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revision 1.819 by jmc, Fri May 18 03:02:47 2007 UTC revision 1.1018 by jmc, Sun Aug 24 22:03:51 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 add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
8      to add mass source/sink of fluid in the interior (3-D generalisation
9      of oceanic real-fresh water flux).
10    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
11    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
12    o new pkg: down_slope
13      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
14      - presently, modify T & S inland (dwnslp_calc_rho.F).
15        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
16      - implementation for ocean in P-coords not tested.
17      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
18    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
19      (to facilitate conversion of oceanic pkg to p-coordinate).
20    o change FIND_RHO to FIND_RHO_2D :
21      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
22    o new pkg: cheapaml
23    
24    checkpoint61b
25    o exch2:
26      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
27      - no longer depend on the order sequence (N,S,E,W).
28      - 3rd exchange no longer needed (tested with 24 tiles).
29      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
30      - exch_UV_A-grid readily available (but not yet tested).
31      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
32      (both are no longer needed) in exch_uv: no effect in forward run; but
33       get truncation error differences with adjoint exch.
34    o exch2:
35     - change index-bounds storage (moved from target to local tile,
36       more intuitive this way) ; rename/remove some variables.
37     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
38    
39    checkpoint61a
40    o exch2/matlab-topology-generator:
41      fix bug in index bounds for N-S internal exchange (hard to tell if this
42      had any effect on the solution).
43    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
44      is exceeded
45    o testreport: modify syntax of awk, so that it works also with
46      awk, and not only with nawk and gawk
47    
48    checkpoint61
49    o autodiff
50      Change default for TAF usage by removing argument '-nonew_arg'
51      This changes TAF subroutine argument list (ordering of active var.)
52      Omission of this flag leads to incompatibility w.r.t. TAMC
53      To restore TAMC-compatibility, need following modifs:
54      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
55      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
56      Tested TAF version is 1.9.22
57      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
58    
59    checkpoint60
60    --->>> This is the last checkpoint for which generating the adjoint
61    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
62    --->>> by default.
63    --->>> Future checkpoints will ommit this flag by default.
64    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
65    o pkg/grdchk: Add gradient check to etan0 perturbations.
66    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
67    o pkg/autodiff: more flexibility in zeroadj.
68      model/src: modifying do_oceanic_phys.F accordingly.
69    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
70    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
71      special setup of gmredi for which the adjoint is stable
72      enough for parameter optimization.
73    o bridging the gap between eddy stress and GM.
74      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
75          along with a change in CPP option (now ALLOW_EDDYPSI).
76      -> when using GM w/ GM_AdvForm:
77          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
78          is applied either in the tracer Eq. or in momentum Eq.
79          depending on data.gmredi (intro. GM_InMomAsStress).
80      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
81      The key modifications are in model/src/taueddy_external_forcing.F
82      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
83    
84    checkpoint59r
85    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
86      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
87      fix option to read coriolis(@ cell-corner) from files with CS-grid.
88    o pkg/mnc: add some attributes to standard 1D-coordinate variables
89    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
90      mass points, when using mnc for output
91      - add runtime parameter (missing_value, missing_value_int) to override
92        default (which is the value of getcon('UNDEF'))
93    o pkg/mnc: prepare mnc for the actual use of missing values with the
94      diagnostics package: small fix in mnc_cw_readwrite.template and more
95      initialisation of never used fields
96      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
97      versions
98    o pkg/thsice/thsice_ini_vars.F added default initial values so that
99      thermodynamics sea ice solver does not blow up when some initial fields
100      are missing.
101    o move from external_forcing_surf.F to ini_forcing.F
102      the p-coord. hack consisting in using pLoad to set phi0surf ;
103      update output of tutorial_global_oce_in_p (affected @ truncation level).
104    o Freshen up a bit hs94.1x64x5, notably:
105      remove rotationPeriod and tRef=5*0. (adjoint only), and add
106      exactConserv=.TRUE.
107    o pkg/generic_advdiff:
108      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
109      applies to files where Temperature & Salinity 2nd Order moments are used.
110    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
111      this uses a dynamically allocated internal state data structure
112      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
113      and requires a fortran 90 compiler
114    
115    checkpoint59q
116    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
117       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
118    o Refresh tutorial_global_oce_biogeo, notably:
119      - change bathymetry (put back seamounts in ACC, use hFacs)
120      - change EOS (POLY3 --> JMD95Z)
121      - use Bryan-Lewis vertical diffusivity
122      - use multidimensional advection
123      - remove old virtual virtual in dic pkg, now done through ptracer pkg
124      - change a couple of parameters in dic pkg
125    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
126    o pkg/obcs: change default to OBCSfixTopo = .true.,
127      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
128      - replace "debugMode" with "debugLevel .GE. debLevB"
129    o implementation of TAF directives for gchem,cfc,dic
130    o remove "exp5" (replaced by tutorial_deep_convection).
131    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
132      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
133      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
134      --> changes results in exp4, seaice_obcs
135    o tutorial_deep_convection :
136      update the set-up and increase resolution and domain size ; start
137      from pseudo initial conditions = output at t=120mn in order to see
138      something happening when running testreport.
139    o pkg/seaice: add os7mp as an advection scheme
140                  add check for advection schemes
141                  add a flag for restoring T and S underneath sea ice
142    o pkg/my82: add netcdf-support and diagnostics
143    o thsice pkg:
144      - Now hsMax limits snow height by turning it into ice following
145        flooding scheme (and now conserving energy)
146      - Slight rewriting of the formula in thsice_calc_thick.F
147      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
148      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
149    
150    checkpoint59p
151    o gchem / dic / cfc :
152      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
153      - add new parameter files: "data.dic" & "data.cfc" ;
154      - various re-arrangement in initialisation & header file ;
155      - fix tutorial_global_oce_biogeo for multi-threaded test.
156    o pkg/dic: test for "pickup_dic" file when restarting ;
157      if no pickup-file, can restart with a re-initialised pH (same as it did
158      before) providing pickupStrictlyMatch is set to False.
159    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
160      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
161    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
162      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
163    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
164     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
165       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
166    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
167       scheme to use for vorticty-term ;
168     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
169       (with default selectVortScheme, return to original discretisation)
170     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
171    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
172    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
173      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
174      also fix diagnostics VISCAHW & VISCA4W.
175    
176    checkpoint59o
177    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
178    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
179      move a few statemens out the main loop into separate loops
180    o pkg/shelfice:
181      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
182        (kg/m^2/s), does not break tests, because in verification/isomip,
183        rhoConstFresh=rhoConst (by accident)
184      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
185      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
186        new file model/src/seawater.F, so that they are available for all pkgs.
187      - convert potential temperature into in-situ temperature. This changes the
188        isomip tests => update tests
189    o add a flag writePickupAtEnd (default=true) to be able to suppress
190      writing a pickup at the last timestep
191    o tools/mpack-1.6 :
192      - disable automake (not working) and autoconf (not needed).
193      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
194        also cleaner with much less compilation warnings.
195    o pkg/profiles:
196      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
197      (for "less than 32 characters name" compiler requirement)
198    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
199      conditions that have a different sampling frequency than S/T/U/V obcs
200    o pkg/diagnostics (stats-diags):
201      - fix global Min/Max in case 1 processor get only empty tiles
202    o genmake2: replace (4 times)
203         make genmake_tc_1.o >> genmake_warnings 2>&1
204      with
205         COMM="$CC $CFLAGS -c genmake_tc_1.c"
206         echo $COMM >> genmake_warnings
207         $COMM >> genmake_warnings 2>&1
208      to make genmake2 always see the value of CC as specified in the optfile.
209    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
210      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
211      - modify verification advect_cs test to test SOM-advection on CS-grid.
212    o pkg/ctrl:
213      - Rewrite of ctrl_map_ini_ecco.F,
214        introducing a generic routine (ctrl_map_ini_gen.F).
215      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
216    
217    checkpoint59n
218    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
219      number in dedicate array "hdiag":
220      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
221        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
222      - many small changes (integer format) for large number of diagnostics
223      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
224        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
225    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
226      usingSphericalGrid, this allows to define the rotated grid coordinates
227      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
228      geographical coordinates according to the inverse of the rotation defined
229      by the Euler angles, so that Coriolis parameter and online-interpolation by
230      exf works with the geographical coordinates on XC/YC/XG/YG.
231      Naturally, this feature does not work with all packages, so some
232      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
233      profiles), because there the coordinates are assumed to be regular
234      spherical grid coordinates.
235    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
236      - introduce isopycnal diffusion coefficient control.
237    o tools/adjoint_options:
238      - additional control vector components.
239    o pkg/mnc: have mnc create marginally meaning full coordinate variables
240      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
241    o pkg/mypackage:
242      - add example of read/write pickup for state-var ;
243      - add entry points to the main code for state-vars diags & write-pickup.
244    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
245      transitions for useExfYearlyFields
246      - add new subroutine that determines the file to read from for
247        use*YearlyFields = .TRUE. and .FALSE.
248      - add a verification experiment to global_with_exf that tests
249        useExfYearlyFields with USE_EXF_INTERPOLATION defined
250    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
251      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
252      subroutines (which could be generated from a template, because they are
253      almost identical), for now they are included in obcs_prescribe_read.F for
254      simplicity
255    o pkg/exf:
256      - add a little more diagnostic to exf_interp_read (in analogy to
257        mds_read_field, can be turned off with debugLevel < debugLevA=1)
258      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
259        ugly but fast by unrolling short inner loops, inserting a unroll=8
260        directive in routine lagran, and splitting a loop and making do while the
261        outermost loop (the latter requires the intoduction of index arrays)
262    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
263    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
264      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
265    o verification/seaice_obcs: updated for restart test and latest options
266    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
267      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
268      for now this is only available for the C-grid code and also within
269      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
270    
271    checkpoint59m
272    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
273      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
274    o gad_som : fix flux output (& diagnostics) to have same units as other  
275      advection scheme fluxes (was previously multiplied by deltaT).  
276    o added verification/seaice_obcs both to test seaice open boundaries
277      and to provide an example matlab scrpt for generating them
278    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
279    o pkg/salt_plume: clean up salt_plume_frac.F to
280      remove redundancy in PlumeMethod 1 and 4
281    o pkg/kpp: added saltplume diagnostics
282    o pkg/obcs and pkg/seaice:
283      - do not set uice and vice to zero when OB*icefile are unspecified
284      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
285      - moved seaice tracer obcs after call to seaice_growth
286    o pkg/salt_plume: added various options for salt plume depth
287      criterion and for vertical distribution of the salt
288    
289    checkpoint59l
290    o pkg/ptracers: new version of ptracers pickup:
291      read meta file and write only fields which are needed to restart.
292      ( same logic as main pickup file ; also using pickupStrictlyMatch )
293    o pkg/seaice:
294      - add timescale for melting due to warm mixed layer as a means of
295        setting SEAICE_availHeatFrac more conveniently
296      - add a CPP-flag/runtime parameter check for flooding algorithm
297      - reformulated availHeat in seaice_growth.F to be independent of AREA
298    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
299      unit changes
300    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
301    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
302      SX vector computer.
303    o pkg/seaice:
304      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
305        seaice forcing fields can now be read only through pkg/exf
306      - removed some unused halos
307    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
308    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
309      or U/VICE from U/VWIND before computing U/VSTRESS
310    
311    checkpoint59k
312    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
313      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
314    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
315      all experiments pass when compile with un-initialised var. checking option.
316    o added pkg/salt_plume
317    o script to test restart (for now, in MITgcm_contrib/jmc_script)
318    o pkg/seaice: new read/write pickup version.
319      read meta file and write only fields which are needed to restart.
320      ( same logic as main pickup file ; also using pickupStrictlyMatch )
321    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
322    o lab_sea.hb87: modify the domain & update output.hb87.txt :
323      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
324      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
325      process. Fixed here by closing the domain at the Northern boundary.
326    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
327    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
328      a set of consecutive levels in/from a 3-D array.
329    o pkg/ptracers:
330      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
331      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
332    
333    checkpoint59j
334    o in pkgs: dic, obcs, offline, rbcs:
335      standard way to compute coeff. for time interpolation between 2 time reccords
336      which retains full precision (& make results less dependent on compiler).
337      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
338    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
339      packages instead of reading ice cover and wind speed separately
340    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
341     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
342      to allow to compile customized code before the update)
343    o cleaning-up:
344      - fix CPP instruction syntax in pkg/obcs
345      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
346        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
347      - fix some threads issue in IO parts.
348    o pkg/dic:
349      - add tons of "_d 0" (--> much better testreports !)
350       and then update outputs of tutorial_global_oce_biogeo
351    o pkg/mom_fluxform:
352      add a special version of momentum advection intended to conserve momentum
353      next to a bathymetry step or a coastline edge. (default = off = #undef)
354    o new read/write pickup version:
355      - for now, only implemented for main (mdsio) pickup file.
356      - write out only what is needed to restart; merge pickup_nh , pickup_ph
357        and main pickup together.
358      - read meta file; read only what is needed to restart; stop if a field
359        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
360        if it make sense (even if the restart is not perfect).
361      - if no meta file, assume that pickup to read corresponds exactly to
362        a pickup that would currently be written.
363      - read pickup written in the old format (until checkpoint59i) if it
364        recognizes an old meta file (no field-list).
365      - add a meta file in exp. which starts from a pickup: 2 cases:
366        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
367         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
368        b) a meta file describing the content of the associated pickup file
369         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
370    o pkg/mdsio & pkg/rw:
371      - new routine to read a meta file ; new set of routine to read
372        Multiple-fields file (with meta file).
373    o added open boundary conditions capability for seaice
374        HSNOW, HSALT, UICE, and VICE
375    
376    checkpoint59i
377    o adjoint:
378      * fix multiDimAdvection adjoint
379        (partial recomputation problem by TAF for fVerT(:,:,kDown)
380        and comlev1 size definition (maxpass vs. max. number of tracers)
381      * verification/global_ocean.90x45x15 adjoint now tests
382        NLFS and multiDimAdvection using DST3 (=30)
383      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
384    o pkg/kpp: add "_d 0" to real constant (if missing);
385      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
386      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
387    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
388      for internal parameters related to restart process (formerly from PARAMS.h)
389      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
390    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
391      as argument. (only atm2d & obcs write_pickup have not yet been updated)
392    o pkg/monitor:
393      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
394      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
395      - account for deep Atmosphere factor and density factor (anelastic)
396    o added open boundary conditions capability for seaice HEFF and AREA
397    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
398      thermodynamics
399      - requires a little reorganization, which affects the testreport results
400        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
401        so that now the conservative form is tested
402      - add a few comments
403    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
404    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
405    o add new diagnostics to seaice: advective, diffusive fluxes (only for
406      multidim-advection, for scheme 2 they are not filled) and transports,
407      thermodynamic growth rates
408    o change units of EmPmR (inside the code, + within coupling interface)
409      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
410      Affects results @ truncation level (cg2d match) and update output of
411       experiments: lab_sea(6), global_ocean.90x40x15(10),
412      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
413      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
414      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
415      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
416    
417    checkpoint59h
418    o pkg/exf:
419      - improve vectorization by moving if-statement out of loops in
420        exf_mapfields, exf_radiation
421      - exf_bulkformulae.F: introduce 2D fields and vectorize code
422    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
423    o testreport:
424      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
425        monitor & update offline_exf_seaice exp. output.
426      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
427    o pkg/seaice:
428      - bug fix in the evp solver: boundary conditions were affected be
429        masking of zMax/zMin (changes results)
430      - minor bug fix in boundary conditions in seaice_calc_strainrates
431        (changes results for no_slip)
432      - seaice_lsr.F: make interpolation of eta dependent on boundaries
433      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
434      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
435        stress formulation and no-slip boundary conditions
436    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
437      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
438    o pkg/seaice: a first HSALT time stepping equation has been checked in
439    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
440      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
441      without requiring DO-IF statements
442    o pkg/thsice:
443      use continuous power-law function for partition of energy between lateral
444      melting/freezing and thinning/thickening ; old code using step function
445      still available with #undef THSICE_FRACEN_POWERLAW
446      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
447    o testreport: change AD testing : check against results/output_adm.txt
448      using same scripts as for forward test.
449    
450    checkpoint59g
451    o adjoint testing: in preparation for changing testreport:
452      - output format: cost and grad written on separated lines
453      - ad output results in directory "results" (instead of "results_ad")
454    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
455    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
456    o pkg/ecco: allow user defined cost function contributions
457    o testreport:
458      Allow to choose (per experiment) the list of tested output variables
459       and the main variable (used to issue a pass/FAIL ) ;
460      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
461      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
462      Also modify printing of summary:
463       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
464       b) echo the list of tested variables in the individual summary.txt of
465          each experiment.
466    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
467      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
468      (but still depend on the tile decompostion of the domain).
469    o pkg/seaice: change a discretization detail to make the B-grid code
470      "more symmetric". This change is likely to remove all "ridges/leads" that
471      where quasi-aligned with the grid in B-grid solutions. It may also be
472      the solution to the stress coupling issues with the B-grid.
473    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
474      remove .cvsignore from input dir. (since testreport no longer run here).
475    o pkg/thsice:
476     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
477     - fix reshaping of sea-ice just after advection:
478       melt all the ice only if ice-volume is too small.
479     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
480       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
481     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
482    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
483      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
484    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
485      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
486      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
487      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
488      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
489      -> update output.txt
490    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
491     this affects truncation error: -> update output.txt of exp:
492      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
493      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
494    
495    checkpoint59f
496    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
497    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
498      a bounded range (in forward mode)
499    o pkg/ecco, ctrl, autodiff and mom_common:
500     internal parameter controls, completements of implementations
501    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
502    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
503      (not seem any difference in testing results).
504    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
505       at face corners.
506    o pkg/generic_advdiff:
507     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
508      loop range indices for computing vertical advection tendency
509      and do the calculation in the interior only (no overlap) ;
510      for now, only implemented for SOM advection (to save CPU time).
511     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
512    o exch2 adjoint
513      First set of changes:
514      - add exch2 hand-written adjoint templates
515      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
516        This will require cleanup in pkg/autodiff/*.F
517        (changed routines currently kept separate in verif. code/)
518      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
519        that used to hide exch2 or cubed-sphere specific code
520        (commented via 'cph-exch2')
521    o pkg/seaice
522      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
523    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
524       output of global_ocean.cs32x15.thsice .
525    
526    checkpoint59e
527    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
528      for B-grid vector (not yet tested) and C-grid vector (<- only used
529      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
530    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
531      (#ifdef ALLOW_SALT_PLUME)
532    o gather_2d/scatter_2d: removed halo regions
533    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
534      scheme and the corresponding test case (under front_relax dir). For now,
535      only available with Skew-flux form and not yet tested in realistic set-up.
536      adjoint: store directives updated, but gradient checks deteriorated,
537      so maybe GM/Redi adjoint is now broken.
538    o seaice adjoint
539      * add AREA, HEFF, HSNOW as control variable
540        (should not change lab_sea results)
541      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
542    o pkg/seaice:
543      * added computation of saltFlux in seaice_growth;
544        For time being, sea ice salinity is assumed constant
545        contribution of snow flooding to freshening of sea ice is neglected.
546        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
547        defaults to 0.0 in order to maintain backward compatibility.
548        Typical values for SEAICE_salinity are 4 to 10 g/kg.
549      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
550      * added SEAICE_availHeatFrac, which specifies fraction of surface level
551        heat content used to melt or grow ice
552      * commented out cap of HICE: it helps keep ice thinner
553      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
554      * applied OBCS T/S mask to HEFFM sea ice mask
555    
556    checkpoint59d
557    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
558     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
559     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
560    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
561     and change default value of parameter "GM_Small_Number";
562     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
563       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
564       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
565    o pkg/ecco: cost function when applying pkg/smooth to controls
566    o pkg/ctrl: add forcingPrecond run time parameter
567    o pkg/seaice:
568     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
569     - fix bug in metric terms of u-equation in LSR solver (implicit part),
570       changes verification/lab_sea
571     - rearrange implicit part of u-equation in LSR solver to make it easier to
572       read, understand, and debug. This causes changes at the truncation level.
573     - fix (serious) bug in the boundary conditions (sign error in the implicit
574       part) of the LSR solver. Changes all LSR results.
575     - fixed problem with HSNOW initialization to avoid thick snow when AREA
576       is initilized with small values - does not change lab_sea results.
577     - added HsnowFile initialization capability
578    o pkg/smooth: addition to model/src and pkg/ctrl so allow
579     initialization of pkg/smooth and application to control vector
580    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
581    o dependencies: pkg/profiles requires pkg/cal
582    o pkg/profiles:
583     - added option ALLOW_PROFILES_GENERICGRID
584         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
585         that interpolation information (grid points and coefficients) is provided
586         within the netcdf input files.
587         -> sample matlab scripts can be found in MITgcm_contrib/gael
588         that allow you to prepare netcdf input files.
589     - also modified: cleaner include statements, cleaner error print statements,
590       cleaner stops when error, and more tests of the netcdf input files consistency.
591    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
592    o pkg/seaice:
593     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
594       requires a new routine: seaice_diagnostics_fill.F
595     - make sure that seaice does not move if not forced (pressure replacement
596       method, Hibler and Ip, 1995), changes results
597     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
598     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
599       It is turned off by default (=-1.), because it changes the results.
600     - make it possible to read AREA from a file, too.
601    
602    checkpoint59c
603    o add S/R and diagnostics for oceanic mixed-layer depth
604    o move GMRedi call after all vertical mixing schemes (including KPP)
605    o pkg/thsice:
606     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
607      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
608    o pkg/obcs:
609     - bug fix for balance code
610    o pkg/seaice:
611      - allow values of SEAICE_elasticParm > 1
612      - add new parameter SEAICE_evpTauRelax as an alternative
613        to SEAICE_elasticParm
614      - make lsr boundary conditions free slip (by default), changes result
615      - add code for no slip boundary conditions for lsr
616      - set minimum of zeta to zero (and not 4e8) (changes results)
617      - add a cap on AREA after advecting AREA if seaice_growth is not called
618    o change calculation of Visbeck K:
619      - no longer depend on tapering scheme; instead, compute slope (limited
620        by GM_maxSlope). this is equivalent to what was comuted before with
621        clipping or linear tappering.
622      - fix vertical averaging (wrong by 1/2 level)
623      - leave the old version (but will not be maintained) within
624        #ifdef OLD_VISBECK_CALC / #endif
625      - update output of exp. ideal_2D_oce
626    o change error catch in calc_r_star to improve vectorization
627  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
628    add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).    add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
629    o adjoint:
630      Re-organized adjoint checkpointing according to Matt Mazloff
631      (but with modifs/completions/cleanups)
632      Storing is now bundled into large arrays to optimized I/O
633      (and second step in cleanup of the_main_loop)
634    
635  checkpoint59b  checkpoint59b
636  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 59  o pkg/exf: some cleaning-up: Line 684  o pkg/exf: some cleaning-up:
684  o pkg/thsice:  o pkg/thsice:
685   fix few little problems, in thsice_calc_thickn.F:   fix few little problems, in thsice_calc_thickn.F:
686    - growth vertically (and not laterally) if iceFrac == iceMaskMax    - growth vertically (and not laterally) if iceFrac == iceMaskMax
687    - melt laterally only if hIce < hThinIce (as the comments say)    - melt only laterally if hIce < hThinIce (as the comments say)
688    and in thsice_extend.F:    and in thsice_extend.F:
689    - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)    - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
690    - 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 96  o in FFIELDS.h: Line 721  o in FFIELDS.h:
721       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
722  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
723  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
724      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
725        are no longer updating the vertical diffusivity array
726        (passed as argument) but are (re-) setting those arrays.
727  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
728    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
729      cgrid-lsr and evp solver      cgrid-lsr and evp solver
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