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revision 1.808 by jmc, Thu May 3 22:57:27 2007 UTC revision 1.1032 by jmc, Wed Oct 22 00:19:33 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 gmredi (Visbeck-variable-K):
8      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
9      - change computation of Visbeck-K where Slope > Smax :        
10        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
11        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
12    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
13      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
14    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
15    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
16      does not become too large (to avoid precision problems in implicit-diffusion
17      solver); update ideal_2D_oce output.
18    o pkg ggl90:
19      - in ggl90_cal.F: compute only one set of visc/diff, used to
20        step forward TKE/T/S/momentum
21      - default value of GGL90viscMax/GGL90diffMax larger and equal (to
22        have Prandlt =1)
23    o gmredi (fm07):
24      - add lower limit on Transition layer thickness + lower limit on 1/lambda
25      - allow to set few more params from data.gmredi
26    o pkg ggl90:
27          - add missing sqrt(2) factor in computation of mixing length
28            scale in ggl90_calc.F
29            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
30    
31    checkpoint61d
32    o adjoint modifs
33      - adapt to new field rhoInSitu
34      - allow to revert from StoreDynVars2D, StoreDynVars3D
35        to individual fields
36        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
37    o store 3-D (in-situ) density in commom block (DYNVARS.h)
38     - save 1 rho computation.
39     - no longer modify T & S inland when using down_slope pkg.
40    o gad_som : allow to switch to SOM advection for T & S without corresponding
41      pickup files (using new S/R: MDS_CHECK4FILE).
42    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
43      (for useSingleCpuIO to work in multi-threaded)
44    o pkg/shelfice:
45     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
46       with SHELFICEtopoFile in data.shelfice
47     - move code for reading ice shelf topography and modifying hFacC into separate
48       subroutines of the shelfice package
49     - separate initialisation of "fixed" and "variable" variables
50     - kTopC is not (yet) replaced by kSurfC, although this is possible
51    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
52    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
53      and rename:
54      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
55      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
56    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
57    
58    checkpoint61c
59    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
60      to add mass source/sink of fluid in the interior (3-D generalisation
61      of oceanic real-fresh water flux).
62    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
63    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
64    o new pkg: down_slope
65      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
66      - presently, modify T & S inland (dwnslp_calc_rho.F).
67        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
68      - implementation for ocean in P-coords not tested.
69      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
70    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
71      (to facilitate conversion of oceanic pkg to p-coordinate).
72    o change FIND_RHO to FIND_RHO_2D :
73      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
74    o new pkg: cheapaml
75    
76    checkpoint61b
77    o exch2:
78      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
79      - no longer depend on the order sequence (N,S,E,W).
80      - 3rd exchange no longer needed (tested with 24 tiles).
81      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
82      - exch_UV_A-grid readily available (but not yet tested).
83      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
84      (both are no longer needed) in exch_uv: no effect in forward run; but
85       get truncation error differences with adjoint exch.
86    o exch2:
87     - change index-bounds storage (moved from target to local tile,
88       more intuitive this way) ; rename/remove some variables.
89     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
90    
91    checkpoint61a
92    o exch2/matlab-topology-generator:
93      fix bug in index bounds for N-S internal exchange (hard to tell if this
94      had any effect on the solution).
95    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
96      is exceeded
97    o testreport: modify syntax of awk, so that it works also with
98      awk, and not only with nawk and gawk
99    
100    checkpoint61
101    o autodiff
102      Change default for TAF usage by removing argument '-nonew_arg'
103      This changes TAF subroutine argument list (ordering of active var.)
104      Omission of this flag leads to incompatibility w.r.t. TAMC
105      To restore TAMC-compatibility, need following modifs:
106      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
107      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
108      Tested TAF version is 1.9.22
109      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
110    
111    checkpoint60
112    --->>> This is the last checkpoint for which generating the adjoint
113    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
114    --->>> by default.
115    --->>> Future checkpoints will ommit this flag by default.
116    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
117    o pkg/grdchk: Add gradient check to etan0 perturbations.
118    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
119    o pkg/autodiff: more flexibility in zeroadj.
120      model/src: modifying do_oceanic_phys.F accordingly.
121    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
122    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
123      special setup of gmredi for which the adjoint is stable
124      enough for parameter optimization.
125    o bridging the gap between eddy stress and GM.
126      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
127          along with a change in CPP option (now ALLOW_EDDYPSI).
128      -> when using GM w/ GM_AdvForm:
129          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
130          is applied either in the tracer Eq. or in momentum Eq.
131          depending on data.gmredi (intro. GM_InMomAsStress).
132      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
133      The key modifications are in model/src/taueddy_external_forcing.F
134      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
135    
136    checkpoint59r
137    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
138      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
139      fix option to read coriolis(@ cell-corner) from files with CS-grid.
140    o pkg/mnc: add some attributes to standard 1D-coordinate variables
141    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
142      mass points, when using mnc for output
143      - add runtime parameter (missing_value, missing_value_int) to override
144        default (which is the value of getcon('UNDEF'))
145    o pkg/mnc: prepare mnc for the actual use of missing values with the
146      diagnostics package: small fix in mnc_cw_readwrite.template and more
147      initialisation of never used fields
148      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
149      versions
150    o pkg/thsice/thsice_ini_vars.F added default initial values so that
151      thermodynamics sea ice solver does not blow up when some initial fields
152      are missing.
153    o move from external_forcing_surf.F to ini_forcing.F
154      the p-coord. hack consisting in using pLoad to set phi0surf ;
155      update output of tutorial_global_oce_in_p (affected @ truncation level).
156    o Freshen up a bit hs94.1x64x5, notably:
157      remove rotationPeriod and tRef=5*0. (adjoint only), and add
158      exactConserv=.TRUE.
159    o pkg/generic_advdiff:
160      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
161      applies to files where Temperature & Salinity 2nd Order moments are used.
162    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
163      this uses a dynamically allocated internal state data structure
164      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
165      and requires a fortran 90 compiler
166    
167    checkpoint59q
168    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
169       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
170    o Refresh tutorial_global_oce_biogeo, notably:
171      - change bathymetry (put back seamounts in ACC, use hFacs)
172      - change EOS (POLY3 --> JMD95Z)
173      - use Bryan-Lewis vertical diffusivity
174      - use multidimensional advection
175      - remove old virtual virtual in dic pkg, now done through ptracer pkg
176      - change a couple of parameters in dic pkg
177    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
178    o pkg/obcs: change default to OBCSfixTopo = .true.,
179      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
180      - replace "debugMode" with "debugLevel .GE. debLevB"
181    o implementation of TAF directives for gchem,cfc,dic
182    o remove "exp5" (replaced by tutorial_deep_convection).
183    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
184      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
185      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
186      --> changes results in exp4, seaice_obcs
187    o tutorial_deep_convection :
188      update the set-up and increase resolution and domain size ; start
189      from pseudo initial conditions = output at t=120mn in order to see
190      something happening when running testreport.
191    o pkg/seaice: add os7mp as an advection scheme
192                  add check for advection schemes
193                  add a flag for restoring T and S underneath sea ice
194    o pkg/my82: add netcdf-support and diagnostics
195    o thsice pkg:
196      - Now hsMax limits snow height by turning it into ice following
197        flooding scheme (and now conserving energy)
198      - Slight rewriting of the formula in thsice_calc_thick.F
199      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
200      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
201    
202    checkpoint59p
203    o gchem / dic / cfc :
204      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
205      - add new parameter files: "data.dic" & "data.cfc" ;
206      - various re-arrangement in initialisation & header file ;
207      - fix tutorial_global_oce_biogeo for multi-threaded test.
208    o pkg/dic: test for "pickup_dic" file when restarting ;
209      if no pickup-file, can restart with a re-initialised pH (same as it did
210      before) providing pickupStrictlyMatch is set to False.
211    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
212      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
213    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
214      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
215    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
216     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
217       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
218    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
219       scheme to use for vorticty-term ;
220     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
221       (with default selectVortScheme, return to original discretisation)
222     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
223    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
224    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
225      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
226      also fix diagnostics VISCAHW & VISCA4W.
227    
228    checkpoint59o
229    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
230    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
231      move a few statemens out the main loop into separate loops
232    o pkg/shelfice:
233      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
234        (kg/m^2/s), does not break tests, because in verification/isomip,
235        rhoConstFresh=rhoConst (by accident)
236      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
237      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
238        new file model/src/seawater.F, so that they are available for all pkgs.
239      - convert potential temperature into in-situ temperature. This changes the
240        isomip tests => update tests
241    o add a flag writePickupAtEnd (default=true) to be able to suppress
242      writing a pickup at the last timestep
243    o tools/mpack-1.6 :
244      - disable automake (not working) and autoconf (not needed).
245      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
246        also cleaner with much less compilation warnings.
247    o pkg/profiles:
248      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
249      (for "less than 32 characters name" compiler requirement)
250    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
251      conditions that have a different sampling frequency than S/T/U/V obcs
252    o pkg/diagnostics (stats-diags):
253      - fix global Min/Max in case 1 processor get only empty tiles
254    o genmake2: replace (4 times)
255         make genmake_tc_1.o >> genmake_warnings 2>&1
256      with
257         COMM="$CC $CFLAGS -c genmake_tc_1.c"
258         echo $COMM >> genmake_warnings
259         $COMM >> genmake_warnings 2>&1
260      to make genmake2 always see the value of CC as specified in the optfile.
261    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
262      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
263      - modify verification advect_cs test to test SOM-advection on CS-grid.
264    o pkg/ctrl:
265      - Rewrite of ctrl_map_ini_ecco.F,
266        introducing a generic routine (ctrl_map_ini_gen.F).
267      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
268    
269    checkpoint59n
270    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
271      number in dedicate array "hdiag":
272      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
273        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
274      - many small changes (integer format) for large number of diagnostics
275      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
276        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
277    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
278      usingSphericalGrid, this allows to define the rotated grid coordinates
279      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
280      geographical coordinates according to the inverse of the rotation defined
281      by the Euler angles, so that Coriolis parameter and online-interpolation by
282      exf works with the geographical coordinates on XC/YC/XG/YG.
283      Naturally, this feature does not work with all packages, so some
284      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
285      profiles), because there the coordinates are assumed to be regular
286      spherical grid coordinates.
287    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
288      - introduce isopycnal diffusion coefficient control.
289    o tools/adjoint_options:
290      - additional control vector components.
291    o pkg/mnc: have mnc create marginally meaning full coordinate variables
292      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
293    o pkg/mypackage:
294      - add example of read/write pickup for state-var ;
295      - add entry points to the main code for state-vars diags & write-pickup.
296    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
297      transitions for useExfYearlyFields
298      - add new subroutine that determines the file to read from for
299        use*YearlyFields = .TRUE. and .FALSE.
300      - add a verification experiment to global_with_exf that tests
301        useExfYearlyFields with USE_EXF_INTERPOLATION defined
302    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
303      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
304      subroutines (which could be generated from a template, because they are
305      almost identical), for now they are included in obcs_prescribe_read.F for
306      simplicity
307    o pkg/exf:
308      - add a little more diagnostic to exf_interp_read (in analogy to
309        mds_read_field, can be turned off with debugLevel < debugLevA=1)
310      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
311        ugly but fast by unrolling short inner loops, inserting a unroll=8
312        directive in routine lagran, and splitting a loop and making do while the
313        outermost loop (the latter requires the intoduction of index arrays)
314    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
315    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
316      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
317    o verification/seaice_obcs: updated for restart test and latest options
318    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
319      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
320      for now this is only available for the C-grid code and also within
321      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
322    
323    checkpoint59m
324    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
325      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
326    o gad_som : fix flux output (& diagnostics) to have same units as other  
327      advection scheme fluxes (was previously multiplied by deltaT).  
328    o added verification/seaice_obcs both to test seaice open boundaries
329      and to provide an example matlab scrpt for generating them
330    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
331    o pkg/salt_plume: clean up salt_plume_frac.F to
332      remove redundancy in PlumeMethod 1 and 4
333    o pkg/kpp: added saltplume diagnostics
334    o pkg/obcs and pkg/seaice:
335      - do not set uice and vice to zero when OB*icefile are unspecified
336      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
337      - moved seaice tracer obcs after call to seaice_growth
338    o pkg/salt_plume: added various options for salt plume depth
339      criterion and for vertical distribution of the salt
340    
341    checkpoint59l
342    o pkg/ptracers: new version of ptracers pickup:
343      read meta file and write only fields which are needed to restart.
344      ( same logic as main pickup file ; also using pickupStrictlyMatch )
345    o pkg/seaice:
346      - add timescale for melting due to warm mixed layer as a means of
347        setting SEAICE_availHeatFrac more conveniently
348      - add a CPP-flag/runtime parameter check for flooding algorithm
349      - reformulated availHeat in seaice_growth.F to be independent of AREA
350    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
351      unit changes
352    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
353    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
354      SX vector computer.
355    o pkg/seaice:
356      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
357        seaice forcing fields can now be read only through pkg/exf
358      - removed some unused halos
359    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
360    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
361      or U/VICE from U/VWIND before computing U/VSTRESS
362    
363    checkpoint59k
364    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
365      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
366    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
367      all experiments pass when compile with un-initialised var. checking option.
368    o added pkg/salt_plume
369    o script to test restart (for now, in MITgcm_contrib/jmc_script)
370    o pkg/seaice: new read/write pickup version.
371      read meta file and write only fields which are needed to restart.
372      ( same logic as main pickup file ; also using pickupStrictlyMatch )
373    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
374    o lab_sea.hb87: modify the domain & update output.hb87.txt :
375      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
376      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
377      process. Fixed here by closing the domain at the Northern boundary.
378    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
379    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
380      a set of consecutive levels in/from a 3-D array.
381    o pkg/ptracers:
382      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
383      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
384    
385    checkpoint59j
386    o in pkgs: dic, obcs, offline, rbcs:
387      standard way to compute coeff. for time interpolation between 2 time reccords
388      which retains full precision (& make results less dependent on compiler).
389      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
390    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
391      packages instead of reading ice cover and wind speed separately
392    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
393     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
394      to allow to compile customized code before the update)
395    o cleaning-up:
396      - fix CPP instruction syntax in pkg/obcs
397      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
398        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
399      - fix some threads issue in IO parts.
400    o pkg/dic:
401      - add tons of "_d 0" (--> much better testreports !)
402       and then update outputs of tutorial_global_oce_biogeo
403    o pkg/mom_fluxform:
404      add a special version of momentum advection intended to conserve momentum
405      next to a bathymetry step or a coastline edge. (default = off = #undef)
406    o new read/write pickup version:
407      - for now, only implemented for main (mdsio) pickup file.
408      - write out only what is needed to restart; merge pickup_nh , pickup_ph
409        and main pickup together.
410      - read meta file; read only what is needed to restart; stop if a field
411        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
412        if it make sense (even if the restart is not perfect).
413      - if no meta file, assume that pickup to read corresponds exactly to
414        a pickup that would currently be written.
415      - read pickup written in the old format (until checkpoint59i) if it
416        recognizes an old meta file (no field-list).
417      - add a meta file in exp. which starts from a pickup: 2 cases:
418        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
419         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
420        b) a meta file describing the content of the associated pickup file
421         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
422    o pkg/mdsio & pkg/rw:
423      - new routine to read a meta file ; new set of routine to read
424        Multiple-fields file (with meta file).
425    o added open boundary conditions capability for seaice
426        HSNOW, HSALT, UICE, and VICE
427    
428    checkpoint59i
429    o adjoint:
430      * fix multiDimAdvection adjoint
431        (partial recomputation problem by TAF for fVerT(:,:,kDown)
432        and comlev1 size definition (maxpass vs. max. number of tracers)
433      * verification/global_ocean.90x45x15 adjoint now tests
434        NLFS and multiDimAdvection using DST3 (=30)
435      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
436    o pkg/kpp: add "_d 0" to real constant (if missing);
437      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
438      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
439    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
440      for internal parameters related to restart process (formerly from PARAMS.h)
441      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
442    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
443      as argument. (only atm2d & obcs write_pickup have not yet been updated)
444    o pkg/monitor:
445      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
446      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
447      - account for deep Atmosphere factor and density factor (anelastic)
448    o added open boundary conditions capability for seaice HEFF and AREA
449    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
450      thermodynamics
451      - requires a little reorganization, which affects the testreport results
452        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
453        so that now the conservative form is tested
454      - add a few comments
455    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
456    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
457    o add new diagnostics to seaice: advective, diffusive fluxes (only for
458      multidim-advection, for scheme 2 they are not filled) and transports,
459      thermodynamic growth rates
460    o change units of EmPmR (inside the code, + within coupling interface)
461      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
462      Affects results @ truncation level (cg2d match) and update output of
463       experiments: lab_sea(6), global_ocean.90x40x15(10),
464      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
465      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
466      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
467      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
468    
469    checkpoint59h
470    o pkg/exf:
471      - improve vectorization by moving if-statement out of loops in
472        exf_mapfields, exf_radiation
473      - exf_bulkformulae.F: introduce 2D fields and vectorize code
474    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
475    o testreport:
476      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
477        monitor & update offline_exf_seaice exp. output.
478      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
479    o pkg/seaice:
480      - bug fix in the evp solver: boundary conditions were affected be
481        masking of zMax/zMin (changes results)
482      - minor bug fix in boundary conditions in seaice_calc_strainrates
483        (changes results for no_slip)
484      - seaice_lsr.F: make interpolation of eta dependent on boundaries
485      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
486      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
487        stress formulation and no-slip boundary conditions
488    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
489      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
490    o pkg/seaice: a first HSALT time stepping equation has been checked in
491    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
492      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
493      without requiring DO-IF statements
494    o pkg/thsice:
495      use continuous power-law function for partition of energy between lateral
496      melting/freezing and thinning/thickening ; old code using step function
497      still available with #undef THSICE_FRACEN_POWERLAW
498      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
499    o testreport: change AD testing : check against results/output_adm.txt
500      using same scripts as for forward test.
501    
502    checkpoint59g
503    o adjoint testing: in preparation for changing testreport:
504      - output format: cost and grad written on separated lines
505      - ad output results in directory "results" (instead of "results_ad")
506    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
507    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
508    o pkg/ecco: allow user defined cost function contributions
509    o testreport:
510      Allow to choose (per experiment) the list of tested output variables
511       and the main variable (used to issue a pass/FAIL ) ;
512      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
513      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
514      Also modify printing of summary:
515       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
516       b) echo the list of tested variables in the individual summary.txt of
517          each experiment.
518    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
519      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
520      (but still depend on the tile decompostion of the domain).
521    o pkg/seaice: change a discretization detail to make the B-grid code
522      "more symmetric". This change is likely to remove all "ridges/leads" that
523      where quasi-aligned with the grid in B-grid solutions. It may also be
524      the solution to the stress coupling issues with the B-grid.
525    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
526      remove .cvsignore from input dir. (since testreport no longer run here).
527    o pkg/thsice:
528     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
529     - fix reshaping of sea-ice just after advection:
530       melt all the ice only if ice-volume is too small.
531     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
532       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
533     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
534    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
535      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
536    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
537      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
538      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
539      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
540      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
541      -> update output.txt
542    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
543     this affects truncation error: -> update output.txt of exp:
544      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
545      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
546    
547    checkpoint59f
548    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
549    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
550      a bounded range (in forward mode)
551    o pkg/ecco, ctrl, autodiff and mom_common:
552     internal parameter controls, completements of implementations
553    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
554    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
555      (not seem any difference in testing results).
556    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
557       at face corners.
558    o pkg/generic_advdiff:
559     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
560      loop range indices for computing vertical advection tendency
561      and do the calculation in the interior only (no overlap) ;
562      for now, only implemented for SOM advection (to save CPU time).
563     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
564    o exch2 adjoint
565      First set of changes:
566      - add exch2 hand-written adjoint templates
567      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
568        This will require cleanup in pkg/autodiff/*.F
569        (changed routines currently kept separate in verif. code/)
570      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
571        that used to hide exch2 or cubed-sphere specific code
572        (commented via 'cph-exch2')
573    o pkg/seaice
574      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
575    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
576       output of global_ocean.cs32x15.thsice .
577    
578    checkpoint59e
579    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
580      for B-grid vector (not yet tested) and C-grid vector (<- only used
581      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
582    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
583      (#ifdef ALLOW_SALT_PLUME)
584    o gather_2d/scatter_2d: removed halo regions
585    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
586      scheme and the corresponding test case (under front_relax dir). For now,
587      only available with Skew-flux form and not yet tested in realistic set-up.
588      adjoint: store directives updated, but gradient checks deteriorated,
589      so maybe GM/Redi adjoint is now broken.
590    o seaice adjoint
591      * add AREA, HEFF, HSNOW as control variable
592        (should not change lab_sea results)
593      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
594    o pkg/seaice:
595      * added computation of saltFlux in seaice_growth;
596        For time being, sea ice salinity is assumed constant
597        contribution of snow flooding to freshening of sea ice is neglected.
598        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
599        defaults to 0.0 in order to maintain backward compatibility.
600        Typical values for SEAICE_salinity are 4 to 10 g/kg.
601      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
602      * added SEAICE_availHeatFrac, which specifies fraction of surface level
603        heat content used to melt or grow ice
604      * commented out cap of HICE: it helps keep ice thinner
605      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
606      * applied OBCS T/S mask to HEFFM sea ice mask
607    
608    checkpoint59d
609    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
610     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
611     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
612    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
613     and change default value of parameter "GM_Small_Number";
614     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
615       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
616       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
617    o pkg/ecco: cost function when applying pkg/smooth to controls
618    o pkg/ctrl: add forcingPrecond run time parameter
619    o pkg/seaice:
620     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
621     - fix bug in metric terms of u-equation in LSR solver (implicit part),
622       changes verification/lab_sea
623     - rearrange implicit part of u-equation in LSR solver to make it easier to
624       read, understand, and debug. This causes changes at the truncation level.
625     - fix (serious) bug in the boundary conditions (sign error in the implicit
626       part) of the LSR solver. Changes all LSR results.
627     - fixed problem with HSNOW initialization to avoid thick snow when AREA
628       is initilized with small values - does not change lab_sea results.
629     - added HsnowFile initialization capability
630    o pkg/smooth: addition to model/src and pkg/ctrl so allow
631     initialization of pkg/smooth and application to control vector
632    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
633    o dependencies: pkg/profiles requires pkg/cal
634    o pkg/profiles:
635     - added option ALLOW_PROFILES_GENERICGRID
636         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
637         that interpolation information (grid points and coefficients) is provided
638         within the netcdf input files.
639         -> sample matlab scripts can be found in MITgcm_contrib/gael
640         that allow you to prepare netcdf input files.
641     - also modified: cleaner include statements, cleaner error print statements,
642       cleaner stops when error, and more tests of the netcdf input files consistency.
643    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
644    o pkg/seaice:
645     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
646       requires a new routine: seaice_diagnostics_fill.F
647     - make sure that seaice does not move if not forced (pressure replacement
648       method, Hibler and Ip, 1995), changes results
649     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
650     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
651       It is turned off by default (=-1.), because it changes the results.
652     - make it possible to read AREA from a file, too.
653    
654    checkpoint59c
655    o add S/R and diagnostics for oceanic mixed-layer depth
656    o move GMRedi call after all vertical mixing schemes (including KPP)
657    o pkg/thsice:
658     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
659      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
660    o pkg/obcs:
661     - bug fix for balance code
662    o pkg/seaice:
663      - allow values of SEAICE_elasticParm > 1
664      - add new parameter SEAICE_evpTauRelax as an alternative
665        to SEAICE_elasticParm
666      - make lsr boundary conditions free slip (by default), changes result
667      - add code for no slip boundary conditions for lsr
668      - set minimum of zeta to zero (and not 4e8) (changes results)
669      - add a cap on AREA after advecting AREA if seaice_growth is not called
670    o change calculation of Visbeck K:
671      - no longer depend on tapering scheme; instead, compute slope (limited
672        by GM_maxSlope). this is equivalent to what was comuted before with
673        clipping or linear tappering.
674      - fix vertical averaging (wrong by 1/2 level)
675      - leave the old version (but will not be maintained) within
676        #ifdef OLD_VISBECK_CALC / #endif
677      - update output of exp. ideal_2D_oce
678    o change error catch in calc_r_star to improve vectorization
679    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
680      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
681    o adjoint:
682      Re-organized adjoint checkpointing according to Matt Mazloff
683      (but with modifs/completions/cleanups)
684      Storing is now bundled into large arrays to optimized I/O
685      (and second step in cleanup of the_main_loop)
686    
687    checkpoint59b
688    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
689      - export/import (between ocean & coupler) fields needed for ocean DIC.
690    o pkg/seaice:
691      - get rid of three more exchanges seaice_calc_viscosities (required
692        different loop boundaries in seaice_lsr and seaice_ocean_stress)
693      - bug fix in seaice_ocean_stress (update of lab_sea required)
694      - reduce loop boundaries to necessary minimum also in seaice_evp
695      - go back to the old way of computing deltaC/Z as the adjoint likes that
696        better
697    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
698      passive tracer to an Age Tracer) + update output.txt
699    o pkg/exf:
700      - implement A-grid / C-grid selection for wind-stress input files.
701      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
702      for now, in exf_bulk_largeyeager04.F only :
703      - change implementation for case where windspeed + 2. components wind-stress
704        are read-in. AND use rhoConstFresh to convert evap.
705    o pkg/seaice:
706      - use correct EXCH_UV for wind-forcing (on A-grid).
707      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
708        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
709    o pkg/exf:
710      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
711      EXF_INTERPOLATION:
712      - merge global_with_exf/code version of exf_interp_read.F
713        to the main code ;
714      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
715        reading the file ; Important: This options needs to be defined to recover
716        previous code.
717        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
718      - no longer loose real*8 precision along the way when using exf_iprec=64.
719    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
720      - change discretisation of evp-solver in order to avoid another exchange
721        (changes lab_sea) and clean up a little
722      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
723        help the adjoint (this also changes the results slightly)
724      - add a few "_d 0" where they had been missing in seaice_evp.F
725      - cleaning up: remove unused seaice_calc_rhs.F
726    o pkg/exf: some cleaning-up:
727      - change various "constants" into runtime parameters
728      - cleaned-up Large&Yeager04 routine which should eventually
729        replace exf_bulkformulae.F (changed names of S/R and CPP)
730        and merged various ALLOW_ATM_WIND options
731     only used with thsice pkg (in thsice_get_exf.F):
732      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
733        which are used when useStabilityFct_overIce=TRUE (= the default)
734      - change default values of ice & snow emissivity and scale downward LW
735        by ice & snow emissivity.
736    o pkg/thsice:
737     fix few little problems, in thsice_calc_thickn.F:
738      - growth vertically (and not laterally) if iceFrac == iceMaskMax
739      - melt only laterally if hIce < hThinIce (as the comments say)
740      and in thsice_extend.F:
741      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
742      - start to form ice as soon as the minimum ice-volume is reachable.
743     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
744      and cpl_aim+ocn
745  o pkg/kpp  o pkg/kpp
  - remove wrong (within bi,bj loops) EXCH calls.  
  - little cleaning (add argument myThid in last position, cvs header ...)  
746   - move computation of surface related input fields to KPP into a new   - move computation of surface related input fields to KPP into a new
747     subroutine kpp_forcing_surf.F     subroutine kpp_forcing_surf.F
748     - remove wrong (within bi,bj loops) EXCH calls.
749     - little cleaning (add argument myThid in last position, cvs header ...)
750     - for now, fix conservation problem by exchanging KPPviscAz (may not
751       be the best fix)
752  o pkg/seaice  o pkg/seaice
753   - check for inconsistent evp parameter/cpp-flag combination   - check for inconsistent evp parameter/cpp-flag combination
754   - remove leftover errIO flat for obsolete name list error handling   - remove leftover errIO flat for obsolete name list error handling
755    o OpenAD
756     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
757    
758  checkpoint59a  checkpoint59a
759  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 31  o in FFIELDS.h: Line 773  o in FFIELDS.h:
773       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
774  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
775  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
776      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
777        are no longer updating the vertical diffusivity array
778        (passed as argument) but are (re-) setting those arrays.
779  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
780    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
781      cgrid-lsr and evp solver      cgrid-lsr and evp solver
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