.F,
330        introducing a generic routine (ctrl_map_ini_gen.F).
331      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
332    
333    checkpoint59n
334    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
335      number in dedicate array "hdiag":
336      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
337        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
338      - many small changes (integer format) for large number of diagnostics
339      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
340        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
341    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
342      usingSphericalGrid, this allows to define the rotated grid coordinates
343      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
344      geographical coordinates according to the inverse of the rotation defined
345      by the Euler angles, so that Coriolis parameter and online-interpolation by
346      exf works with the geographical coordinates on XC/YC/XG/YG.
347      Naturally, this feature does not work with all packages, so some
348      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
349      profiles), because there the coordinates are assumed to be regular
350      spherical grid coordinates.
351    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
352      - introduce isopycnal diffusion coefficient control.
353    o tools/adjoint_options:
354      - additional control vector components.
355    o pkg/mnc: have mnc create marginally meaning full coordinate variables
356      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
357    o pkg/mypackage:
358      - add example of read/write pickup for state-var ;
359      - add entry points to the main code for state-vars diags & write-pickup.
360    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
361      transitions for useExfYearlyFields
362      - add new subroutine that determines the file to read from for
363        use*YearlyFields = .TRUE. and .FALSE.
364      - add a verification experiment to global_with_exf that tests
365        useExfYearlyFields with USE_EXF_INTERPOLATION defined
366    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
367      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
368      subroutines (which could be generated from a template, because they are
369      almost identical), for now they are included in obcs_prescribe_read.F for
370      simplicity
371    o pkg/exf:
372      - add a little more diagnostic to exf_interp_read (in analogy to
373        mds_read_field, can be turned off with debugLevel < debugLevA=1)
374      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
375        ugly but fast by unrolling short inner loops, inserting a unroll=8
376        directive in routine lagran, and splitting a loop and making do while the
377        outermost loop (the latter requires the intoduction of index arrays)
378    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
379    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
380      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
381    o verification/seaice_obcs: updated for restart test and latest options
382    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
383      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
384      for now this is only available for the C-grid code and also within
385      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
386    
387    checkpoint59m
388    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
389      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
390    o gad_som : fix flux output (& diagnostics) to have same units as other  
391      advection scheme fluxes (was previously multiplied by deltaT).  
392    o added verification/seaice_obcs both to test seaice open boundaries
393      and to provide an example matlab scrpt for generating them
394    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
395    o pkg/salt_plume: clean up salt_plume_frac.F to
396      remove redundancy in PlumeMethod 1 and 4
397    o pkg/kpp: added saltplume diagnostics
398    o pkg/obcs and pkg/seaice:
399      - do not set uice and vice to zero when OB*icefile are unspecified
400      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
401      - moved seaice tracer obcs after call to seaice_growth
402    o pkg/salt_plume: added various options for salt plume depth
403      criterion and for vertical distribution of the salt
404    
405    checkpoint59l
406    o pkg/ptracers: new version of ptracers pickup:
407      read meta file and write only fields which are needed to restart.
408      ( same logic as main pickup file ; also using pickupStrictlyMatch )
409    o pkg/seaice:
410      - add timescale for melting due to warm mixed layer as a means of
411        setting SEAICE_availHeatFrac more conveniently
412      - add a CPP-flag/runtime parameter check for flooding algorithm
413      - reformulated availHeat in seaice_growth.F to be independent of AREA
414    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
415      unit changes
416    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
417    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
418      SX vector computer.
419    o pkg/seaice:
420      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
421        seaice forcing fields can now be read only through pkg/exf
422      - removed some unused halos
423    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
424    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
425      or U/VICE from U/VWIND before computing U/VSTRESS
426    
427    checkpoint59k
428    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
429      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
430    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
431      all experiments pass when compile with un-initialised var. checking option.
432    o added pkg/salt_plume
433    o script to test restart (for now, in MITgcm_contrib/jmc_script)
434    o pkg/seaice: new read/write pickup version.
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: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
438    o lab_sea.hb87: modify the domain & update output.hb87.txt :
439      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
440      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
441      process. Fixed here by closing the domain at the Northern boundary.
442    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
443    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
444      a set of consecutive levels in/from a 3-D array.
445    o pkg/ptracers:
446      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
447      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
448    
449    checkpoint59j
450    o in pkgs: dic, obcs, offline, rbcs:
451      standard way to compute coeff. for time interpolation between 2 time reccords
452      which retains full precision (& make results less dependent on compiler).
453      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
454    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
455      packages instead of reading ice cover and wind speed separately
456    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
457     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
458      to allow to compile customized code before the update)
459    o cleaning-up:
460      - fix CPP instruction syntax in pkg/obcs
461      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
462        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
463      - fix some threads issue in IO parts.
464    o pkg/dic:
465      - add tons of "_d 0" (--> much better testreports !)
466       and then update outputs of tutorial_global_oce_biogeo
467    o pkg/mom_fluxform:
468      add a special version of momentum advection intended to conserve momentum
469      next to a bathymetry step or a coastline edge. (default = off = #undef)
470    o new read/write pickup version:
471      - for now, only implemented for main (mdsio) pickup file.
472      - write out only what is needed to restart; merge pickup_nh , pickup_ph
473        and main pickup together.
474      - read meta file; read only what is needed to restart; stop if a field
475        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
476        if it make sense (even if the restart is not perfect).
477      - if no meta file, assume that pickup to read corresponds exactly to
478        a pickup that would currently be written.
479      - read pickup written in the old format (until checkpoint59i) if it
480        recognizes an old meta file (no field-list).
481      - add a meta file in exp. which starts from a pickup: 2 cases:
482        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
483         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
484        b) a meta file describing the content of the associated pickup file
485         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
486    o pkg/mdsio & pkg/rw:
487      - new routine to read a meta file ; new set of routine to read
488        Multiple-fields file (with meta file).
489    o added open boundary conditions capability for seaice
490        HSNOW, HSALT, UICE, and VICE
491    
492    checkpoint59i
493    o adjoint:
494      * fix multiDimAdvection adjoint
495        (partial recomputation problem by TAF for fVerT(:,:,kDown)
496        and comlev1 size definition (maxpass vs. max. number of tracers)
497      * verification/global_ocean.90x45x15 adjoint now tests
498        NLFS and multiDimAdvection using DST3 (=30)
499      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
500    o pkg/kpp: add "_d 0" to real constant (if missing);
501      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
502      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
503    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
504      for internal parameters related to restart process (formerly from PARAMS.h)
505      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
506    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
507      as argument. (only atm2d & obcs write_pickup have not yet been updated)
508    o pkg/monitor:
509      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
510      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
511      - account for deep Atmosphere factor and density factor (anelastic)
512    o added open boundary conditions capability for seaice HEFF and AREA
513    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
514      thermodynamics
515      - requires a little reorganization, which affects the testreport results
516        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
517        so that now the conservative form is tested
518      - add a few comments
519    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
520    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
521    o add new diagnostics to seaice: advective, diffusive fluxes (only for
522      multidim-advection, for scheme 2 they are not filled) and transports,
523      thermodynamic growth rates
524    o change units of EmPmR (inside the code, + within coupling interface)
525      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
526      Affects results @ truncation level (cg2d match) and update output of
527       experiments: lab_sea(6), global_ocean.90x40x15(10),
528      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
529      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
530      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
531      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
532    
533    checkpoint59h
534    o pkg/exf:
535      - improve vectorization by moving if-statement out of loops in
536        exf_mapfields, exf_radiation
537      - exf_bulkformulae.F: introduce 2D fields and vectorize code
538    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
539    o testreport:
540      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
541        monitor & update offline_exf_seaice exp. output.
542      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
543    o pkg/seaice:
544      - bug fix in the evp solver: boundary conditions were affected be
545        masking of zMax/zMin (changes results)
546      - minor bug fix in boundary conditions in seaice_calc_strainrates
547        (changes results for no_slip)
548      - seaice_lsr.F: make interpolation of eta dependent on boundaries
549      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
550      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
551        stress formulation and no-slip boundary conditions
552    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
553      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
554    o pkg/seaice: a first HSALT time stepping equation has been checked in
555    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
556      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
557      without requiring DO-IF statements
558    o pkg/thsice:
559      use continuous power-law function for partition of energy between lateral
560      melting/freezing and thinning/thickening ; old code using step function
561      still available with #undef THSICE_FRACEN_POWERLAW
562      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
563    o testreport: change AD testing : check against results/output_adm.txt
564      using same scripts as for forward test.
565    
566    checkpoint59g
567    o adjoint testing: in preparation for changing testreport:
568      - output format: cost and grad written on separated lines
569      - ad output results in directory "results" (instead of "results_ad")
570    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
571    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
572    o pkg/ecco: allow user defined cost function contributions
573    o testreport:
574      Allow to choose (per experiment) the list of tested output variables
575       and the main variable (used to issue a pass/FAIL ) ;
576      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
577      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
578      Also modify printing of summary:
579       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
580       b) echo the list of tested variables in the individual summary.txt of
581          each experiment.
582    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
583      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
584      (but still depend on the tile decompostion of the domain).
585    o pkg/seaice: change a discretization detail to make the B-grid code
586      "more symmetric". This change is likely to remove all "ridges/leads" that
587      where quasi-aligned with the grid in B-grid solutions. It may also be
588      the solution to the stress coupling issues with the B-grid.
589    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
590      remove .cvsignore from input dir. (since testreport no longer run here).
591    o pkg/thsice:
592     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
593     - fix reshaping of sea-ice just after advection:
594       melt all the ice only if ice-volume is too small.
595     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
596       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
597     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
598    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
599      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
600    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
601      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
602      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
603      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
604      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
605      -> update output.txt
606    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
607     this affects truncation error: -> update output.txt of exp:
608      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
609      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
610    
611    checkpoint59f
612    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
613    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
614      a bounded range (in forward mode)
615    o pkg/ecco, ctrl, autodiff and mom_common:
616     internal parameter controls, completements of implementations
617    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
618    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
619      (not seem any difference in testing results).
620    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
621       at face corners.
622    o pkg/generic_advdiff:
623     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
624      loop range indices for computing vertical advection tendency
625      and do the calculation in the interior only (no overlap) ;
626      for now, only implemented for SOM advection (to save CPU time).
627     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
628    o exch2 adjoint
629      First set of changes:
630      - add exch2 hand-written adjoint templates
631      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
632        This will require cleanup in pkg/autodiff/*.F
633        (changed routines currently kept separate in verif. code/)
634      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
635        that used to hide exch2 or cubed-sphere specific code
636        (commented via 'cph-exch2')
637    o pkg/seaice
638      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
639    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
640       output of global_ocean.cs32x15.thsice .
641    
642    checkpoint59e
643    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
644      for B-grid vector (not yet tested) and C-grid vector (<- only used
645      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
646    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
647      (#ifdef ALLOW_SALT_PLUME)
648    o gather_2d/scatter_2d: removed halo regions
649    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
650      scheme and the corresponding test case (under front_relax dir). For now,
651      only available with Skew-flux form and not yet tested in realistic set-up.
652      adjoint: store directives updated, but gradient checks deteriorated,
653      so maybe GM/Redi adjoint is now broken.
654    o seaice adjoint
655      * add AREA, HEFF, HSNOW as control variable
656        (should not change lab_sea results)
657      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
658    o pkg/seaice:
659      * added computation of saltFlux in seaice_growth;
660        For time being, sea ice salinity is assumed constant
661        contribution of snow flooding to freshening of sea ice is neglected.
662        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
663        defaults to 0.0 in order to maintain backward compatibility.
664        Typical values for SEAICE_salinity are 4 to 10 g/kg.
665      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
666      * added SEAICE_availHeatFrac, which specifies fraction of surface level
667        heat content used to melt or grow ice
668      * commented out cap of HICE: it helps keep ice thinner
669      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
670      * applied OBCS T/S mask to HEFFM sea ice mask
671    
672    checkpoint59d
673    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
674     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
675     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
676    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
677     and change default value of parameter "GM_Small_Number";
678     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
679       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
680       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
681    o pkg/ecco: cost function when applying pkg/smooth to controls
682    o pkg/ctrl: add forcingPrecond run time parameter
683    o pkg/seaice:
684     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
685     - fix bug in metric terms of u-equation in LSR solver (implicit part),
686       changes verification/lab_sea
687     - rearrange implicit part of u-equation in LSR solver to make it easier to
688       read, understand, and debug. This causes changes at the truncation level.
689     - fix (serious) bug in the boundary conditions (sign error in the implicit
690       part) of the LSR solver. Changes all LSR results.
691     - fixed problem with HSNOW initialization to avoid thick snow when AREA
692       is initilized with small values - does not change lab_sea results.
693     - added HsnowFile initialization capability
694    o pkg/smooth: addition to model/src and pkg/ctrl so allow
695     initialization of pkg/smooth and application to control vector
696    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
697    o dependencies: pkg/profiles requires pkg/cal
698    o pkg/profiles:
699     - added option ALLOW_PROFILES_GENERICGRID
700         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
701         that interpolation information (grid points and coefficients) is provided
702         within the netcdf input files.
703         -> sample matlab scripts can be found in MITgcm_contrib/gael
704         that allow you to prepare netcdf input files.
705     - also modified: cleaner include statements, cleaner error print statements,
706       cleaner stops when error, and more tests of the netcdf input files consistency.
707    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
708    o pkg/seaice:
709     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
710       requires a new routine: seaice_diagnostics_fill.F
711     - make sure that seaice does not move if not forced (pressure replacement
712       method, Hibler and Ip, 1995), changes results
713     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
714     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
715       It is turned off by default (=-1.), because it changes the results.
716     - make it possible to read AREA from a file, too.
717    
718    checkpoint59c
719    o add S/R and diagnostics for oceanic mixed-layer depth
720    o move GMRedi call after all vertical mixing schemes (including KPP)
721    o pkg/thsice:
722     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
723      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
724    o pkg/obcs:
725     - bug fix for balance code
726    o pkg/seaice:
727      - allow values of SEAICE_elasticParm > 1
728      - add new parameter SEAICE_evpTauRelax as an alternative
729        to SEAICE_elasticParm
730      - make lsr boundary conditions free slip (by default), changes result
731      - add code for no slip boundary conditions for lsr
732      - set minimum of zeta to zero (and not 4e8) (changes results)
733      - add a cap on AREA after advecting AREA if seaice_growth is not called
734    o change calculation of Visbeck K:
735      - no longer depend on tapering scheme; instead, compute slope (limited
736        by GM_maxSlope). this is equivalent to what was comuted before with
737        clipping or linear tappering.
738      - fix vertical averaging (wrong by 1/2 level)
739      - leave the old version (but will not be maintained) within
740        #ifdef OLD_VISBECK_CALC / #endif
741      - update output of exp. ideal_2D_oce
742    o change error catch in calc_r_star to improve vectorization
743    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
744      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
745    o adjoint:
746      Re-organized adjoint checkpointing according to Matt Mazloff
747      (but with modifs/completions/cleanups)
748      Storing is now bundled into large arrays to optimized I/O
749      (and second step in cleanup of the_main_loop)
750    
751    checkpoint59b
752    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
753      - export/import (between ocean & coupler) fields needed for ocean DIC.
754    o pkg/seaice:
755      - get rid of three more exchanges seaice_calc_viscosities (required
756        different loop boundaries in seaice_lsr and seaice_ocean_stress)
757      - bug fix in seaice_ocean_stress (update of lab_sea required)
758      - reduce loop boundaries to necessary minimum also in seaice_evp
759      - go back to the old way of computing deltaC/Z as the adjoint likes that
760        better
761    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
762      passive tracer to an Age Tracer) + update output.txt
763    o pkg/exf:
764      - implement A-grid / C-grid selection for wind-stress input files.
765      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
766      for now, in exf_bulk_largeyeager04.F only :
767      - change implementation for case where windspeed + 2. components wind-stress
768        are read-in. AND use rhoConstFresh to convert evap.
769    o pkg/seaice:
770      - use correct EXCH_UV for wind-forcing (on A-grid).
771      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
772        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
773    o pkg/exf:
774      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
775      EXF_INTERPOLATION:
776      - merge global_with_exf/code version of exf_interp_read.F
777        to the main code ;
778      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
779        reading the file ; Important: This options needs to be defined to recover
780        previous code.
781        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
782      - no longer loose real*8 precision along the way when using exf_iprec=64.
783    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
784      - change discretisation of evp-solver in order to avoid another exchange
785        (changes lab_sea) and clean up a little
786      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
787        help the adjoint (this also changes the results slightly)
788      - add a few "_d 0" where they had been missing in seaice_evp.F
789      - cleaning up: remove unused seaice_calc_rhs.F
790    o pkg/exf: some cleaning-up:
791      - change various "constants" into runtime parameters
792      - cleaned-up Large&Yeager04 routine which should eventually
793        replace exf_bulkformulae.F (changed names of S/R and CPP)
794        and merged various ALLOW_ATM_WIND options
795     only used with thsice pkg (in thsice_get_exf.F):
796      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
797        which are used when useStabilityFct_overIce=TRUE (= the default)
798      - change default values of ice & snow emissivity and scale downward LW
799        by ice & snow emissivity.
800    o pkg/thsice:
801     fix few little problems, in thsice_calc_thickn.F:
802      - growth vertically (and not laterally) if iceFrac == iceMaskMax
803      - melt only laterally if hIce < hThinIce (as the comments say)
804      and in thsice_extend.F:
805      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
806      - start to form ice as soon as the minimum ice-volume is reachable.
807     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
808      and cpl_aim+ocn
809    o pkg/kpp
810     - move computation of surface related input fields to KPP into a new
811       subroutine kpp_forcing_surf.F
812     - remove wrong (within bi,bj loops) EXCH calls.
813     - little cleaning (add argument myThid in last position, cvs header ...)
814     - for now, fix conservation problem by exchanging KPPviscAz (may not
815       be the best fix)
816    o pkg/seaice
817     - check for inconsistent evp parameter/cpp-flag combination
818     - remove leftover errIO flat for obsolete name list error handling
819    o OpenAD
820     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
821    
822    checkpoint59a
823    o pkg/seaice: some parameter clarifications and a little bit of clean up
824    o pkg/thsice: rename run-time parameters:
825       himin       -> hIceMin
826       himin0      -> hThinIce
827       hihig       -> hThickIce
828       i0          -> i0swFrac
829       transCoef   -> bMeltCoef
830       frac_energy -> fracMelting
831      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
832       with default values (for now) that do not change the results.
833      remove old version of thsice vars advection in pkg/seaice.
834    o in FFIELDS.h:
835      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
836      - make pLoad & sIceLoad always available (but still only used if
837         ATMOSPHERIC_LOADING is #define).
838    o pkg/kpp: replaced _KPP_RL with _RL
839    o bug fixes for vertical diffusivity computations when both KPP and
840        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
841        are no longer updating the vertical diffusivity array
842        (passed as argument) but are (re-) setting those arrays.
843    o pkg/seaice: fix bug in evp solver, while doing that
844      - change (improve?) discretization of stress computations for both
845        cgrid-lsr and evp solver
846      - add a new routine to compute strain rates
847      - the above changes lab_sea results
848      - add no slip conditions for evp solver (off by default), lsr-version
849        may follow
850      - fix exchange for shear at Z-points (does not change lab_sea)
851      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
852        (to force the user to pick a time step since there is not "safe" way
853        of choosing it)
854      - add principal stress diagnostics
855      - rearrange fields for evp a little to avoid having to call a: too many
856        exchanges and b: exchanges for stress trensor components which we do
857        not have.
858      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
859        of evp, complete rewrite for lsr case (latter is does not yet work
860        in all cases)
861    o pkg/kpp: add code to have mixing in shelf ice caverns
862      - add myThid to all kpp routines (long overdue)
863    
864    checkpoint59
865    o pkg/exf:
866      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
867        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
868      - move exf header files from lower_case.h to UPPER_CASE.h ;
869        add missing cvs Header & Name
870      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
871      - add namelist param. selectStressGridPosition, exf_monFreq
872      - retire many _CLIM routines, and remove data.exf_clim
873        + params moved to data.exf
874        + climsst, climsss now handled by exf_set_gen, i.e.
875          climss?period=0 refers to constant field,
876          climss?period=-12 to monthly forcing
877      - split up namelists in data.exf
878    o pkg/seaice:
879      - remove seaice_exch and seaice_exch_uv
880      - remove superfluous exchange of theta
881      - add myThid to seaice_budget_ocean/ice
882      - add new interface for atmospheric wind forcing (C-grid only)
883        + new routine
884        + two new field (taux, tauy for stress over ice)
885        + removed one global field (DAIRN) for C-grid case only
886    o pkg/thsise
887      - 2nd set of modifs for thsice adjoint in conjunction with exf
888    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
889    
890    checkpoint58y_post
891    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
892      vertical diffusivity, similar to that in MOM4; turned on using
893      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
894      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
895    o Added capability for 3D specification of background vertical diffusion
896      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
897      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
898      "data" file that contains the 3D vertical diffusivity coefficients.
899    o ice dynamics (pkg/seaice) with thsice thermodynamics:
900      - add code within pkg thsice to advect & diffuse sea-ice fields
901      similar to (and will replace) what has been added in  seaice_advdiff.F,
902      but: - conserving Mass, Heat & Salt.
903           - better when using non-linear advection scheme (not yet fully tested)
904           - can also be used in atmospheric set-up (for now, only the diffusion).
905    
906    checkpoint58x_post
907    o IO option for global-file compact format:
908      - add options when generating topology (utils/exch2/matlab-topology-generator)
909      - add I/O capability (pkg/mdsio).
910      - adapt utils/matlab/rdmds.m to read this format.
911      for now long-line format not yet supported by pkg/mdsio (& exch2).
912    o shelfice: add a few diagnostics
913    
914    checkpoint58w_post
915    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
916      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
917      (and replace horiVertRatio in NH code).
918      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
919                         and tutorial_plume_on_slope (sensitive to truncation)
920    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
921      directly to drive seaice model (C-grid only)
922    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
923     - reintroduce computation of wind from stress,
924     - compute tau (in exf_bulkformulae.F) from windstress averaged to
925       mass points to avoid tau = 0
926     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
927    o rdmnc.m: make it work with "global" files created with gluemnc
928    o rdmnc.m : some improvements in dealing with singleton dimension
929      (tested on all testreport mnc output files).
930    o genmake2: disable pkg/profiles if netcdf test fails.
931    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
932    o move call to cal_readparms up to make calendar parameters/variable available
933      to all packages
934    
935    checkpoint58v_post
936    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
937      useDynP_inEos_Zc tested.
938    o pkg/exf: changes to properly interpolate/mask/scale initial fields
939    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
940      and portions thereof.  See read_cs.txt for description and examples.
941    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
942      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
943      following the great-circle arc between those 2 points.
944    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
945      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
946    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
947     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
948     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
949     - still needs work (not working with some options ; efficiency to improve)
950       and serious testing.
951     - use this scheme for temperature & salinity in 2 advection test exp.:
952       advect_xy & advect_xz, respectively.
953    
954    checkpoint58u_post
955    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
956    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
957    o testreport: add option "-skipdir" to skip some test.
958    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
959      momentum calculation.
960    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
961    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
962      remove checkpoint.F and the_correction_step.F (no longer used);
963      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
964    o add option (linFSConserveTr) to correct for tracer source/sink due to
965      Linear Free surface
966    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
967    o pkg/thsice: fix reading mnc-pickups
968    
969    checkpoint58t_post
970    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
971    o pkg/mdsio:
972     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
973       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
974       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
975     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
976     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
977       either MDS_READ_FIELD or MDS_WRITE_FIELD )
978     - new S/R (to replace MDSWRITEMETA), which allows to write more
979       informations (variable names, time ...) to meta files.
980     - modify rdmds.m to give back the meta file content.
981    o pkg/diagnostics: change vertical interpolation to be safer, and more
982       flexible (define p-levels to interpolate to in data.diagnostics);
983      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
984       diagnostic pointer.
985    o pkg/seaice: more cleaning up of seaice_growth, added many comments
986    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
987    o fix multi-category seaice:
988     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
989       SEAICE_MULTICATEGORY
990     - fix short wave heat flux
991    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
992       and allow to use EVP solver. Change forward lab_sea: test both EVP
993       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
994    o Initial check-in of lab_sea adjoint
995      (very similar to natl_box_adjoint/code_seaice)
996      * used C-grid and EVP solver
997      * used KPP, GM/Redi
998      * uses inAdExact=.TRUE.
999      * gradient checks fail for both ADM and TLM
1000        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
1001        f.d. gradients actually seem more problematic than ADM, TLM gradients;
1002        issue is related to forward mismatch between g77 an ifort
1003    o pkg/seaice: overhaul of thermodynamics
1004     - growth.F and groatb.F are replaced by new routine seaice_growth.F
1005     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
1006     - move a few global fields out of SEAICE.h into seaice_growth.F and
1007       make them 2D (FICE/QNETO/ ...)
1008     - remove FO (it is the same as QNETO)
1009     - introduce a few local fields to avoid modifying external fields such
1010       as atemp, etc.
1011    
1012    checkpoint58s_post
1013    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
1014      changed exf_set_gen.F so that
1015        genperiod=0 means input file is one time-constant field and
1016        genperiod=-12 means input file contains 12 monthly means
1017    o CG2D: use pre-computed solver main-diagonal (stored in common block);
1018      this affects truncation error ; generate new output file for exp. which
1019      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
1020        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
1021        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
1022        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
1023        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
1024        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
1025    o start implementation of deep-atmosphere and anelastic formulation
1026    o verification: remove 2nd copy of input files and use script "prepare_run"
1027      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
1028    o mom_common/vecinv/fluxform: fix a few initialisation isssues
1029    o profiles: fix for multithreaded case
1030    
1031    o diagnostics: rename few diags:
1032      s/'PRESSURE'/'RCENTER '/g
1033      s/'TICE    '/'oceFreez'/g
1034      s/'TAUX    '/'oceTAUX '/g
1035      s/'TAUY    '/'oceTAUY '/g
1036      s/'SWFLUX  '/'oceQsw  '/g
1037      s/DIFx/DFxE/g
1038      s/DIFy/DFyE/g
1039      and add few ocean-forcing diagnostics:
1040      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
1041    o modifications to pkg/seaice/growth.F and budget.F, which change results of
1042      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
1043      as actual snow thickness.  It now refers everywhere to effective snow
1044      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
1045    
1046    checkpoint58r_post
1047    o modifications to pkg/seaice/growth.F, which change results of
1048      lab_sea experiment: fixes pertain to melting snow over open water, to
1049      masking EVAP under sea ice, and to using the correct AREA variable for
1050      computations of EVAP, PRECIP, HSNOW, and GHEFF
1051    o add ability to read bathy, salt, and theta using MNC (off by def)
1052    o add flooding algorithm and advection of HSNOW for pkg/seaice;
1053      both are turned off by default and do no change any results
1054    o seaice advection with pkg/thsice: a step toward the use of non-linear
1055      advection scheme, but #ifdef or commented out for now (requires more EXCH).
1056    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
1057      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
1058      in natl_box (affects results @ truncation level: update output.txt)
1059    o multi-threading and IO:
1060      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
1061      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
1062        (needed to work with SingleCpuIO): tested in all verif. exp.
1063    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
1064      affects the results (but none of the verification test uses this scheme).
1065    o Adding some pkg/diagnostics capability to pkg/seaice
1066      (will certainly be subject to changes)
1067    o ctrl: adding new control variables:
1068      lwflux, lwdown, evap, snowprecip, apressure, runoff
1069    
1070    checkpoint58q_post
1071    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
1072      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
1073      high_res_cube configuration by 4% on Columbia.
1074    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
1075      add (in global_with_exf/code) a version of EXF_INTERP_READ without
1076      dynamical allocation (seems to work in multi-threaded).
1077    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
1078      single CPU io) so that TAF does not have to see EESUPPORT.h
1079    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
1080    
1081    checkpoint58p_post
1082    o obcs: stop if obcs is used with useCDscheme = .true.
1083    o shelfice:
1084     - fix a sign error so that no slip at shelfice interface works
1085     - remove stop for combination non-hydrostatic code and shelfice. That does
1086       not mean, that the results are correct, but at least they are numerically
1087       stable
1088    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
1089    o added adjoint exch routined for all exch*3d* routines
1090      and updated flow directives
1091    
1092    checkpoint58o_post
1093    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
1094      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
1095    o change controling S/R for writing pickup file (new S/R do_write_pickup)
1096      and clean-up reading/writing of pickup files.
1097    o fix local version of read/write pickup (NH part) in rotating_tank/code
1098    o simplify EXCH interface:
1099     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
1100     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
1101    o added the regrid package
1102    o shelfice:
1103     - add a simple boundary layer scheme to reduce noise
1104     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
1105    
1106    checkpoint58n_post
1107    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
1108       local variable (not in common block).
1109    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
1110      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
1111      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
1112        to work with SingleCpuIO.
1113    o add "_d 0" to real constant of pkg/cfc subroutines ;
1114       update exp. cfc_exemple & tutorial_cfc_offline output files.
1115    o multi-threading and IO:
1116      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
1117        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
1118      - barrier before and after reading.
1119      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
1120      - avoid using MDS_WRITELOCAL for LAND pkg output.
1121      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
1122        common-block variables ; Allows multi-threading with master-thread IO.
1123    o change default MAX_NO_THREADS from 32 to 4 ;
1124      and stop cleanly when MAX_NO_THREADS is too small.
1125    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
1126    
1127    checkpoint58m_post
1128    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
1129       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
1130    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
1131       keep global_ocean.90x40x15 (for AD testing) with former secondary test
1132       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
1133    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
1134        add MITgcm_tutorials (= code + all the tutorials)
1135    o ecco, option to compute cost for total ssh (mean+anom)
1136    o consistent with addition of ptracer and ssh in pkg/profiles
1137    o profiles: adding ptracer and ssh
1138    o testreport: change multi-test output-file name
1139      (from output.txt.{name} to output.{name}.txt)
1140    o profiles: now ok for mutli-tiles case
1141    o seaice: add 4 parameters for different advection schemes for area,
1142      (effective) seaice thickness, enthalphy, and snow height. Their default
1143      is the standard parameter SEAICEadvScheme
1144    o calc_gw:
1145     - add cosFacU in zonal viscous flux (harmonic.visc.).
1146     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
1147       of tutorial_plume_on_slope.
1148    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
1149    o calc_gw: true flux-form, account for horizontal grid spacing.
1150      update rotating_tank results, but not plume_on_slope (affected at
1151      truncation level, 11 digits).
1152    
1153    checkpoint58l_post
1154    o calc_gw:
1155     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
1156     - remove side-drag for now (need to fix it); update plume_on_slope results.
1157     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
1158  o commit code to make SST/SSS weights spatially variable  o commit code to make SST/SSS weights spatially variable
1159    (based on either variable in-situ or variable initial T/S weights)    (based on either variable in-situ or variable initial T/S weights)
1160  o pkg/ecco:  o pkg/ecco:
# Line 15  o pkg/ecco: Line 1165  o pkg/ecco:
1165      (sflxumm, sfluxmm2, bal_sfluxmm)      (sflxumm, sfluxmm2, bal_sfluxmm)
1166    * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,    * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
1167      including separate counting and multipliers      including separate counting and multipliers
1168    o pkg/rbcs
1169      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
1170    
1171  checkpoint58k_post  checkpoint58k_post
1172  o testreport:  o testreport:
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