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revision 1.825 by mlosch, Wed May 30 10:56:27 2007 UTC revision 1.1045 by mlosch, Wed Nov 26 15:27:02 2008 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/obcs: fix a CPP-flag, bug reported by Jeff Blundell
8    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
9      a still unfixed compiler/optimization bug
10    
11    checkpoint61f
12    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
13      update results of global_ocean.cs32x15.icedyn test.
14    o move getcon.F from model/src to pkg/fizhi.
15    o pkg/exf: add parameter for extrapolation of temp up to the surface
16       and option to prevent negative evap (in bulk_largeyeager04 only).
17    o Prather Advection scheme: fix tracer conservation for divergent flow
18      (e.g., when using NonLin Free-Surface).
19    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
20    o gmredi (Visbeck-variable-K):
21     - add more parameters to Visbeck-variable-K.
22     - use a 5 points average for dSigmaR in Visbeck-K calculation
23       (more "homogenous": same stencil and same weights as in dSigmaH)
24     - update output of ideal_2D_oce experiment.
25    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
26      (#undef REAL4_IS_SLOW)
27     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
28       coordinate variable
29     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
30       (surface forcing fields), removes some of the functionality
31     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
32     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
33       probably not all: copy _RS surface flux fields to RL field before
34       calling DIAGNOSTICS_FILL
35     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
36       real*4 (CALL EXCH_*_RS) versions.
37     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
38       (generate new output).
39    
40    checkpoint61e
41    o gmredi (Visbeck-variable-K):
42      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
43      - change computation of Visbeck-K where Slope > Smax :        
44        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
45        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
46    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
47      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
48    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
49    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
50      does not become too large (to avoid precision problems in implicit-diffusion
51      solver); update ideal_2D_oce output.
52    o pkg ggl90:
53      - in ggl90_cal.F: compute only one set of visc/diff, used to
54        step forward TKE/T/S/momentum
55      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
56        have Prandlt =1)
57    o gmredi (fm07):
58      - add lower limit on Transition layer thickness + lower limit on 1/lambda
59      - allow to set few more params from data.gmredi
60    o pkg ggl90:
61          - add missing sqrt(2) factor in computation of mixing length
62            scale in ggl90_calc.F
63            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
64    
65    checkpoint61d
66    o adjoint modifs
67      - adapt to new field rhoInSitu
68      - allow to revert from StoreDynVars2D, StoreDynVars3D
69        to individual fields
70        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
71    o store 3-D (in-situ) density in commom block (DYNVARS.h)
72     - save 1 rho computation.
73     - no longer modify T & S inland when using down_slope pkg.
74    o gad_som : allow to switch to SOM advection for T & S without corresponding
75      pickup files (using new S/R: MDS_CHECK4FILE).
76    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
77      (for useSingleCpuIO to work in multi-threaded)
78    o pkg/shelfice:
79     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
80       with SHELFICEtopoFile in data.shelfice
81     - move code for reading ice shelf topography and modifying hFacC into separate
82       subroutines of the shelfice package
83     - separate initialisation of "fixed" and "variable" variables
84     - kTopC is not (yet) replaced by kSurfC, although this is possible
85    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
86    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
87      and rename:
88      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
89      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
90    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
91    
92    checkpoint61c
93    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
94      to add mass source/sink of fluid in the interior (3-D generalisation
95      of oceanic real-fresh water flux).
96    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
97    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
98    o new pkg: down_slope
99      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
100      - presently, modify T & S inland (dwnslp_calc_rho.F).
101        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
102      - implementation for ocean in P-coords not tested.
103      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
104    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
105      (to facilitate conversion of oceanic pkg to p-coordinate).
106    o change FIND_RHO to FIND_RHO_2D :
107      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
108    o new pkg: cheapaml
109    
110    checkpoint61b
111    o exch2:
112      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
113      - no longer depend on the order sequence (N,S,E,W).
114      - 3rd exchange no longer needed (tested with 24 tiles).
115      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
116      - exch_UV_A-grid readily available (but not yet tested).
117      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
118      (both are no longer needed) in exch_uv: no effect in forward run; but
119       get truncation error differences with adjoint exch.
120    o exch2:
121     - change index-bounds storage (moved from target to local tile,
122       more intuitive this way) ; rename/remove some variables.
123     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
124    
125    checkpoint61a
126    o exch2/matlab-topology-generator:
127      fix bug in index bounds for N-S internal exchange (hard to tell if this
128      had any effect on the solution).
129    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
130      is exceeded
131    o testreport: modify syntax of awk, so that it works also with
132      awk, and not only with nawk and gawk
133    
134    checkpoint61
135    o autodiff
136      Change default for TAF usage by removing argument '-nonew_arg'
137      This changes TAF subroutine argument list (ordering of active var.)
138      Omission of this flag leads to incompatibility w.r.t. TAMC
139      To restore TAMC-compatibility, need following modifs:
140      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
141      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
142      Tested TAF version is 1.9.22
143      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
144    
145    checkpoint60
146    --->>> This is the last checkpoint for which generating the adjoint
147    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
148    --->>> by default.
149    --->>> Future checkpoints will ommit this flag by default.
150    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
151    o pkg/grdchk: Add gradient check to etan0 perturbations.
152    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
153    o pkg/autodiff: more flexibility in zeroadj.
154      model/src: modifying do_oceanic_phys.F accordingly.
155    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
156    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
157      special setup of gmredi for which the adjoint is stable
158      enough for parameter optimization.
159    o bridging the gap between eddy stress and GM.
160      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
161          along with a change in CPP option (now ALLOW_EDDYPSI).
162      -> when using GM w/ GM_AdvForm:
163          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
164          is applied either in the tracer Eq. or in momentum Eq.
165          depending on data.gmredi (intro. GM_InMomAsStress).
166      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
167      The key modifications are in model/src/taueddy_external_forcing.F
168      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
169    
170    checkpoint59r
171    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
172      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
173      fix option to read coriolis(@ cell-corner) from files with CS-grid.
174    o pkg/mnc: add some attributes to standard 1D-coordinate variables
175    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
176      mass points, when using mnc for output
177      - add runtime parameter (missing_value, missing_value_int) to override
178        default (which is the value of getcon('UNDEF'))
179    o pkg/mnc: prepare mnc for the actual use of missing values with the
180      diagnostics package: small fix in mnc_cw_readwrite.template and more
181      initialisation of never used fields
182      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
183      versions
184    o pkg/thsice/thsice_ini_vars.F added default initial values so that
185      thermodynamics sea ice solver does not blow up when some initial fields
186      are missing.
187    o move from external_forcing_surf.F to ini_forcing.F
188      the p-coord. hack consisting in using pLoad to set phi0surf ;
189      update output of tutorial_global_oce_in_p (affected @ truncation level).
190    o Freshen up a bit hs94.1x64x5, notably:
191      remove rotationPeriod and tRef=5*0. (adjoint only), and add
192      exactConserv=.TRUE.
193    o pkg/generic_advdiff:
194      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
195      applies to files where Temperature & Salinity 2nd Order moments are used.
196    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
197      this uses a dynamically allocated internal state data structure
198      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
199      and requires a fortran 90 compiler
200    
201    checkpoint59q
202    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
203       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
204    o Refresh tutorial_global_oce_biogeo, notably:
205      - change bathymetry (put back seamounts in ACC, use hFacs)
206      - change EOS (POLY3 --> JMD95Z)
207      - use Bryan-Lewis vertical diffusivity
208      - use multidimensional advection
209      - remove old virtual virtual in dic pkg, now done through ptracer pkg
210      - change a couple of parameters in dic pkg
211    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
212    o pkg/obcs: change default to OBCSfixTopo = .true.,
213      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
214      - replace "debugMode" with "debugLevel .GE. debLevB"
215    o implementation of TAF directives for gchem,cfc,dic
216    o remove "exp5" (replaced by tutorial_deep_convection).
217    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
218      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
219      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
220      --> changes results in exp4, seaice_obcs
221    o tutorial_deep_convection :
222      update the set-up and increase resolution and domain size ; start
223      from pseudo initial conditions = output at t=120mn in order to see
224      something happening when running testreport.
225    o pkg/seaice: add os7mp as an advection scheme
226                  add check for advection schemes
227                  add a flag for restoring T and S underneath sea ice
228    o pkg/my82: add netcdf-support and diagnostics
229    o thsice pkg:
230      - Now hsMax limits snow height by turning it into ice following
231        flooding scheme (and now conserving energy)
232      - Slight rewriting of the formula in thsice_calc_thick.F
233      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
234      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
235    
236    checkpoint59p
237    o gchem / dic / cfc :
238      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
239      - add new parameter files: "data.dic" & "data.cfc" ;
240      - various re-arrangement in initialisation & header file ;
241      - fix tutorial_global_oce_biogeo for multi-threaded test.
242    o pkg/dic: test for "pickup_dic" file when restarting ;
243      if no pickup-file, can restart with a re-initialised pH (same as it did
244      before) providing pickupStrictlyMatch is set to False.
245    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
246      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
247    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
248      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
249    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
250     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
251       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
252    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
253       scheme to use for vorticty-term ;
254     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
255       (with default selectVortScheme, return to original discretisation)
256     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
257    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
258    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
259      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
260      also fix diagnostics VISCAHW & VISCA4W.
261    
262    checkpoint59o
263    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
264    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
265      move a few statemens out the main loop into separate loops
266    o pkg/shelfice:
267      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
268        (kg/m^2/s), does not break tests, because in verification/isomip,
269        rhoConstFresh=rhoConst (by accident)
270      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
271      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
272        new file model/src/seawater.F, so that they are available for all pkgs.
273      - convert potential temperature into in-situ temperature. This changes the
274        isomip tests => update tests
275    o add a flag writePickupAtEnd (default=true) to be able to suppress
276      writing a pickup at the last timestep
277    o tools/mpack-1.6 :
278      - disable automake (not working) and autoconf (not needed).
279      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
280        also cleaner with much less compilation warnings.
281    o pkg/profiles:
282      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
283      (for "less than 32 characters name" compiler requirement)
284    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
285      conditions that have a different sampling frequency than S/T/U/V obcs
286    o pkg/diagnostics (stats-diags):
287      - fix global Min/Max in case 1 processor get only empty tiles
288    o genmake2: replace (4 times)
289         make genmake_tc_1.o >> genmake_warnings 2>&1
290      with
291         COMM="$CC $CFLAGS -c genmake_tc_1.c"
292         echo $COMM >> genmake_warnings
293         $COMM >> genmake_warnings 2>&1
294      to make genmake2 always see the value of CC as specified in the optfile.
295    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
296      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
297      - modify verification advect_cs test to test SOM-advection on CS-grid.
298    o pkg/ctrl:
299      - Rewrite of ctrl_map_ini_ecco.F,
300        introducing a generic routine (ctrl_map_ini_gen.F).
301      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
302    
303    checkpoint59n
304    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
305      number in dedicate array "hdiag":
306      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
307        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
308      - many small changes (integer format) for large number of diagnostics
309      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
310        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
311    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
312      usingSphericalGrid, this allows to define the rotated grid coordinates
313      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
314      geographical coordinates according to the inverse of the rotation defined
315      by the Euler angles, so that Coriolis parameter and online-interpolation by
316      exf works with the geographical coordinates on XC/YC/XG/YG.
317      Naturally, this feature does not work with all packages, so some
318      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
319      profiles), because there the coordinates are assumed to be regular
320      spherical grid coordinates.
321    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
322      - introduce isopycnal diffusion coefficient control.
323    o tools/adjoint_options:
324      - additional control vector components.
325    o pkg/mnc: have mnc create marginally meaning full coordinate variables
326      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
327    o pkg/mypackage:
328      - add example of read/write pickup for state-var ;
329      - add entry points to the main code for state-vars diags & write-pickup.
330    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
331      transitions for useExfYearlyFields
332      - add new subroutine that determines the file to read from for
333        use*YearlyFields = .TRUE. and .FALSE.
334      - add a verification experiment to global_with_exf that tests
335        useExfYearlyFields with USE_EXF_INTERPOLATION defined
336    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
337      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
338      subroutines (which could be generated from a template, because they are
339      almost identical), for now they are included in obcs_prescribe_read.F for
340      simplicity
341    o pkg/exf:
342      - add a little more diagnostic to exf_interp_read (in analogy to
343        mds_read_field, can be turned off with debugLevel < debugLevA=1)
344      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
345        ugly but fast by unrolling short inner loops, inserting a unroll=8
346        directive in routine lagran, and splitting a loop and making do while the
347        outermost loop (the latter requires the intoduction of index arrays)
348    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
349    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
350      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
351    o verification/seaice_obcs: updated for restart test and latest options
352    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
353      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
354      for now this is only available for the C-grid code and also within
355      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
356    
357    checkpoint59m
358    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
359      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
360    o gad_som : fix flux output (& diagnostics) to have same units as other  
361      advection scheme fluxes (was previously multiplied by deltaT).  
362    o added verification/seaice_obcs both to test seaice open boundaries
363      and to provide an example matlab scrpt for generating them
364    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
365    o pkg/salt_plume: clean up salt_plume_frac.F to
366      remove redundancy in PlumeMethod 1 and 4
367    o pkg/kpp: added saltplume diagnostics
368    o pkg/obcs and pkg/seaice:
369      - do not set uice and vice to zero when OB*icefile are unspecified
370      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
371      - moved seaice tracer obcs after call to seaice_growth
372    o pkg/salt_plume: added various options for salt plume depth
373      criterion and for vertical distribution of the salt
374    
375    checkpoint59l
376    o pkg/ptracers: new version of ptracers pickup:
377      read meta file and write only fields which are needed to restart.
378      ( same logic as main pickup file ; also using pickupStrictlyMatch )
379    o pkg/seaice:
380      - add timescale for melting due to warm mixed layer as a means of
381        setting SEAICE_availHeatFrac more conveniently
382      - add a CPP-flag/runtime parameter check for flooding algorithm
383      - reformulated availHeat in seaice_growth.F to be independent of AREA
384    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
385      unit changes
386    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
387    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
388      SX vector computer.
389    o pkg/seaice:
390      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
391        seaice forcing fields can now be read only through pkg/exf
392      - removed some unused halos
393    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
394    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
395      or U/VICE from U/VWIND before computing U/VSTRESS
396    
397    checkpoint59k
398    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
399      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
400    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
401      all experiments pass when compile with un-initialised var. checking option.
402    o added pkg/salt_plume
403    o script to test restart (for now, in MITgcm_contrib/jmc_script)
404    o pkg/seaice: new read/write pickup version.
405      read meta file and write only fields which are needed to restart.
406      ( same logic as main pickup file ; also using pickupStrictlyMatch )
407    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
408    o lab_sea.hb87: modify the domain & update output.hb87.txt :
409      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
410      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
411      process. Fixed here by closing the domain at the Northern boundary.
412    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
413    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
414      a set of consecutive levels in/from a 3-D array.
415    o pkg/ptracers:
416      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
417      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
418    
419    checkpoint59j
420    o in pkgs: dic, obcs, offline, rbcs:
421      standard way to compute coeff. for time interpolation between 2 time reccords
422      which retains full precision (& make results less dependent on compiler).
423      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
424    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
425      packages instead of reading ice cover and wind speed separately
426    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
427     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
428      to allow to compile customized code before the update)
429    o cleaning-up:
430      - fix CPP instruction syntax in pkg/obcs
431      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
432        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
433      - fix some threads issue in IO parts.
434    o pkg/dic:
435      - add tons of "_d 0" (--> much better testreports !)
436       and then update outputs of tutorial_global_oce_biogeo
437    o pkg/mom_fluxform:
438      add a special version of momentum advection intended to conserve momentum
439      next to a bathymetry step or a coastline edge. (default = off = #undef)
440    o new read/write pickup version:
441      - for now, only implemented for main (mdsio) pickup file.
442      - write out only what is needed to restart; merge pickup_nh , pickup_ph
443        and main pickup together.
444      - read meta file; read only what is needed to restart; stop if a field
445        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
446        if it make sense (even if the restart is not perfect).
447      - if no meta file, assume that pickup to read corresponds exactly to
448        a pickup that would currently be written.
449      - read pickup written in the old format (until checkpoint59i) if it
450        recognizes an old meta file (no field-list).
451      - add a meta file in exp. which starts from a pickup: 2 cases:
452        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
453         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
454        b) a meta file describing the content of the associated pickup file
455         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
456    o pkg/mdsio & pkg/rw:
457      - new routine to read a meta file ; new set of routine to read
458        Multiple-fields file (with meta file).
459    o added open boundary conditions capability for seaice
460        HSNOW, HSALT, UICE, and VICE
461    
462    checkpoint59i
463    o adjoint:
464      * fix multiDimAdvection adjoint
465        (partial recomputation problem by TAF for fVerT(:,:,kDown)
466        and comlev1 size definition (maxpass vs. max. number of tracers)
467      * verification/global_ocean.90x45x15 adjoint now tests
468        NLFS and multiDimAdvection using DST3 (=30)
469      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
470    o pkg/kpp: add "_d 0" to real constant (if missing);
471      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
472      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
473    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
474      for internal parameters related to restart process (formerly from PARAMS.h)
475      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
476    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
477      as argument. (only atm2d & obcs write_pickup have not yet been updated)
478    o pkg/monitor:
479      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
480      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
481      - account for deep Atmosphere factor and density factor (anelastic)
482    o added open boundary conditions capability for seaice HEFF and AREA
483    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
484      thermodynamics
485      - requires a little reorganization, which affects the testreport results
486        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
487        so that now the conservative form is tested
488      - add a few comments
489    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
490    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
491    o add new diagnostics to seaice: advective, diffusive fluxes (only for
492      multidim-advection, for scheme 2 they are not filled) and transports,
493      thermodynamic growth rates
494    o change units of EmPmR (inside the code, + within coupling interface)
495      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
496      Affects results @ truncation level (cg2d match) and update output of
497       experiments: lab_sea(6), global_ocean.90x40x15(10),
498      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
499      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
500      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
501      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
502    
503    checkpoint59h
504    o pkg/exf:
505      - improve vectorization by moving if-statement out of loops in
506        exf_mapfields, exf_radiation
507      - exf_bulkformulae.F: introduce 2D fields and vectorize code
508    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
509    o testreport:
510      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
511        monitor & update offline_exf_seaice exp. output.
512      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
513    o pkg/seaice:
514      - bug fix in the evp solver: boundary conditions were affected be
515        masking of zMax/zMin (changes results)
516      - minor bug fix in boundary conditions in seaice_calc_strainrates
517        (changes results for no_slip)
518      - seaice_lsr.F: make interpolation of eta dependent on boundaries
519      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
520      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
521        stress formulation and no-slip boundary conditions
522    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
523      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
524    o pkg/seaice: a first HSALT time stepping equation has been checked in
525    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
526      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
527      without requiring DO-IF statements
528    o pkg/thsice:
529      use continuous power-law function for partition of energy between lateral
530      melting/freezing and thinning/thickening ; old code using step function
531      still available with #undef THSICE_FRACEN_POWERLAW
532      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
533    o testreport: change AD testing : check against results/output_adm.txt
534      using same scripts as for forward test.
535    
536    checkpoint59g
537    o adjoint testing: in preparation for changing testreport:
538      - output format: cost and grad written on separated lines
539      - ad output results in directory "results" (instead of "results_ad")
540    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
541    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
542    o pkg/ecco: allow user defined cost function contributions
543    o testreport:
544      Allow to choose (per experiment) the list of tested output variables
545       and the main variable (used to issue a pass/FAIL ) ;
546      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
547      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
548      Also modify printing of summary:
549       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
550       b) echo the list of tested variables in the individual summary.txt of
551          each experiment.
552    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
553      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
554      (but still depend on the tile decompostion of the domain).
555    o pkg/seaice: change a discretization detail to make the B-grid code
556      "more symmetric". This change is likely to remove all "ridges/leads" that
557      where quasi-aligned with the grid in B-grid solutions. It may also be
558      the solution to the stress coupling issues with the B-grid.
559    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
560      remove .cvsignore from input dir. (since testreport no longer run here).
561    o pkg/thsice:
562     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
563     - fix reshaping of sea-ice just after advection:
564       melt all the ice only if ice-volume is too small.
565     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
566       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
567     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
568    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
569      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
570    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
571      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
572      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
573      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
574      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
575      -> update output.txt
576    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
577     this affects truncation error: -> update output.txt of exp:
578      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
579      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
580    
581    checkpoint59f
582    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
583    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
584      a bounded range (in forward mode)
585    o pkg/ecco, ctrl, autodiff and mom_common:
586     internal parameter controls, completements of implementations
587    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
588    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
589      (not seem any difference in testing results).
590    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
591       at face corners.
592    o pkg/generic_advdiff:
593     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
594      loop range indices for computing vertical advection tendency
595      and do the calculation in the interior only (no overlap) ;
596      for now, only implemented for SOM advection (to save CPU time).
597     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
598    o exch2 adjoint
599      First set of changes:
600      - add exch2 hand-written adjoint templates
601      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
602        This will require cleanup in pkg/autodiff/*.F
603        (changed routines currently kept separate in verif. code/)
604      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
605        that used to hide exch2 or cubed-sphere specific code
606        (commented via 'cph-exch2')
607    o pkg/seaice
608      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
609    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
610       output of global_ocean.cs32x15.thsice .
611    
612    checkpoint59e
613    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
614      for B-grid vector (not yet tested) and C-grid vector (<- only used
615      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
616    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
617      (#ifdef ALLOW_SALT_PLUME)
618    o gather_2d/scatter_2d: removed halo regions
619    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
620      scheme and the corresponding test case (under front_relax dir). For now,
621      only available with Skew-flux form and not yet tested in realistic set-up.
622      adjoint: store directives updated, but gradient checks deteriorated,
623      so maybe GM/Redi adjoint is now broken.
624    o seaice adjoint
625      * add AREA, HEFF, HSNOW as control variable
626        (should not change lab_sea results)
627      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
628    o pkg/seaice:
629      * added computation of saltFlux in seaice_growth;
630        For time being, sea ice salinity is assumed constant
631        contribution of snow flooding to freshening of sea ice is neglected.
632        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
633        defaults to 0.0 in order to maintain backward compatibility.
634        Typical values for SEAICE_salinity are 4 to 10 g/kg.
635      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
636      * added SEAICE_availHeatFrac, which specifies fraction of surface level
637        heat content used to melt or grow ice
638      * commented out cap of HICE: it helps keep ice thinner
639      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
640      * applied OBCS T/S mask to HEFFM sea ice mask
641    
642    checkpoint59d
643    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
644     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
645     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
646    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
647     and change default value of parameter "GM_Small_Number";
648     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
649       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
650       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
651    o pkg/ecco: cost function when applying pkg/smooth to controls
652    o pkg/ctrl: add forcingPrecond run time parameter
653    o pkg/seaice:
654     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
655     - fix bug in metric terms of u-equation in LSR solver (implicit part),
656       changes verification/lab_sea
657     - rearrange implicit part of u-equation in LSR solver to make it easier to
658       read, understand, and debug. This causes changes at the truncation level.
659     - fix (serious) bug in the boundary conditions (sign error in the implicit
660       part) of the LSR solver. Changes all LSR results.
661     - fixed problem with HSNOW initialization to avoid thick snow when AREA
662       is initilized with small values - does not change lab_sea results.
663     - added HsnowFile initialization capability
664    o pkg/smooth: addition to model/src and pkg/ctrl so allow
665     initialization of pkg/smooth and application to control vector
666    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
667    o dependencies: pkg/profiles requires pkg/cal
668    o pkg/profiles:
669     - added option ALLOW_PROFILES_GENERICGRID
670         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
671         that interpolation information (grid points and coefficients) is provided
672         within the netcdf input files.
673         -> sample matlab scripts can be found in MITgcm_contrib/gael
674         that allow you to prepare netcdf input files.
675     - also modified: cleaner include statements, cleaner error print statements,
676       cleaner stops when error, and more tests of the netcdf input files consistency.
677    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
678    o pkg/seaice:
679     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
680       requires a new routine: seaice_diagnostics_fill.F
681     - make sure that seaice does not move if not forced (pressure replacement
682       method, Hibler and Ip, 1995), changes results
683     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
684     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
685       It is turned off by default (=-1.), because it changes the results.
686     - make it possible to read AREA from a file, too.
687    
688    checkpoint59c
689    o add S/R and diagnostics for oceanic mixed-layer depth
690    o move GMRedi call after all vertical mixing schemes (including KPP)
691    o pkg/thsice:
692     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
693      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
694  o pkg/obcs:  o pkg/obcs:
695   - bug fix for balance code   - bug fix for balance code
696  o pkg/seaice:  o pkg/seaice:
697    - allow values of SEAICE_elasticParm > 1    - allow values of SEAICE_elasticParm > 1
698    - add new parameter SEAICE_evpTauRelax as an alternative to SEAICE_elasticParm    - add new parameter SEAICE_evpTauRelax as an alternative
699        to SEAICE_elasticParm
700    - make lsr boundary conditions free slip (by default), changes result    - make lsr boundary conditions free slip (by default), changes result
701    - add code for no slip boundary conditions for lsr    - add code for no slip boundary conditions for lsr
702    - set minimum of zeta to zero (and not 4e8) (changes results)    - set minimum of zeta to zero (and not 4e8) (changes results)
703      - add a cap on AREA after advecting AREA if seaice_growth is not called
704  o change calculation of Visbeck K:  o change calculation of Visbeck K:
705    - no longer depend on tapering scheme; instead, compute slope (limited    - no longer depend on tapering scheme; instead, compute slope (limited
706      by GM_maxSlope). this is equivalent to what was comuted before with      by GM_maxSlope). this is equivalent to what was comuted before with
707      clipping or linear tappering.      clipping or linear tappering.
708    - fix vertical averaging (wrong by 1 level)    - fix vertical averaging (wrong by 1/2 level)
709    - leave the old version (but will not be maintained) within    - leave the old version (but will not be maintained) within
710      #ifdef OLD_VISBECK_CALC / #endif      #ifdef OLD_VISBECK_CALC / #endif
711      - update output of exp. ideal_2D_oce
712  o change error catch in calc_r_star to improve vectorization  o change error catch in calc_r_star to improve vectorization
713  o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and  o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
714    add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).    add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
715    o adjoint:
716      Re-organized adjoint checkpointing according to Matt Mazloff
717      (but with modifs/completions/cleanups)
718      Storing is now bundled into large arrays to optimized I/O
719      (and second step in cleanup of the_main_loop)
720    
721  checkpoint59b  checkpoint59b
722  o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):  o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
# Line 75  o pkg/exf: some cleaning-up: Line 770  o pkg/exf: some cleaning-up:
770  o pkg/thsice:  o pkg/thsice:
771   fix few little problems, in thsice_calc_thickn.F:   fix few little problems, in thsice_calc_thickn.F:
772    - growth vertically (and not laterally) if iceFrac == iceMaskMax    - growth vertically (and not laterally) if iceFrac == iceMaskMax
773    - melt laterally only if hIce < hThinIce (as the comments say)    - melt only laterally if hIce < hThinIce (as the comments say)
774    and in thsice_extend.F:    and in thsice_extend.F:
775    - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)    - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
776    - start to form ice as soon as the minimum ice-volume is reachable.    - start to form ice as soon as the minimum ice-volume is reachable.
# Line 112  o in FFIELDS.h: Line 807  o in FFIELDS.h:
807       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
808  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
809  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
810      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
811        are no longer updating the vertical diffusivity array
812        (passed as argument) but are (re-) setting those arrays.
813  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
814    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
815      cgrid-lsr and evp solver      cgrid-lsr and evp solver
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