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revision 1.801 by jmc, Fri Apr 27 16:33:53 2007 UTC revision 1.1026 by dfer, Mon Sep 29 14:05:54 2008 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg ggl90:
8          - add missing sqrt(2) factor in computation of mixing length
9            scale in ggl90_calc.F
10            (see Eq. (2.35) in Blanke and Delecluse, JPO, 1993)
11    
12    checkpoint61d
13    o adjoint modifs
14      - adapt to new field rhoInSitu
15      - allow to revert from StoreDynVars2D, StoreDynVars3D
16        to individual fields
17        (switches AUTODIFF_USE_OLDSTORE_2D, AUTODIFF_USE_OLDSTORE_3D)
18    o store 3-D (in-situ) density in commom block (DYNVARS.h)
19     - save 1 rho computation.
20     - no longer modify T & S inland when using down_slope pkg.
21    o gad_som : allow to switch to SOM advection for T & S without corresponding
22      pickup files (using new S/R: MDS_CHECK4FILE).
23    o keep removing _BEGIN/_END_MASTER between MDSIO S/R call
24      (for useSingleCpuIO to work in multi-threaded)
25    o pkg/shelfice:
26     - disentangle parameters: retire shelfIceFile in data/PARM05 and substitute
27       with SHELFICEtopoFile in data.shelfice
28     - move code for reading ice shelf topography and modifying hFacC into separate
29       subroutines of the shelfice package
30     - separate initialisation of "fixed" and "variable" variables
31     - kTopC is not (yet) replaced by kSurfC, although this is possible
32    o fix broken diagnostic SIatmFW and changed the units from m/s to kg/m^2/s
33    o add initialisation of deepFac if using Pcoords (new S/R set_grid_factors)
34      and rename:
35      ini_phiref.F          --> set_ref_state.F  (+ set anelastic factors)
36      ini_reference_state.F --> load_ref_files.F (- set anelastic factors)
37    o change FIND_RHO_SCALAR : return rho (instead of rho - rhoConst)
38    
39    checkpoint61c
40    o add option ALLOW_ADDFLUID and run-time selector "selectAddFluid"
41      to add mass source/sink of fluid in the interior (3-D generalisation
42      of oceanic real-fresh water flux).
43    o pkg/monitor: fix recip_dr argument in mon_advcflw2 call (-> advcfl_W_hf_max)
44    o vermix test experiment: switch from LINEAR EOS to MDJWF (not tested before)
45    o new pkg: down_slope
46      density-driven downsloping flow parameterisation (Tellus, 1999, 412-430).
47      - presently, modify T & S inland (dwnslp_calc_rho.F).
48        can be avoided if rho was stored in common bloc and used in calc_phi_hyd.
49      - implementation for ocean in P-coords not tested.
50      - add secondary test to global_ocean.90x40x15 (input.dwnslp) to check this pkg.
51    o move kSurfC,kSurfW & kSurfS from SURFACE.h to GRID.h (next to kLowC)
52      (to facilitate conversion of oceanic pkg to p-coordinate).
53    o change FIND_RHO to FIND_RHO_2D :
54      pass arguments tFld & sFld as local (tile) 2D-arrays ; +fix EOS_CHECK.
55    o new pkg: cheapaml
56    
57    checkpoint61b
58    o exch2:
59      change index bounds in rx2_cube exchanges (new S/R: EXCH2_GET_UV_BOUNDS)
60      - no longer depend on the order sequence (N,S,E,W).
61      - 3rd exchange no longer needed (tested with 24 tiles).
62      - same modif to hand-written adjoint S/R (global_ocean.cs32x15: zero diff)
63      - exch_UV_A-grid readily available (but not yet tested).
64      comment out 3rd exch call and remove copy of V to U at SE & NE face-corners
65      (both are no longer needed) in exch_uv: no effect in forward run; but
66       get truncation error differences with adjoint exch.
67    o exch2:
68     - change index-bounds storage (moved from target to local tile,
69       more intuitive this way) ; rename/remove some variables.
70     - change utils/exch2/matlab-topology-generator & code_mods accordingly.
71    
72    checkpoint61a
73    o exch2/matlab-topology-generator:
74      fix bug in index bounds for N-S internal exchange (hard to tell if this
75      had any effect on the solution).
76    o pkg/mnc: small fix in mnc_handle_err: make sure that length of msgbuf
77      is exceeded
78    o testreport: modify syntax of awk, so that it works also with
79      awk, and not only with nawk and gawk
80    
81    checkpoint61
82    o autodiff
83      Change default for TAF usage by removing argument '-nonew_arg'
84      This changes TAF subroutine argument list (ordering of active var.)
85      Omission of this flag leads to incompatibility w.r.t. TAMC
86      To restore TAMC-compatibility, need following modifs:
87      * use adoptfile tools/adjoint_options/adjoint_tamc_compatibility
88      * use CPP option #define AUTODIFF_TAMC_COMPATIBILITY
89      Tested TAF version is 1.9.22
90      N.B.: exch2 hand-written adjoint code currently not TAMC compatible
91    
92    checkpoint60
93    --->>> This is the last checkpoint for which generating the adjoint
94    --->>> is done via the TAMC-compatibility TAF-flag "-nonewarg"
95    --->>> by default.
96    --->>> Future checkpoints will ommit this flag by default.
97    o pkg/generic_advdiff, os7mp: simplify and avoid division by zero.
98    o pkg/grdchk: Add gradient check to etan0 perturbations.
99    o pkg/exf: read ice area from file (#ifdef ALLOW_ICE_AREAMASK).
100    o pkg/autodiff: more flexibility in zeroadj.
101      model/src: modifying do_oceanic_phys.F accordingly.
102    o pkg/ctrl: Bounds for (kapgm,kapredi,eddypsi) parameter estimation.
103    o model/src and pkg/gmredi: GMREDI_WITH_STABLE_ADJOINT CPP option
104      special setup of gmredi for which the adjoint is stable
105      enough for parameter optimization.
106    o bridging the gap between eddy stress and GM.
107      -> eddyTau is replaced with eddyPsi (eddyTau = f x rho0 x eddyPsi)
108          along with a change in CPP option (now ALLOW_EDDYPSI).
109      -> when using GM w/ GM_AdvForm:
110          The total eddy streamfunction (Psi = eddyPsi + K x Slope)
111          is applied either in the tracer Eq. or in momentum Eq.
112          depending on data.gmredi (intro. GM_InMomAsStress).
113      -> ALLOW_EDDYPSI_CONTROL for estimation purpose.
114      The key modifications are in model/src/taueddy_external_forcing.F
115      pkg/gmredi/gmredi_calc_*F pkg/gmredi/gmredi_*transport.F
116    
117    checkpoint59r
118    o new S/R (pkg/mdsio/mdsio_facef_read.F) reading of sNx+1 x sNy+1 array
119      from per-face file (take S/R READSYMTILE_RS out of ini_curvilinear_grid.F);
120      fix option to read coriolis(@ cell-corner) from files with CS-grid.
121    o pkg/mnc: add some attributes to standard 1D-coordinate variables
122    o pkg/diagnostics: enforce missing_value attribute for scalar variables at
123      mass points, when using mnc for output
124      - add runtime parameter (missing_value, missing_value_int) to override
125        default (which is the value of getcon('UNDEF'))
126    o pkg/mnc: prepare mnc for the actual use of missing values with the
127      diagnostics package: small fix in mnc_cw_readwrite.template and more
128      initialisation of never used fields
129      - replace mnc_common.h and mnc_id_header.h with corresponding upper case
130      versions
131    o pkg/thsice/thsice_ini_vars.F added default initial values so that
132      thermodynamics sea ice solver does not blow up when some initial fields
133      are missing.
134    o move from external_forcing_surf.F to ini_forcing.F
135      the p-coord. hack consisting in using pLoad to set phi0surf ;
136      update output of tutorial_global_oce_in_p (affected @ truncation level).
137    o Freshen up a bit hs94.1x64x5, notably:
138      remove rotationPeriod and tRef=5*0. (adjoint only), and add
139      exactConserv=.TRUE.
140    o pkg/generic_advdiff:
141      change option GAD_ALLOW_SOM_ADVECT to GAD_ALLOW_TS_SOM_ADV which only
142      applies to files where Temperature & Salinity 2nd Order moments are used.
143    o pkg/ptracers: add second-order moment advection schemes (80 and 81);
144      this uses a dynamically allocated internal state data structure
145      (#define PTRACERS_ALLOW_DYN_STATE in PTRACERS_OPTIONS.h)
146      and requires a fortran 90 compiler
147    
148    checkpoint59q
149    o pkg/mom_vecinv: Add energy & enstrophy conserving scheme (selectVortScheme=3)
150       (from Sadourny, described by Burridge & Haseler, ECMWF Rep.4, 1977)
151    o Refresh tutorial_global_oce_biogeo, notably:
152      - change bathymetry (put back seamounts in ACC, use hFacs)
153      - change EOS (POLY3 --> JMD95Z)
154      - use Bryan-Lewis vertical diffusivity
155      - use multidimensional advection
156      - remove old virtual virtual in dic pkg, now done through ptracer pkg
157      - change a couple of parameters in dic pkg
158    o pkg/ctrl: change formula in adctrl_bound.F and add a parameter to ctrl_map_ini_gen.F
159    o pkg/obcs: change default to OBCSfixTopo = .true.,
160      - set OBCSfixTopo=.false. in exp4/input/data.obcs to reproduce old result
161      - replace "debugMode" with "debugLevel .GE. debLevB"
162    o implementation of TAF directives for gchem,cfc,dic
163    o remove "exp5" (replaced by tutorial_deep_convection).
164    o pkg/obcs: add code to fix topography gradients normal to open boundaries;
165      this requires computing the index fields OB_Jn/Js/Ie/Iw in obcs_readparms;
166      the code can be turned on by setting OBCSfixTopo = .true. in data.obcs
167      --> changes results in exp4, seaice_obcs
168    o tutorial_deep_convection :
169      update the set-up and increase resolution and domain size ; start
170      from pseudo initial conditions = output at t=120mn in order to see
171      something happening when running testreport.
172    o pkg/seaice: add os7mp as an advection scheme
173                  add check for advection schemes
174                  add a flag for restoring T and S underneath sea ice
175    o pkg/my82: add netcdf-support and diagnostics
176    o thsice pkg:
177      - Now hsMax limits snow height by turning it into ice following
178        flooding scheme (and now conserving energy)
179      - Slight rewriting of the formula in thsice_calc_thick.F
180      - Parameter rhowi eliminated to be replaced by floodFac = (rhosw-rhoi)/rhos
181      --> changes results of global_ocean.cs32x15.icedyn and global_ocean.cs32x15.thsice
182    
183    checkpoint59p
184    o gchem / dic / cfc :
185      - add useDIC, useCFC , read from "data.gchem" (& hold in GCHEM.h);
186      - add new parameter files: "data.dic" & "data.cfc" ;
187      - various re-arrangement in initialisation & header file ;
188      - fix tutorial_global_oce_biogeo for multi-threaded test.
189    o pkg/dic: test for "pickup_dic" file when restarting ;
190      if no pickup-file, can restart with a re-initialised pH (same as it did
191      before) providing pickupStrictlyMatch is set to False.
192    o change argument list of S/R PTRACERS_WRITE_PICKUP & MYPACKAGE_WRITE_PICKUP
193      + fix call to S/R GGL90_WRITE_PICKUP & DIC_WRITE_PICKUP
194    o add a "warning" (to Error msg file) when an Active Tracer is not using AB-2
195      and staggerTimeStep is off (needed for stability of Internal-wave dynamics).
196    o move out of PARAMS.h & data the last pieces of old-ptracer code: tauTr1ClimRelax,
197     & lambdaTr1ClimRelax ; put those 2 params in PTRACERS_PARAMS.h & data.ptracers
198       (note: not clear to me what lambdaTr1ClimRelax is still used for ...)
199    o pkg/mom_vecinv: - new parameter "selectVortScheme" to select which
200       scheme to use for vorticty-term ;
201     - compute upwindVorticity=T case within mom_vi_u/v_coriolis_c4.F
202       (with default selectVortScheme, return to original discretisation)
203     - remove weird combination (e.g.: upwindVorticity & highOrderVorticity)
204    o pkg/seaice: add a line to the summary to indicate grid type (B/C)
205    o in mom_calc_visc, fix average value of viscAh_W & viscA4_W next to the
206      bottom ; only used with variable horizontal viscosity and non-hydrostatic.
207      also fix diagnostics VISCAHW & VISCA4W.
208    
209    checkpoint59o
210    o dome/code/obcs_calc.F: avoid division by zero (detected using gfortran).
211    o change the loop ordering in most gad_*_adv_x.F to improve vectorization:
212      move a few statemens out the main loop into separate loops
213    o pkg/shelfice:
214      - sort out freshwater flux; convert freshwater fluxes to mass fluxes
215        (kg/m^2/s), does not break tests, because in verification/isomip,
216        rhoConstFresh=rhoConst (by accident)
217      - rearrange computation of tLoc, sLoc, pLoc to make code more efficient
218      - move S/R find_rho_scalar, pkg/ecco/sw_ptmp.F, pkg/ecco/sw_adtg.F into
219        new file model/src/seawater.F, so that they are available for all pkgs.
220      - convert potential temperature into in-situ temperature. This changes the
221        isomip tests => update tests
222    o add a flag writePickupAtEnd (default=true) to be able to suppress
223      writing a pickup at the last timestep
224    o tools/mpack-1.6 :
225      - disable automake (not working) and autoconf (not needed).
226      - update to version 1.6.4 which fix MD5 code on some 64 bits platforms
227        also cleaner with much less compilation warnings.
228    o pkg/profiles:
229      rename profiles_interp_mean_genericgrid as profiles_interp_mean_gg
230      (for "less than 32 characters name" compiler requirement)
231    o pkg/obcs and pkg/exf: added capability to specify seaice open boundary
232      conditions that have a different sampling frequency than S/T/U/V obcs
233    o pkg/diagnostics (stats-diags):
234      - fix global Min/Max in case 1 processor get only empty tiles
235    o genmake2: replace (4 times)
236         make genmake_tc_1.o >> genmake_warnings 2>&1
237      with
238         COMM="$CC $CFLAGS -c genmake_tc_1.c"
239         echo $COMM >> genmake_warnings
240         $COMM >> genmake_warnings 2>&1
241      to make genmake2 always see the value of CC as specified in the optfile.
242    o generic_advdiff: - prather advection scheme (SOM) coded for CS-grid.
243      - add diagnostics for 1srt & 2nd Order moments and sub-grid variance.
244      - modify verification advect_cs test to test SOM-advection on CS-grid.
245    o pkg/ctrl:
246      - Rewrite of ctrl_map_ini_ecco.F,
247        introducing a generic routine (ctrl_map_ini_gen.F).
248      - Modification of ctrl_bound/adctrl_bound handling control vector bounds.
249    
250    checkpoint59n
251    o pkg/diagnostics: for large number of diagnostics, store diagnostic mate
252      number in dedicate array "hdiag":
253      - new version of S/R DIAGNOSTICS_ADD2LIST : DIAGNOSTICS_ADDTOLIST
254        with 1 more argument (mate number); modify old version DIAGNOSTICS_ADD2LIST.
255      - many small changes (integer format) for large number of diagnostics
256      - start to use DIAGNOSTICS_ADDTOLIST (necessary for diagnostics with
257        a counter mate) in pkg diagnostics, ptracers, thsice & aim_v23.
258    o add parameter rotateGrid and Euler angles EulerPhi/Theta/Psi. For
259      usingSphericalGrid, this allows to define the rotated grid coordinates
260      via phiMin/thetaMin/dxSpacing/dySpacing, etc., but then re-compute the
261      geographical coordinates according to the inverse of the rotation defined
262      by the Euler angles, so that Coriolis parameter and online-interpolation by
263      exf works with the geographical coordinates on XC/YC/XG/YG.
264      Naturally, this feature does not work with all packages, so some
265      combinations are prohibited in config_summary (flt, flt_zonal, ecco,
266      profiles), because there the coordinates are assumed to be regular
267      spherical grid coordinates.
268    o pkg/gmredi,ctrl,ecco,autodiff,grdchk and model/src,inc:
269      - introduce isopycnal diffusion coefficient control.
270    o tools/adjoint_options:
271      - additional control vector components.
272    o pkg/mnc: have mnc create marginally meaning full coordinate variables
273      (that is the grid indices) if usingCurvilinearGrid and NOT EXCH2
274    o pkg/mypackage:
275      - add example of read/write pickup for state-var ;
276      - add entry points to the main code for state-vars diags & write-pickup.
277    o pkg/exf: rewrite of exf_getffieldrec.F to properly deal with year
278      transitions for useExfYearlyFields
279      - add new subroutine that determines the file to read from for
280        use*YearlyFields = .TRUE. and .FALSE.
281      - add a verification experiment to global_with_exf that tests
282        useExfYearlyFields with USE_EXF_INTERPOLATION defined
283    o pkg/obcs/exf: add useOBCSYearlyFields (=.FALSE.) to obcs with exf in
284      analogy to useExfYearlyFields; rearrange obcs_prescribe_read: two new
285      subroutines (which could be generated from a template, because they are
286      almost identical), for now they are included in obcs_prescribe_read.F for
287      simplicity
288    o pkg/exf:
289      - add a little more diagnostic to exf_interp_read (in analogy to
290        mds_read_field, can be turned off with debugLevel < debugLevA=1)
291      - improve vectorizability of exf_interp for TARGET_NEC_SX, makes code
292        ugly but fast by unrolling short inner loops, inserting a unroll=8
293        directive in routine lagran, and splitting a loop and making do while the
294        outermost loop (the latter requires the intoduction of index arrays)
295    o pkg/obcs: replace obcs_apply_area/heff/hsalt/hsnow with obcs_apply_seaice
296    o pkg/seaice: moved DIFFERENT_MULTIPLE from seaice_model to seaice_dynsolver
297      http://forge.csail.mit.edu/pipermail/mitgcm-devel/2008-January/003173.html
298    o verification/seaice_obcs: updated for restart test and latest options
299    o pkg/seaice: add a new flag SEAICEuseTEM to use a slightly different
300      ice rheology (so-called truncated ellipse, that gets rid of tensile stress);
301      for now this is only available for the C-grid code and also within
302      #ifdef SEAICE_ALLOW_TEM, because this option may slow down the EVP code
303    
304    checkpoint59m
305    o pkg/seaice: use different time constant for melting (SEAICE_gamma_t)
306      and freezing (SEAICE_gamma_t_frz) ice due to mixed layer temperature
307    o gad_som : fix flux output (& diagnostics) to have same units as other  
308      advection scheme fluxes (was previously multiplied by deltaT).  
309    o added verification/seaice_obcs both to test seaice open boundaries
310      and to provide an example matlab scrpt for generating them
311    o added verification/lab_sea/input.salt_plume for testing pkg/salt_plume
312    o pkg/salt_plume: clean up salt_plume_frac.F to
313      remove redundancy in PlumeMethod 1 and 4
314    o pkg/kpp: added saltplume diagnostics
315    o pkg/obcs and pkg/seaice:
316      - do not set uice and vice to zero when OB*icefile are unspecified
317      - OBCS_SEAICE_AVOID_CONVERGENCE is undefined by default
318      - moved seaice tracer obcs after call to seaice_growth
319    o pkg/salt_plume: added various options for salt plume depth
320      criterion and for vertical distribution of the salt
321    
322    checkpoint59l
323    o pkg/ptracers: new version of ptracers pickup:
324      read meta file and write only fields which are needed to restart.
325      ( same logic as main pickup file ; also using pickupStrictlyMatch )
326    o pkg/seaice:
327      - add timescale for melting due to warm mixed layer as a means of
328        setting SEAICE_availHeatFrac more conveniently
329      - add a CPP-flag/runtime parameter check for flooding algorithm
330      - reformulated availHeat in seaice_growth.F to be independent of AREA
331    o change units attribute of EmPmR netcdf variables to kg/m^2/s to reflect recent
332      unit changes
333    o pkg/obcs: added OBCS_SEAICE_AVOID_CONVERGENCE constraint
334    o cg2d.F: add 3 compiler directives that speed up this routine by 30% on a NEC
335      SX vector computer.
336    o pkg/seaice:
337      - removed SEAICE_FFIELDS.h and seaice_get_forcing.F
338        seaice forcing fields can now be read only through pkg/exf
339      - removed some unused halos
340    o no longer write pickup from THE_MODEL_MAIN but always from FORWARD_STEP
341    o pkg/exf: added useRelativeWind EXF_PARAM.h option for subtracting U/VVEL
342      or U/VICE from U/VWIND before computing U/VSTRESS
343    
344    checkpoint59k
345    o pkg/seaice: ICE2WATR=SEAICE_rhoIce/rhoConst for consistency between
346      dynamics and thermodynamics. Set ICE2WATR=0.92 to reproduce older results.
347    o fix un-initialised variable problem (in mom_vecinv & shap_filt):
348      all experiments pass when compile with un-initialised var. checking option.
349    o added pkg/salt_plume
350    o script to test restart (for now, in MITgcm_contrib/jmc_script)
351    o pkg/seaice: new read/write pickup version.
352      read meta file and write only fields which are needed to restart.
353      ( same logic as main pickup file ; also using pickupStrictlyMatch )
354    o pkg/seaice: fix bug in seaice_ocean_stress (call of seaice_calc_strainrates)
355    o lab_sea.hb87: modify the domain & update output.hb87.txt :
356      lat-long grid & no-slip BC in seaice-dynamics produce different sigma12
357      at j=1 & j=Ny+1 : this case is not treated correctly in the restart
358      process. Fixed here by closing the domain at the Northern boundary.
359    o pkg/rw: cleaning-up: call directly new MDSIO S/R MDS_READ/WRITE_FIELD.
360    o pkg/mdsio: add new arguments to MDS_READ/WRITE_FIELD for reading/writing
361      a set of consecutive levels in/from a 3-D array.
362    o pkg/ptracers:
363      use a 2 characters string ioLabel to identify tracer (if more than 99 tracers).
364      to-do: fix pkg/diagnostics when large number of diagnostics are defined.
365    
366    checkpoint59j
367    o in pkgs: dic, obcs, offline, rbcs:
368      standard way to compute coeff. for time interpolation between 2 time reccords
369      which retains full precision (& make results less dependent on compiler).
370      update output of exp: tutorial_cfc_offline & tutorial_global_oce_biogeo.
371    o pkg/cfc: if compiled with exf and seaice, cfc now can use fields from those
372      packages instead of reading ice cover and wind speed separately
373    o split PTRACERS.h in 2 header files: PTRACERS_FIELDS.h & PTRACERS_PARAMS.h
374     (keep a temporary version of PTRACERS.h in verification/OpenAD/code_ad_openad
375      to allow to compile customized code before the update)
376    o cleaning-up:
377      - fix CPP instruction syntax in pkg/obcs
378      - replace (some) call to MDSIO S/R with call to RW interface S/R ; and
379        add #ifdef ALLOW_MDSIO elsewhere (allows to compile without pkg/mdsio)
380      - fix some threads issue in IO parts.
381    o pkg/dic:
382      - add tons of "_d 0" (--> much better testreports !)
383       and then update outputs of tutorial_global_oce_biogeo
384    o pkg/mom_fluxform:
385      add a special version of momentum advection intended to conserve momentum
386      next to a bathymetry step or a coastline edge. (default = off = #undef)
387    o new read/write pickup version:
388      - for now, only implemented for main (mdsio) pickup file.
389      - write out only what is needed to restart; merge pickup_nh , pickup_ph
390        and main pickup together.
391      - read meta file; read only what is needed to restart; stop if a field
392        is missing (if pickupStrictlyMatch=T, = the default) or try to restart
393        if it make sense (even if the restart is not perfect).
394      - if no meta file, assume that pickup to read corresponds exactly to
395        a pickup that would currently be written.
396      - read pickup written in the old format (until checkpoint59i) if it
397        recognizes an old meta file (no field-list).
398      - add a meta file in exp. which starts from a pickup: 2 cases:
399        a) minimal meta file (with just file precision) + pickupStrictlyMatch=F
400         e.g.: global_ocean.90x40x15/input/pickup.0000036000.meta
401        b) a meta file describing the content of the associated pickup file
402         e.g.: tutorial_global_oce_biogeo/input/pickup.0004248000.meta
403    o pkg/mdsio & pkg/rw:
404      - new routine to read a meta file ; new set of routine to read
405        Multiple-fields file (with meta file).
406    o added open boundary conditions capability for seaice
407        HSNOW, HSALT, UICE, and VICE
408    
409    checkpoint59i
410    o adjoint:
411      * fix multiDimAdvection adjoint
412        (partial recomputation problem by TAF for fVerT(:,:,kDown)
413        and comlev1 size definition (maxpass vs. max. number of tracers)
414      * verification/global_ocean.90x45x15 adjoint now tests
415        NLFS and multiDimAdvection using DST3 (=30)
416      * verification/lab_sea now tests multiDimAdvection using DST3 (=30)
417    o pkg/kpp: add "_d 0" to real constant (if missing);
418      update output of exp: natl_box (10.digits); vermix (std, 7.digits)
419      and lab_sea, 3.FW (only 6,4,6 digits match) & AD (8.digits).
420    o prepare for "clever pickup" implementation: add new header file "RESTART.h"
421      for internal parameters related to restart process (formerly from PARAMS.h)
422      and add startAB parameter to argument list of S/R ADAMS_BASHFORTH2.
423    o more standard interface to {PKG}_WRITE_PICKUP with pickup suffix passed
424      as argument. (only atm2d & obcs write_pickup have not yet been updated)
425    o pkg/monitor:
426      - use GLOBAL_SUM_TILE instead of _GLOBAL_SUM
427      - fix mon_stats_rs (statistics over the full domain, even where field is zero)
428      - account for deep Atmosphere factor and density factor (anelastic)
429    o added open boundary conditions capability for seaice HEFF and AREA
430    o pkg/shelfice: add option for convservative form of Hellmer&Olbers (1989)
431      thermodynamics
432      - requires a little reorganization, which affects the testreport results
433        of isomip.htd (only 7 digits of cg2d agree) => update/modify experiment,
434        so that now the conservative form is tested
435      - add a few comments
436    o add missing cvs Header: or Name: in eesupp/*, pkg/* & verification/code*
437    o add a little bit of code to gad_os7mp_adv_?.F to help vectorization
438    o add new diagnostics to seaice: advective, diffusive fluxes (only for
439      multidim-advection, for scheme 2 they are not filled) and transports,
440      thermodynamic growth rates
441    o change units of EmPmR (inside the code, + within coupling interface)
442      from m/s to kg/m2/s (mass flux) but leave input file unchanged.
443      Affects results @ truncation level (cg2d match) and update output of
444       experiments: lab_sea(6), global_ocean.90x40x15(10),
445      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
446      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
447      Coupled set-up: allow to restart from previous pickups (cpl_oldPickup=T).
448      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
449    
450    checkpoint59h
451    o pkg/exf:
452      - improve vectorization by moving if-statement out of loops in
453        exf_mapfields, exf_radiation
454      - exf_bulkformulae.F: introduce 2D fields and vectorize code
455    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
456    o testreport:
457      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
458        monitor & update offline_exf_seaice exp. output.
459      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
460    o pkg/seaice:
461      - bug fix in the evp solver: boundary conditions were affected be
462        masking of zMax/zMin (changes results)
463      - minor bug fix in boundary conditions in seaice_calc_strainrates
464        (changes results for no_slip)
465      - seaice_lsr.F: make interpolation of eta dependent on boundaries
466      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
467      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
468        stress formulation and no-slip boundary conditions
469    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
470      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
471    o pkg/seaice: a first HSALT time stepping equation has been checked in
472    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
473      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
474      without requiring DO-IF statements
475    o pkg/thsice:
476      use continuous power-law function for partition of energy between lateral
477      melting/freezing and thinning/thickening ; old code using step function
478      still available with #undef THSICE_FRACEN_POWERLAW
479      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
480    o testreport: change AD testing : check against results/output_adm.txt
481      using same scripts as for forward test.
482    
483    checkpoint59g
484    o adjoint testing: in preparation for changing testreport:
485      - output format: cost and grad written on separated lines
486      - ad output results in directory "results" (instead of "results_ad")
487    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
488    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
489    o pkg/ecco: allow user defined cost function contributions
490    o testreport:
491      Allow to choose (per experiment) the list of tested output variables
492       and the main variable (used to issue a pass/FAIL ) ;
493      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
494      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
495      Also modify printing of summary:
496       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
497       b) echo the list of tested variables in the individual summary.txt of
498          each experiment.
499    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
500      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
501      (but still depend on the tile decompostion of the domain).
502    o pkg/seaice: change a discretization detail to make the B-grid code
503      "more symmetric". This change is likely to remove all "ridges/leads" that
504      where quasi-aligned with the grid in B-grid solutions. It may also be
505      the solution to the stress coupling issues with the B-grid.
506    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
507      remove .cvsignore from input dir. (since testreport no longer run here).
508    o pkg/thsice:
509     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
510     - fix reshaping of sea-ice just after advection:
511       melt all the ice only if ice-volume is too small.
512     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
513       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
514     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
515    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
516      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
517    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
518      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
519      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
520      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
521      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
522      -> update output.txt
523    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
524     this affects truncation error: -> update output.txt of exp:
525      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
526      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
527    
528    checkpoint59f
529    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
530    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
531      a bounded range (in forward mode)
532    o pkg/ecco, ctrl, autodiff and mom_common:
533     internal parameter controls, completements of implementations
534    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
535    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
536      (not seem any difference in testing results).
537    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
538       at face corners.
539    o pkg/generic_advdiff:
540     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
541      loop range indices for computing vertical advection tendency
542      and do the calculation in the interior only (no overlap) ;
543      for now, only implemented for SOM advection (to save CPU time).
544     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
545    o exch2 adjoint
546      First set of changes:
547      - add exch2 hand-written adjoint templates
548      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
549        This will require cleanup in pkg/autodiff/*.F
550        (changed routines currently kept separate in verif. code/)
551      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
552        that used to hide exch2 or cubed-sphere specific code
553        (commented via 'cph-exch2')
554    o pkg/seaice
555      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
556    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
557       output of global_ocean.cs32x15.thsice .
558    
559    checkpoint59e
560    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
561      for B-grid vector (not yet tested) and C-grid vector (<- only used
562      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
563    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
564      (#ifdef ALLOW_SALT_PLUME)
565    o gather_2d/scatter_2d: removed halo regions
566    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
567      scheme and the corresponding test case (under front_relax dir). For now,
568      only available with Skew-flux form and not yet tested in realistic set-up.
569      adjoint: store directives updated, but gradient checks deteriorated,
570      so maybe GM/Redi adjoint is now broken.
571    o seaice adjoint
572      * add AREA, HEFF, HSNOW as control variable
573        (should not change lab_sea results)
574      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
575    o pkg/seaice:
576      * added computation of saltFlux in seaice_growth;
577        For time being, sea ice salinity is assumed constant
578        contribution of snow flooding to freshening of sea ice is neglected.
579        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
580        defaults to 0.0 in order to maintain backward compatibility.
581        Typical values for SEAICE_salinity are 4 to 10 g/kg.
582      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
583      * added SEAICE_availHeatFrac, which specifies fraction of surface level
584        heat content used to melt or grow ice
585      * commented out cap of HICE: it helps keep ice thinner
586      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
587      * applied OBCS T/S mask to HEFFM sea ice mask
588    
589    checkpoint59d
590    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
591     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
592     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
593    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
594     and change default value of parameter "GM_Small_Number";
595     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
596       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
597       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
598    o pkg/ecco: cost function when applying pkg/smooth to controls
599    o pkg/ctrl: add forcingPrecond run time parameter
600    o pkg/seaice:
601     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
602     - fix bug in metric terms of u-equation in LSR solver (implicit part),
603       changes verification/lab_sea
604     - rearrange implicit part of u-equation in LSR solver to make it easier to
605       read, understand, and debug. This causes changes at the truncation level.
606     - fix (serious) bug in the boundary conditions (sign error in the implicit
607       part) of the LSR solver. Changes all LSR results.
608     - fixed problem with HSNOW initialization to avoid thick snow when AREA
609       is initilized with small values - does not change lab_sea results.
610     - added HsnowFile initialization capability
611    o pkg/smooth: addition to model/src and pkg/ctrl so allow
612     initialization of pkg/smooth and application to control vector
613    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
614    o dependencies: pkg/profiles requires pkg/cal
615    o pkg/profiles:
616     - added option ALLOW_PROFILES_GENERICGRID
617         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
618         that interpolation information (grid points and coefficients) is provided
619         within the netcdf input files.
620         -> sample matlab scripts can be found in MITgcm_contrib/gael
621         that allow you to prepare netcdf input files.
622     - also modified: cleaner include statements, cleaner error print statements,
623       cleaner stops when error, and more tests of the netcdf input files consistency.
624    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
625    o pkg/seaice:
626     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
627       requires a new routine: seaice_diagnostics_fill.F
628     - make sure that seaice does not move if not forced (pressure replacement
629       method, Hibler and Ip, 1995), changes results
630     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
631     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
632       It is turned off by default (=-1.), because it changes the results.
633     - make it possible to read AREA from a file, too.
634    
635    checkpoint59c
636    o add S/R and diagnostics for oceanic mixed-layer depth
637    o move GMRedi call after all vertical mixing schemes (including KPP)
638    o pkg/thsice:
639     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
640      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
641    o pkg/obcs:
642     - bug fix for balance code
643    o pkg/seaice:
644      - allow values of SEAICE_elasticParm > 1
645      - add new parameter SEAICE_evpTauRelax as an alternative
646        to SEAICE_elasticParm
647      - make lsr boundary conditions free slip (by default), changes result
648      - add code for no slip boundary conditions for lsr
649      - set minimum of zeta to zero (and not 4e8) (changes results)
650      - add a cap on AREA after advecting AREA if seaice_growth is not called
651    o change calculation of Visbeck K:
652      - no longer depend on tapering scheme; instead, compute slope (limited
653        by GM_maxSlope). this is equivalent to what was comuted before with
654        clipping or linear tappering.
655      - fix vertical averaging (wrong by 1/2 level)
656      - leave the old version (but will not be maintained) within
657        #ifdef OLD_VISBECK_CALC / #endif
658      - update output of exp. ideal_2D_oce
659    o change error catch in calc_r_star to improve vectorization
660    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
661      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
662    o adjoint:
663      Re-organized adjoint checkpointing according to Matt Mazloff
664      (but with modifs/completions/cleanups)
665      Storing is now bundled into large arrays to optimized I/O
666      (and second step in cleanup of the_main_loop)
667    
668    checkpoint59b
669    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
670      - export/import (between ocean & coupler) fields needed for ocean DIC.
671    o pkg/seaice:
672      - get rid of three more exchanges seaice_calc_viscosities (required
673        different loop boundaries in seaice_lsr and seaice_ocean_stress)
674      - bug fix in seaice_ocean_stress (update of lab_sea required)
675      - reduce loop boundaries to necessary minimum also in seaice_evp
676      - go back to the old way of computing deltaC/Z as the adjoint likes that
677        better
678    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
679      passive tracer to an Age Tracer) + update output.txt
680    o pkg/exf:
681      - implement A-grid / C-grid selection for wind-stress input files.
682      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
683      for now, in exf_bulk_largeyeager04.F only :
684      - change implementation for case where windspeed + 2. components wind-stress
685        are read-in. AND use rhoConstFresh to convert evap.
686    o pkg/seaice:
687      - use correct EXCH_UV for wind-forcing (on A-grid).
688      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
689        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
690    o pkg/exf:
691      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
692      EXF_INTERPOLATION:
693      - merge global_with_exf/code version of exf_interp_read.F
694        to the main code ;
695      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
696        reading the file ; Important: This options needs to be defined to recover
697        previous code.
698        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
699      - no longer loose real*8 precision along the way when using exf_iprec=64.
700    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
701      - change discretisation of evp-solver in order to avoid another exchange
702        (changes lab_sea) and clean up a little
703      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
704        help the adjoint (this also changes the results slightly)
705      - add a few "_d 0" where they had been missing in seaice_evp.F
706      - cleaning up: remove unused seaice_calc_rhs.F
707    o pkg/exf: some cleaning-up:
708      - change various "constants" into runtime parameters
709      - cleaned-up Large&Yeager04 routine which should eventually
710        replace exf_bulkformulae.F (changed names of S/R and CPP)
711        and merged various ALLOW_ATM_WIND options
712     only used with thsice pkg (in thsice_get_exf.F):
713      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
714        which are used when useStabilityFct_overIce=TRUE (= the default)
715      - change default values of ice & snow emissivity and scale downward LW
716        by ice & snow emissivity.
717    o pkg/thsice:
718     fix few little problems, in thsice_calc_thickn.F:
719      - growth vertically (and not laterally) if iceFrac == iceMaskMax
720      - melt only laterally if hIce < hThinIce (as the comments say)
721      and in thsice_extend.F:
722      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
723      - start to form ice as soon as the minimum ice-volume is reachable.
724     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
725      and cpl_aim+ocn
726    o pkg/kpp
727     - move computation of surface related input fields to KPP into a new
728       subroutine kpp_forcing_surf.F
729     - remove wrong (within bi,bj loops) EXCH calls.
730     - little cleaning (add argument myThid in last position, cvs header ...)
731     - for now, fix conservation problem by exchanging KPPviscAz (may not
732       be the best fix)
733    o pkg/seaice
734     - check for inconsistent evp parameter/cpp-flag combination
735     - remove leftover errIO flat for obsolete name list error handling
736    o OpenAD
737     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
738    
739    checkpoint59a
740    o pkg/seaice: some parameter clarifications and a little bit of clean up
741    o pkg/thsice: rename run-time parameters:
742       himin       -> hIceMin
743       himin0      -> hThinIce
744       hihig       -> hThickIce
745       i0          -> i0swFrac
746       transCoef   -> bMeltCoef
747       frac_energy -> fracMelting
748      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
749       with default values (for now) that do not change the results.
750      remove old version of thsice vars advection in pkg/seaice.
751  o in FFIELDS.h:  o in FFIELDS.h:
752    - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD    - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
753    - make pLoad & sIceLoad always available (but still only used if    - make pLoad & sIceLoad always available (but still only used if
754       ATMOSPHERIC_LOADING is #define).       ATMOSPHERIC_LOADING is #define).
755  o pkg/kpp: replaced _KPP_RL with _RL  o pkg/kpp: replaced _KPP_RL with _RL
756  o bug fixes for vertical diffusivity computations when both KPP and  o bug fixes for vertical diffusivity computations when both KPP and
757      3D diffusivity arrays are used.      3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
758        are no longer updating the vertical diffusivity array
759        (passed as argument) but are (re-) setting those arrays.
760  o pkg/seaice: fix bug in evp solver, while doing that  o pkg/seaice: fix bug in evp solver, while doing that
761    - change (improve?) discretization of stress computations for both    - change (improve?) discretization of stress computations for both
762      cgrid-lsr and evp solver      cgrid-lsr and evp solver
# Line 30  o pkg/seaice: fix bug in evp solver, whi Line 776  o pkg/seaice: fix bug in evp solver, whi
776      of evp, complete rewrite for lsr case (latter is does not yet work      of evp, complete rewrite for lsr case (latter is does not yet work
777      in all cases)      in all cases)
778  o pkg/kpp: add code to have mixing in shelf ice caverns  o pkg/kpp: add code to have mixing in shelf ice caverns
779      - add myThid to all kpp routines (long overdue)
780    
781  checkpoint59  checkpoint59
782  o pkg/exf:  o pkg/exf:
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