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revision 1.811 by mlosch, Wed May 9 14:32:05 2007 UTC revision 1.1025 by heimbach, Thu Sep 25 16:10:48 2008 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint61d
8    o adjoint modifs
9      - adapt to new field rhoInSitu
10      - allow to revert from StoreDynVars2D, StoreDynVars3D
11        to individual fields
12        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
13    o store 3-D (in-situ) density in commom block (DYNVARS.h)
14     - save 1 rho computation.
15     - no longer modify T & S inland when using down_slope pkg.
16    o gad_som : allow to switch to SOM advection for T & S without corresponding
17      pickup files (using new S/R: MDS_CHECK4FILE).
18    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
19      (for useSingleCpuIO to work in multi-threaded)
20    o pkg/shelfice:
21     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
22       with SHELFICEtopoFile in data.shelfice
23     - move code for reading ice shelf topography and modifying hFacC into separate
24       subroutines of the shelfice package
25     - separate initialisation of "fixed" and "variable" variables
26     - kTopC is not (yet) replaced by kSurfC, although this is possible
27    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
28    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
29      and rename:
30      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
31      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
32    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
33    
34    checkpoint61c
35    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
36      to add mass source/sink of fluid in the interior (3-D generalisation
37      of oceanic real-fresh water flux).
38    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
39    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
40    o new pkg: down_slope
41      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
42      - presently, modify T & S inland (dwnslp_calc_rho.F).
43        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
44      - implementation for ocean in P-coords not tested.
45      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
46    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
47      (to facilitate conversion of oceanic pkg to p-coordinate).
48    o change FIND_RHO to FIND_RHO_2D :
49      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
50    o new pkg: cheapaml
51    
52    checkpoint61b
53    o exch2:
54      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
55      - no longer depend on the order sequence (N,S,E,W).
56      - 3rd exchange no longer needed (tested with 24 tiles).
57      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
58      - exch_UV_A-grid readily available (but not yet tested).
59      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
60      (both are no longer needed) in exch_uv: no effect in forward run; but
61       get truncation error differences with adjoint exch.
62    o exch2:
63     - change index-bounds storage (moved from target to local tile,
64       more intuitive this way) ; rename/remove some variables.
65     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
66    
67    checkpoint61a
68    o exch2/matlab-topology-generator:
69      fix bug in index bounds for N-S internal exchange (hard to tell if this
70      had any effect on the solution).
71    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
72      is exceeded
73    o testreport: modify syntax of awk, so that it works also with
74      awk, and not only with nawk and gawk
75    
76    checkpoint61
77    o autodiff
78      Change default for TAF usage by removing argument '-nonew_arg'
79      This changes TAF subroutine argument list (ordering of active var.)
80      Omission of this flag leads to incompatibility w.r.t. TAMC
81      To restore TAMC-compatibility, need following modifs:
82      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
83      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
84      Tested TAF version is 1.9.22
85      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
86    
87    checkpoint60
88    --->>> This is the last checkpoint for which generating the adjoint
89    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
90    --->>> by default.
91    --->>> Future checkpoints will ommit this flag by default.
92    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
93    o pkg/grdchk: Add gradient check to etan0 perturbations.
94    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
95    o pkg/autodiff: more flexibility in zeroadj.
96      model/src: modifying do_oceanic_phys.F accordingly.
97    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
98    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
99      special setup of gmredi for which the adjoint is stable
100      enough for parameter optimization.
101    o bridging the gap between eddy stress and GM.
102      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
103          along with a change in CPP option (now ALLOW_EDDYPSI).
104      -> when using GM w/ GM_AdvForm:
105          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
106          is applied either in the tracer Eq. or in momentum Eq.
107          depending on data.gmredi (intro. GM_InMomAsStress).
108      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
109      The key modifications are in model/src/taueddy_external_forcing.F
110      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
111    
112    checkpoint59r
113    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
114      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
115      fix option to read coriolis(@ cell-corner) from files with CS-grid.
116    o pkg/mnc: add some attributes to standard 1D-coordinate variables
117    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
118      mass points, when using mnc for output
119      - add runtime parameter (missing_value, missing_value_int) to override
120        default (which is the value of getcon('UNDEF'))
121    o pkg/mnc: prepare mnc for the actual use of missing values with the
122      diagnostics package: small fix in mnc_cw_readwrite.template and more
123      initialisation of never used fields
124      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
125      versions
126    o pkg/thsice/thsice_ini_vars.F added default initial values so that
127      thermodynamics sea ice solver does not blow up when some initial fields
128      are missing.
129    o move from external_forcing_surf.F to ini_forcing.F
130      the p-coord. hack consisting in using pLoad to set phi0surf ;
131      update output of tutorial_global_oce_in_p (affected @ truncation level).
132    o Freshen up a bit hs94.1x64x5, notably:
133      remove rotationPeriod and tRef=5*0. (adjoint only), and add
134      exactConserv=.TRUE.
135    o pkg/generic_advdiff:
136      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
137      applies to files where Temperature & Salinity 2nd Order moments are used.
138    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
139      this uses a dynamically allocated internal state data structure
140      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
141      and requires a fortran 90 compiler
142    
143    checkpoint59q
144    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
145       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
146    o Refresh tutorial_global_oce_biogeo, notably:
147      - change bathymetry (put back seamounts in ACC, use hFacs)
148      - change EOS (POLY3 --> JMD95Z)
149      - use Bryan-Lewis vertical diffusivity
150      - use multidimensional advection
151      - remove old virtual virtual in dic pkg, now done through ptracer pkg
152      - change a couple of parameters in dic pkg
153    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
154    o pkg/obcs: change default to OBCSfixTopo = .true.,
155      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
156      - replace "debugMode" with "debugLevel .GE. debLevB"
157    o implementation of TAF directives for gchem,cfc,dic
158    o remove "exp5" (replaced by tutorial_deep_convection).
159    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
160      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
161      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
162      --> changes results in exp4, seaice_obcs
163    o tutorial_deep_convection :
164      update the set-up and increase resolution and domain size ; start
165      from pseudo initial conditions = output at t=120mn in order to see
166      something happening when running testreport.
167    o pkg/seaice: add os7mp as an advection scheme
168                  add check for advection schemes
169                  add a flag for restoring T and S underneath sea ice
170    o pkg/my82: add netcdf-support and diagnostics
171    o thsice pkg:
172      - Now hsMax limits snow height by turning it into ice following
173        flooding scheme (and now conserving energy)
174      - Slight rewriting of the formula in thsice_calc_thick.F
175      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
176      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
177    
178    checkpoint59p
179    o gchem / dic / cfc :
180      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
181      - add new parameter files: "data.dic" & "data.cfc" ;
182      - various re-arrangement in initialisation & header file ;
183      - fix tutorial_global_oce_biogeo for multi-threaded test.
184    o pkg/dic: test for "pickup_dic" file when restarting ;
185      if no pickup-file, can restart with a re-initialised pH (same as it did
186      before) providing pickupStrictlyMatch is set to False.
187    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
188      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
189    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
190      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
191    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
192     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
193       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
194    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
195       scheme to use for vorticty-term ;
196     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
197       (with default selectVortScheme, return to original discretisation)
198     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
199    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
200    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
201      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
202      also fix diagnostics VISCAHW & VISCA4W.
203    
204    checkpoint59o
205    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
206    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
207      move a few statemens out the main loop into separate loops
208    o pkg/shelfice:
209      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
210        (kg/m^2/s), does not break tests, because in verification/isomip,
211        rhoConstFresh=rhoConst (by accident)
212      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
213      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
214        new file model/src/seawater.F, so that they are available for all pkgs.
215      - convert potential temperature into in-situ temperature. This changes the
216        isomip tests => update tests
217    o add a flag writePickupAtEnd (default=true) to be able to suppress
218      writing a pickup at the last timestep
219    o tools/mpack-1.6 :
220      - disable automake (not working) and autoconf (not needed).
221      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
222        also cleaner with much less compilation warnings.
223    o pkg/profiles:
224      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
225      (for "less than 32 characters name" compiler requirement)
226    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
227      conditions that have a different sampling frequency than S/T/U/V obcs
228    o pkg/diagnostics (stats-diags):
229      - fix global Min/Max in case 1 processor get only empty tiles
230    o genmake2: replace (4 times)
231         make genmake_tc_1.o >> genmake_warnings 2>&1
232      with
233         COMM="$CC $CFLAGS -c genmake_tc_1.c"
234         echo $COMM >> genmake_warnings
235         $COMM >> genmake_warnings 2>&1
236      to make genmake2 always see the value of CC as specified in the optfile.
237    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
238      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
239      - modify verification advect_cs test to test SOM-advection on CS-grid.
240    o pkg/ctrl:
241      - Rewrite of ctrl_map_ini_ecco.F,
242        introducing a generic routine (ctrl_map_ini_gen.F).
243      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
244    
245    checkpoint59n
246    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
247      number in dedicate array "hdiag":
248      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
249        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
250      - many small changes (integer format) for large number of diagnostics
251      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
252        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
253    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
254      usingSphericalGrid, this allows to define the rotated grid coordinates
255      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
256      geographical coordinates according to the inverse of the rotation defined
257      by the Euler angles, so that Coriolis parameter and online-interpolation by
258      exf works with the geographical coordinates on XC/YC/XG/YG.
259      Naturally, this feature does not work with all packages, so some
260      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
261      profiles), because there the coordinates are assumed to be regular
262      spherical grid coordinates.
263    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
264      - introduce isopycnal diffusion coefficient control.
265    o tools/adjoint_options:
266      - additional control vector components.
267    o pkg/mnc: have mnc create marginally meaning full coordinate variables
268      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
269    o pkg/mypackage:
270      - add example of read/write pickup for state-var ;
271      - add entry points to the main code for state-vars diags & write-pickup.
272    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
273      transitions for useExfYearlyFields
274      - add new subroutine that determines the file to read from for
275        use*YearlyFields = .TRUE. and .FALSE.
276      - add a verification experiment to global_with_exf that tests
277        useExfYearlyFields with USE_EXF_INTERPOLATION defined
278    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
279      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
280      subroutines (which could be generated from a template, because they are
281      almost identical), for now they are included in obcs_prescribe_read.F for
282      simplicity
283    o pkg/exf:
284      - add a little more diagnostic to exf_interp_read (in analogy to
285        mds_read_field, can be turned off with debugLevel < debugLevA=1)
286      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
287        ugly but fast by unrolling short inner loops, inserting a unroll=8
288        directive in routine lagran, and splitting a loop and making do while the
289        outermost loop (the latter requires the intoduction of index arrays)
290    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
291    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
292      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
293    o verification/seaice_obcs: updated for restart test and latest options
294    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
295      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
296      for now this is only available for the C-grid code and also within
297      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
298    
299    checkpoint59m
300    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
301      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
302    o gad_som : fix flux output (& diagnostics) to have same units as other  
303      advection scheme fluxes (was previously multiplied by deltaT).  
304    o added verification/seaice_obcs both to test seaice open boundaries
305      and to provide an example matlab scrpt for generating them
306    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
307    o pkg/salt_plume: clean up salt_plume_frac.F to
308      remove redundancy in PlumeMethod 1 and 4
309    o pkg/kpp: added saltplume diagnostics
310    o pkg/obcs and pkg/seaice:
311      - do not set uice and vice to zero when OB*icefile are unspecified
312      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
313      - moved seaice tracer obcs after call to seaice_growth
314    o pkg/salt_plume: added various options for salt plume depth
315      criterion and for vertical distribution of the salt
316    
317    checkpoint59l
318    o pkg/ptracers: new version of ptracers pickup:
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:
322      - add timescale for melting due to warm mixed layer as a means of
323        setting SEAICE_availHeatFrac more conveniently
324      - add a CPP-flag/runtime parameter check for flooding algorithm
325      - reformulated availHeat in seaice_growth.F to be independent of AREA
326    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
327      unit changes
328    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
329    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
330      SX vector computer.
331    o pkg/seaice:
332      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
333        seaice forcing fields can now be read only through pkg/exf
334      - removed some unused halos
335    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
336    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
337      or U/VICE from U/VWIND before computing U/VSTRESS
338    
339    checkpoint59k
340    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
341      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
342    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
343      all experiments pass when compile with un-initialised var. checking option.
344    o added pkg/salt_plume
345    o script to test restart (for now, in MITgcm_contrib/jmc_script)
346    o pkg/seaice: new read/write pickup version.
347      read meta file and write only fields which are needed to restart.
348      ( same logic as main pickup file ; also using pickupStrictlyMatch )
349    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
350    o lab_sea.hb87: modify the domain & update output.hb87.txt :
351      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
352      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
353      process. Fixed here by closing the domain at the Northern boundary.
354    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
355    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
356      a set of consecutive levels in/from a 3-D array.
357    o pkg/ptracers:
358      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
359      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
360    
361    checkpoint59j
362    o in pkgs: dic, obcs, offline, rbcs:
363      standard way to compute coeff. for time interpolation between 2 time reccords
364      which retains full precision (& make results less dependent on compiler).
365      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
366    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
367      packages instead of reading ice cover and wind speed separately
368    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
369     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
370      to allow to compile customized code before the update)
371    o cleaning-up:
372      - fix CPP instruction syntax in pkg/obcs
373      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
374        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
375      - fix some threads issue in IO parts.
376    o pkg/dic:
377      - add tons of "_d 0" (--> much better testreports !)
378       and then update outputs of tutorial_global_oce_biogeo
379    o pkg/mom_fluxform:
380      add a special version of momentum advection intended to conserve momentum
381      next to a bathymetry step or a coastline edge. (default = off = #undef)
382    o new read/write pickup version:
383      - for now, only implemented for main (mdsio) pickup file.
384      - write out only what is needed to restart; merge pickup_nh , pickup_ph
385        and main pickup together.
386      - read meta file; read only what is needed to restart; stop if a field
387        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
388        if it make sense (even if the restart is not perfect).
389      - if no meta file, assume that pickup to read corresponds exactly to
390        a pickup that would currently be written.
391      - read pickup written in the old format (until checkpoint59i) if it
392        recognizes an old meta file (no field-list).
393      - add a meta file in exp. which starts from a pickup: 2 cases:
394        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
395         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
396        b) a meta file describing the content of the associated pickup file
397         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
398    o pkg/mdsio & pkg/rw:
399      - new routine to read a meta file ; new set of routine to read
400        Multiple-fields file (with meta file).
401    o added open boundary conditions capability for seaice
402        HSNOW, HSALT, UICE, and VICE
403    
404    checkpoint59i
405    o adjoint:
406      * fix multiDimAdvection adjoint
407        (partial recomputation problem by TAF for fVerT(:,:,kDown)
408        and comlev1 size definition (maxpass vs. max. number of tracers)
409      * verification/global_ocean.90x45x15 adjoint now tests
410        NLFS and multiDimAdvection using DST3 (=30)
411      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
412    o pkg/kpp: add "_d 0" to real constant (if missing);
413      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
414      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
415    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
416      for internal parameters related to restart process (formerly from PARAMS.h)
417      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
418    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
419      as argument. (only atm2d & obcs write_pickup have not yet been updated)
420    o pkg/monitor:
421      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
422      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
423      - account for deep Atmosphere factor and density factor (anelastic)
424    o added open boundary conditions capability for seaice HEFF and AREA
425    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
426      thermodynamics
427      - requires a little reorganization, which affects the testreport results
428        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
429        so that now the conservative form is tested
430      - add a few comments
431    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
432    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
433    o add new diagnostics to seaice: advective, diffusive fluxes (only for
434      multidim-advection, for scheme 2 they are not filled) and transports,
435      thermodynamic growth rates
436    o change units of EmPmR (inside the code, + within coupling interface)
437      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
438      Affects results @ truncation level (cg2d match) and update output of
439       experiments: lab_sea(6), global_ocean.90x40x15(10),
440      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
441      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
442      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
443      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
444    
445    checkpoint59h
446    o pkg/exf:
447      - improve vectorization by moving if-statement out of loops in
448        exf_mapfields, exf_radiation
449      - exf_bulkformulae.F: introduce 2D fields and vectorize code
450    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
451    o testreport:
452      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
453        monitor & update offline_exf_seaice exp. output.
454      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
455    o pkg/seaice:
456      - bug fix in the evp solver: boundary conditions were affected be
457        masking of zMax/zMin (changes results)
458      - minor bug fix in boundary conditions in seaice_calc_strainrates
459        (changes results for no_slip)
460      - seaice_lsr.F: make interpolation of eta dependent on boundaries
461      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
462      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
463        stress formulation and no-slip boundary conditions
464    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
465      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
466    o pkg/seaice: a first HSALT time stepping equation has been checked in
467    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
468      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
469      without requiring DO-IF statements
470    o pkg/thsice:
471      use continuous power-law function for partition of energy between lateral
472      melting/freezing and thinning/thickening ; old code using step function
473      still available with #undef THSICE_FRACEN_POWERLAW
474      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
475    o testreport: change AD testing : check against results/output_adm.txt
476      using same scripts as for forward test.
477    
478    checkpoint59g
479    o adjoint testing: in preparation for changing testreport:
480      - output format: cost and grad written on separated lines
481      - ad output results in directory "results" (instead of "results_ad")
482    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
483    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
484    o pkg/ecco: allow user defined cost function contributions
485    o testreport:
486      Allow to choose (per experiment) the list of tested output variables
487       and the main variable (used to issue a pass/FAIL ) ;
488      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
489      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
490      Also modify printing of summary:
491       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
492       b) echo the list of tested variables in the individual summary.txt of
493          each experiment.
494    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
495      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
496      (but still depend on the tile decompostion of the domain).
497    o pkg/seaice: change a discretization detail to make the B-grid code
498      "more symmetric". This change is likely to remove all "ridges/leads" that
499      where quasi-aligned with the grid in B-grid solutions. It may also be
500      the solution to the stress coupling issues with the B-grid.
501    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
502      remove .cvsignore from input dir. (since testreport no longer run here).
503    o pkg/thsice:
504     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
505     - fix reshaping of sea-ice just after advection:
506       melt all the ice only if ice-volume is too small.
507     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
508       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
509     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
510    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
511      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
512    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
513      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
514      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
515      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
516      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
517      -> update output.txt
518    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
519     this affects truncation error: -> update output.txt of exp:
520      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
521      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
522    
523    checkpoint59f
524    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
525    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
526      a bounded range (in forward mode)
527    o pkg/ecco, ctrl, autodiff and mom_common:
528     internal parameter controls, completements of implementations
529    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
530    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
531      (not seem any difference in testing results).
532    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
533       at face corners.
534    o pkg/generic_advdiff:
535     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
536      loop range indices for computing vertical advection tendency
537      and do the calculation in the interior only (no overlap) ;
538      for now, only implemented for SOM advection (to save CPU time).
539     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
540    o exch2 adjoint
541      First set of changes:
542      - add exch2 hand-written adjoint templates
543      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
544        This will require cleanup in pkg/autodiff/*.F
545        (changed routines currently kept separate in verif. code/)
546      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
547        that used to hide exch2 or cubed-sphere specific code
548        (commented via 'cph-exch2')
549    o pkg/seaice
550      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
551    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
552       output of global_ocean.cs32x15.thsice .
553    
554    checkpoint59e
555    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
556      for B-grid vector (not yet tested) and C-grid vector (<- only used
557      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
558    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
559      (#ifdef ALLOW_SALT_PLUME)
560    o gather_2d/scatter_2d: removed halo regions
561    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
562      scheme and the corresponding test case (under front_relax dir). For now,
563      only available with Skew-flux form and not yet tested in realistic set-up.
564      adjoint: store directives updated, but gradient checks deteriorated,
565      so maybe GM/Redi adjoint is now broken.
566    o seaice adjoint
567      * add AREA, HEFF, HSNOW as control variable
568        (should not change lab_sea results)
569      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
570    o pkg/seaice:
571      * added computation of saltFlux in seaice_growth;
572        For time being, sea ice salinity is assumed constant
573        contribution of snow flooding to freshening of sea ice is neglected.
574        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
575        defaults to 0.0 in order to maintain backward compatibility.
576        Typical values for SEAICE_salinity are 4 to 10 g/kg.
577      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
578      * added SEAICE_availHeatFrac, which specifies fraction of surface level
579        heat content used to melt or grow ice
580      * commented out cap of HICE: it helps keep ice thinner
581      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
582      * applied OBCS T/S mask to HEFFM sea ice mask
583    
584    checkpoint59d
585    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
586     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
587     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
588    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
589     and change default value of parameter "GM_Small_Number";
590     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
591       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
592       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
593    o pkg/ecco: cost function when applying pkg/smooth to controls
594    o pkg/ctrl: add forcingPrecond run time parameter
595    o pkg/seaice:
596     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
597     - fix bug in metric terms of u-equation in LSR solver (implicit part),
598       changes verification/lab_sea
599     - rearrange implicit part of u-equation in LSR solver to make it easier to
600       read, understand, and debug. This causes changes at the truncation level.
601     - fix (serious) bug in the boundary conditions (sign error in the implicit
602       part) of the LSR solver. Changes all LSR results.
603     - fixed problem with HSNOW initialization to avoid thick snow when AREA
604       is initilized with small values - does not change lab_sea results.
605     - added HsnowFile initialization capability
606    o pkg/smooth: addition to model/src and pkg/ctrl so allow
607     initialization of pkg/smooth and application to control vector
608    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
609    o dependencies: pkg/profiles requires pkg/cal
610    o pkg/profiles:
611     - added option ALLOW_PROFILES_GENERICGRID
612         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
613         that interpolation information (grid points and coefficients) is provided
614         within the netcdf input files.
615         -> sample matlab scripts can be found in MITgcm_contrib/gael
616         that allow you to prepare netcdf input files.
617     - also modified: cleaner include statements, cleaner error print statements,
618       cleaner stops when error, and more tests of the netcdf input files consistency.
619    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
620    o pkg/seaice:
621     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
622       requires a new routine: seaice_diagnostics_fill.F
623     - make sure that seaice does not move if not forced (pressure replacement
624       method, Hibler and Ip, 1995), changes results
625     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
626     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
627       It is turned off by default (=-1.), because it changes the results.
628     - make it possible to read AREA from a file, too.
629    
630    checkpoint59c
631    o add S/R and diagnostics for oceanic mixed-layer depth
632    o move GMRedi call after all vertical mixing schemes (including KPP)
633    o pkg/thsice:
634     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
635      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
636    o pkg/obcs:
637     - bug fix for balance code
638    o pkg/seaice:
639      - allow values of SEAICE_elasticParm > 1
640      - add new parameter SEAICE_evpTauRelax as an alternative
641        to SEAICE_elasticParm
642      - make lsr boundary conditions free slip (by default), changes result
643      - add code for no slip boundary conditions for lsr
644      - set minimum of zeta to zero (and not 4e8) (changes results)
645      - add a cap on AREA after advecting AREA if seaice_growth is not called
646    o change calculation of Visbeck K:
647      - no longer depend on tapering scheme; instead, compute slope (limited
648        by GM_maxSlope). this is equivalent to what was comuted before with
649        clipping or linear tappering.
650      - fix vertical averaging (wrong by 1/2 level)
651      - leave the old version (but will not be maintained) within
652        #ifdef OLD_VISBECK_CALC / #endif
653      - update output of exp. ideal_2D_oce
654    o change error catch in calc_r_star to improve vectorization
655    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
656      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
657    o adjoint:
658      Re-organized adjoint checkpointing according to Matt Mazloff
659      (but with modifs/completions/cleanups)
660      Storing is now bundled into large arrays to optimized I/O
661      (and second step in cleanup of the_main_loop)
662    
663    checkpoint59b
664    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
665      - export/import (between ocean & coupler) fields needed for ocean DIC.
666    o pkg/seaice:
667      - get rid of three more exchanges seaice_calc_viscosities (required
668        different loop boundaries in seaice_lsr and seaice_ocean_stress)
669      - bug fix in seaice_ocean_stress (update of lab_sea required)
670      - reduce loop boundaries to necessary minimum also in seaice_evp
671      - go back to the old way of computing deltaC/Z as the adjoint likes that
672        better
673    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
674      passive tracer to an Age Tracer) + update output.txt
675    o pkg/exf:
676      - implement A-grid / C-grid selection for wind-stress input files.
677      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
678      for now, in exf_bulk_largeyeager04.F only :
679      - change implementation for case where windspeed + 2. components wind-stress
680        are read-in. AND use rhoConstFresh to convert evap.
681    o pkg/seaice:
682      - use correct EXCH_UV for wind-forcing (on A-grid).
683      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
684        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
685    o pkg/exf:
686      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
687      EXF_INTERPOLATION:
688      - merge global_with_exf/code version of exf_interp_read.F
689        to the main code ;
690      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
691        reading the file ; Important: This options needs to be defined to recover
692        previous code.
693        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
694      - no longer loose real*8 precision along the way when using exf_iprec=64.
695  o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)  o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
696      - change discretisation of evp-solver in order to avoid another exchange
697        (changes lab_sea) and clean up a little
698      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
699        help the adjoint (this also changes the results slightly)
700      - add a few "_d 0" where they had been missing in seaice_evp.F
701      - cleaning up: remove unused seaice_calc_rhs.F
702  o pkg/exf: some cleaning-up:  o pkg/exf: some cleaning-up:
703    - change various "constants" into runtime parameters    - change various "constants" into runtime parameters
704    - cleaned-up Large&Yeager04 routine which should eventually    - cleaned-up Large&Yeager04 routine which should eventually
# Line 18  o pkg/exf: some cleaning-up: Line 712  o pkg/exf: some cleaning-up:
712  o pkg/thsice:  o pkg/thsice:
713   fix few little problems, in thsice_calc_thickn.F:   fix few little problems, in thsice_calc_thickn.F:
714    - growth vertically (and not laterally) if iceFrac == iceMaskMax    - growth vertically (and not laterally) if iceFrac == iceMaskMax
715    - melt laterally only if hIce < hThinIce (as the comments say)    - melt only laterally if hIce < hThinIce (as the comments say)
716    and in thsice_extend.F:    and in thsice_extend.F:
717    - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)    - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
718    - 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 34  o pkg/kpp Line 728  o pkg/kpp
728  o pkg/seaice  o pkg/seaice
729   - check for inconsistent evp parameter/cpp-flag combination   - check for inconsistent evp parameter/cpp-flag combination
730   - remove leftover errIO flat for obsolete name list error handling   - remove leftover errIO flat for obsolete name list error handling
731    o OpenAD
732     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
733    
734  checkpoint59a  checkpoint59a
735  o pkg/seaice: some parameter clarifications and a little bit of clean up  o pkg/seaice: some parameter clarifications and a little bit of clean up
# Line 53  o in FFIELDS.h: Line 749  o in FFIELDS.h:
749       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
750  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
751  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
752      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
753        are no longer updating the vertical diffusivity array
754        (passed as argument) but are (re-) setting those arrays.
755  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
756    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
757      cgrid-lsr and evp solver      cgrid-lsr and evp solver
Legend:
Removed from v.1.811  
changed lines
  Added in v.1.1025
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