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revision 1.1881 by m_bates, Tue Jun 18 21:30:33 2013 UTC revision 1.1983 by mlosch, Tue Apr 29 14:23:52 2014 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/seaice: remove global variable TICE (not needed)
8      - replace by TICES or local variable where necessary (cost_seaice_test,
9        seaice_diagnostics_state)
10      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
11      - use specific read/write routines for reading and writing individual leves
12        of a multilevel field
13    o pkg/ctrl & model/inc:
14      - move additional anomaly fields of control vars (related to options:
15         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
16        from DYNVARS.h into new header file: CTRL_FIELDS.h
17    o pkg/seaice: some small modifications to the ridging code
18      - make fw2ObyRidge a global variable and add the freshwater flux to
19        seaice_growth
20      - pass actual thickness from seaice_prepare_ridging, so that it is
21        computed only in one place and compute it in the same way as in
22        seaice_growth
23      - initialise more fields in seaice_do_ridging that where cause floating
24        point exceptions over land
25    o pkg/seaice: preparations for ridging code and first real ridging code
26      - move most of "PART 1" of S/R seaice_growth into a new and separate
27        S/R seaice_reg_ridge that will both regularize the state variable after
28        advection call the actual ridging routine;
29      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
30        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
31      - remove ridging code from seaice_advdiff
32      - clean up remaining part 1 of seaice_growth in an attempt to make it
33        more readable (this is probably subjective)
34      - call seaice_itd_redist once in the initialisation phase to have the initial
35        conditions in the correct category
36      - finally: add new ridging routine for ITD code
37    
38    checkpoint64v (2014/04/11)
39    o pkg/ecco:
40      - add runtime parameters mdt[start,end]date[1,2]
41      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
42    o pkg/seaice:
43      - make deltaC a global variable, so that it can be used in ridging code
44      - first step towards ridging: introduce new routines that compute
45        ice strength based on ridging parameters
46      - add diagnostic for HSNOWITD
47      - add opnWtrFrac as a global variable (required for ridging scheme)
48    o pkg/salt_plume + pkg/seaice/seaice_growth.F
49      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
50        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
51    o verification/hs94.1x64x5:
52      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
53      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
54    o autodiff:
55      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
56        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
57        For now, only in pkgs used in verification/hs94.1x64x5.
58      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
59        which are specific to TAF/TAMC).
60      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
61        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
62        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
63      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
64        building mitgcmuv_ad (make adAll).
65    o pkg/ecco:
66      - cost_gencost_seaicev4.F:
67         reformulate proxy cost as function of sst and local param SEAICE_freeze
68         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
69      - add stop statement if old names siv4-[sst,vol] are used
70      - add snapshots + cost reports for atmospheric longwave
71      - remove factor 0.1 in front of wtau[u,v]
72      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
73         ALLOW_TMI_SST_COST_CONTRIBUTION
74    o pkg/atm_phys:
75      - add some diagnostics for Short-wave and for convection S/R.
76    o pkg/seaice/seaice_growth:
77      - fix a bug in the lateral melt parameterization for SEAICE_ITD
78        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
79      - rearrange loop order for better vector code in the same code block
80      - rewrite the floeDiameter formula to have fewer divisions
81      -  (miraculously) none of this changes the results of seaice_itd
82    o pkg/smooth:
83      - move param smooth2Ddiffnbt to pkg/ecco
84    o pkg/salt_plume:
85      - salt_plume_frac.F:
86         clean up local param names
87         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
88    o pkg/rw:
89      - add RS version of S/R READ_MFLDS_LEV.
90    o pkg/streamice:
91      - fix the restart test by writing/reading pickup_streamice files.
92    o pkg/seaice:
93      - refine checks for jfnk-related parameters
94      - comment out if statement with SEAICEuseIMEX parameter as long as there
95        is no IMEX code to avoid confusion and surprises
96    
97    checkpoint64u (2014/03/07)
98    o verification/MLAdjust:
99      - rename secondary test suffix:
100         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
101         0.leithD -> AhFlxF  + switch to flux-form
102         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
103         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
104    o pkg/mom_vecinv:
105      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
106        to be before mom_calc_visc.F)
107      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
108      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
109        this is simpler for the adjoint and for diagnostics.
110    o model/src + pkg/momentum:
111      - add input files for  2-D additional Western and Southern cell-edge wall
112         (e.g., to add "thin-wall" where it is =1).
113      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
114        using 2nd hFacZ that is computed from initial (fix domain) hFac
115      - known limitations of thin wall implementation: not yet coded for sigma
116        coords; not working with CD-scheme neither.
117    o pkg/seaice:
118      - rename recently introduced parameters from (wrong name) AB to
119        BDF (backward difference time discretisation)
120      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
121    o tools/adjoint_options:
122      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
123    
124    checkpoint64t (2014/02/01)
125    o pkg/ecco
126      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
127        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
128      - replace hard-coded record number and period which only work for monthly
129        with read-in runtime param that works for other periods (month,day,year)
130    o pkg/thsice
131      - corrected store directive fixes thsice adjoint gradient checks
132    o genmake2 & testreport:
133      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
134        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
135        Update testreport accordingly. No need to set "export OPENAD=true"
136        in adjoint_options/adjoint_oad anymore (will be removed later).
137    o pkg/shelfice:
138      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
139        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
140        so that surface forcing applies to k=kSurf if using pkg/shelfice.
141    o pkg/ctrl, pkg/grdchk, pkg/ecco:
142      - Changes to make GENARR more modular (i.e. invisible if not used)
143    o model/src/temp_integrate.F and salt_integrate.F
144      - re-include store directives that were removed on Dec 27th.
145    o model/src/external_forcing_surf.F
146      - add storage directives for EmPmR and PmEpR to avoid recomputation of
147        seaice_model in the adjoint that is problematic when seaice_model is
148        turned off in the adjoint. The resolved issue dated back to July when
149        EXTERNAL_FORCING_SURF call was moved.
150        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
151    o pkg/exf/exf_check.F
152      - fix a small bug again (originally found by Wentao Liu, now found again)
153      - streamline error output
154    o pkg/streamice and aim_v23:
155      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
156        Apple's /usr/bin/cpp knows what to do:
157        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
158        Target: x86_64-apple-darwin13.0.0
159    
160    checkpoint64s (2014/01/05)
161    o tools/adjoint_options:
162      - switch to fastopt.net TAF server (instead of default fastopt.de) for
163        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
164    o model/src:
165      - remove some unnecessary TAF storage directives in forward_step.F and
166        in dynamics.F (note: not always removed by TAF, e.g., double storage
167        of kappaRU,kappaRV in former version of dynamics.F).
168    o model/src & pkg/ptracers:
169      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
170        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
171        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
172      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
173      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
174      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
175    o useSingleCpuInput separates single-CPU input from single-CPU output;
176        for now only implemented for in exf_interp_read.F
177    o verification/advect_xy:
178      - fix missing EXCH call in local version of ini_salt.F and update output.
179    o momentum diagnostics:
180      - fix which deltaT is used in Total-Tendency diagnostics.
181      - fix typo in diagnostics for momentum tendency from AB.
182    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
183        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
184    
185    checkpoint64r (2013/12/08)
186    o verification/*/results:
187      - Update reference output of experiments that were passing with just 13 digits
188         (make it easier to detect future changes in results)
189    o model/src & pkg/ptracers:
190      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
191        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
192        to inside ptracers_integrate.F ; remove ptracers_advection.F
193    o coupling interface pkgs:
194        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
195      - change the config check to test the agreement of Ocean Depth
196        with ATM land/sea mask (instead of ATM orography);
197      - send to coupler the number of coupler time-steps to do for this run:
198        this allows to check for consistency and don't need anymore to be
199        specified in parameter file "data";
200      in coupler:
201      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
202      - improve report to log-file of config setting (pass log-file unit to few S/R)
203    o pkg/compon_communic:
204      - add coupling send/receive for non-tiled integer vector;
205      - add S/R to check and stop if any proc has an error (similar to
206        eesupp/src/stop_if_error.F but single thread and across Comm_World).
207    o pkg/exch2:
208      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
209        through list of all tiles my proc owns.
210    o model/src:
211      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
212        from rTrans) to simplify dependencies (no need to store rTrans anymore in
213        calling S/R); this affects AD results at machine truncation level:
214        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
215        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
216    o tools/build_options:
217      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
218    o coupling interface pkgs:
219        [compon_communic, atm_compon_interf & ocn_compon_interf]
220      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
221        to each S/R that needs it; remove un-used variables.
222      - change component tile registration (cpl_register.F in both compon_interf
223        and mitcomponent_tile_register.F) to pass the full list of tiles
224        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
225      - with pkg/exch2: adopt the same convention used for I/O to define mapping
226        towards coupler global array (unless W2_useE2ioLayOut=F):
227         a) can now use different tiling between atm & ocn comp.
228         b) no needs to modify the run-Off map when changing tiling (was needed
229            even if using the same tiling between atm & ocn).
230         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
231            full land tiles); not yet tested.
232      - check for valid mapping from comp. tile to coupler global array
233      - improve report of tile registration results to log file.
234    o pkg/exch2:
235      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
236        tile-registration (CPL_REGISTER);
237      - activate (un-comment) definition and setting of "W2_tileIndex" list to
238        store the local bi,bj indices of each tile;
239      - also print bi,bj in local report to log file;
240      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
241        Jun 2009 modif of pkg/exch2).
242    o testing on baudelaire:
243      - run 2 tests at a time: no significant slow down (since enough cpu) and
244        get the full set of test done earlier
245      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
246    o model/src/thermodynamics.F and routines called from it:
247      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
248        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
249        velocity (outp) by adding bolus velocity.
250      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
251        mass transport from velocity + lateral grid cell area
252      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
253      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
254     in thermodynamics.F
255      - remove k from thermodynamics.F and move it to temp_integrate.F
256        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
257        loop).
258      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
259        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
260        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
261        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
262      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
263        global_ocean.90x40x15, tutorial_global_oce_biogeo and
264        tutorial_tracer_adjsens (+ TLM output).
265    o tools/OAD_support and (verification/*/) code_oad:
266      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
267        module conversion ; remove unneeded CPP_EEOPTIONS.h.
268      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
269        version (closer to model/inc/CPP_OPTIONS.h).
270    o model/src:
271      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
272        retired list of parameters (routine FREEZE has been replace by surface
273        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
274    o pkg/gmredi:
275      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
276        velocity (same scheme but affects machine truncation) for GM_AdvForm.
277      - update output of FWD experiments: front_relax.bvp,
278        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
279    
280    checkpoint64q (2013/11/17)
281    o verification:
282      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
283        tutorial_global_oce_biogeo and global_ocean.90x40x15.
284      - generate new output (growth & melt) for seaice_itd experiment after
285        updating the input pickup_seaice files (previously wrong).
286    o pkg/cost:
287      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
288        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
289        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
290          cannot be applied to var in common block).
291        o allows to get results independent of tile-per-proc setting (if using
292          slower GLOBAL_SUM_SEND_RECV option).
293      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
294        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
295        forward gradients: update output).
296      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
297        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
298    o pkg/mom_common:
299      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
300        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
301        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
302        ensure that all field value that are used are set.
303    o tutorial_deep_convection (smag3d):
304      - add missing scaling in mom_calc_smag_3d.F;
305      - set smag3D_coeff in input.smag3d such that results do not change.
306    o pkg/dic:
307      - change dic_cost.F to compute cost on each tile first and then apply
308        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
309        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
310      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
311    o eesupp/src & pkg/mdsio:
312      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
313        (from pkg/mdsio) since they are no longer used for tape IO.
314      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
315        (+ keep a copy in pkg/atm_ocn_coupler).
316    o verification/isomip:
317      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
318    o tools/build_options:
319      - optfile linux_amd64_ifort11, fast (no ieee) case:
320        to get a working restart for all experiments, add "-fp-model source"
321        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
322    
323    checkpoint64p (2013/10/20)
324    o pkg/autodiff:
325      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
326        criteria, return to simple (default) tape IO format.
327    o pkg/mdsio (+ eesupp/src):
328      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
329        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
330      - fix globalFile and singleCpuIO options using simpler global mapping.
331      - new pairs of scatter/gather vector S/R (one for each type, generated from
332        template) corresponding to simpler global mapping.
333      - adread_write.F: switch to new S/R (but leave old calls commented) and write
334        to globalFile when parameter globalFiles is set to True.
335      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
336    o pkg/autodiff:
337      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
338        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
339        missing, just add a STOP if array type do not match.
340    o pkg/exf:
341      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
342         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
343         and rename array obsSIce to exf_iceFraction.
344    o tutorial_deep_convection:
345      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
346        for now all in this exp. code dir.
347      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
348        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
349    o eesupp/src:
350      - added SINGLE_DISK_IO option because reading of parameter files on
351        very large number of processors did not work with existing set-up
352    
353    checkpoint64o (2013/09/25)
354    o pkg/atm_phys & atm_compon_interf:
355      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
356    o tools/build_options:
357      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
358        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
359        remove CPP setting (was identical to genmake2 default).
360    o pkg/gmredi & model/src: Some updating and work done on the residual model.
361      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
362      - fixed up the calculation of the eddy stress and how it is added to the
363        external forcing via taueddy_external_forcing.F
364      - at the moment, it is very experimental and only works with the variable eddy
365        diffusivity calculated in gmredi_k3d.F
366    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
367        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
368    o testreport (& tools/do_tst_2+2):
369      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
370    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
371      - remove CPP='cpp -traditional -P' (this is genmake2 default)
372      - add switch (for big setups) to use 'medium' memory-model (but leave it
373        commented out for now). Note: needed with FC 19 to compile big setups.
374    o pkg/atm_compon_interf:
375      - regroup per field origin (model & pkgs) the coupling storage routines
376         (which accumalate in time each coupling field)
377      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
378        update accordingly + simplify aim_do_physics.F
379    
380    checkpoint64n (2013/08/26)
381    o pkg/bbl:
382      - update formulation to reduce dispersion of tracer properties in bbl
383      - replaced horizontal and vertical transport parameters with velocities
384      - changes results for verification/global_with_exf.yearly
385    o verification/halfpipe_streamice:
386      - change to matrix construction; update both Fwd & AD output.
387    o verification/tutorial_tracer_adjsens:
388      - OpenAD test: switch to vector-invariant momentum since fluxform with
389        rStar causes problems with OpenAD; update output.
390    o tools:
391      - genmake2: define a common prefix for all temp-file names ; move them
392        to local /tmp disk (but would be easy to move them back);
393      - xmakedepend: apply the same switch for temp-files.
394    o pkg/offline:
395      - changes for use with rStar (NLFS): assume that we continue to provide
396        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
397        output files) and apply r* scaling at each time-step (function of the time
398        varying Eta field); use normal pickup files (needed for restart with NLFS).
399    o adjoint with OpenAD:
400      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
401        package openad.  This package has to be compiled for all runs with OpenAD
402        instead of specifying code_oad_all as a modification directory.
403      - link the fortran templates from tools/OAD_support to the build directory
404        for preprocessing to avoid conflicts between different setups compiled
405        simultaneously and simplify cleanup.
406    o pkg/exf:
407      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
408        main model or other pkgs are exchanged in EXF_MAPFIELDS).
409    o model/src:
410      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
411        (similar to do_fields_blocking_exchanges.F).
412    o tools/genmake2:
413      - remove TAF output src code just before calling staf (when not doing a fresh
414        built, will stop if things go wrong with staf).
415      - fix target "adobj" (left from TAF version-2 transition)
416    o pkg/diagnostics:
417      - add a parameter to track the status of pkg/diagnostics activation;
418        this replace/extend the use of logical param "settingDiags" (to check
419        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
420        New S/R to print error message and stop when pkgStatus is not right.
421      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
422    
423    checkpoint64m (2013/08/13)
424    o model/inc:
425      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
426        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
427    o pkg/kpp & aim_v23:
428      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
429    o pkg/seaice:
430      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
431        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
432      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
433    o eesupp/src:
434      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
435        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
436    o switch to TAF version-2:
437      - add flow directives to "freeze" naming convention for ad-routines that
438        are used in I/O routines of adjoint state and associated common blocks
439        that are used in adcommon.h (backward compatible with version-1)
440      - update all ad-optfiles (in tools/adjoint_options + few local to some
441        verification exp) to switch to latest TAF version (currently 2.5.5);
442        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
443        out except for diva).
444      - the major change with TAF version-2 is that both the differentiated
445        routines and the forward routines (new) are returned as part of the TAF
446        output source code. Update genmake2 accordingly.
447      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
448        with version-2 when compared to TLM or FWD gradient); other experiments
449        output show minor changes (machine truncation level); update the few AD &
450        TLM output with 12 matching digits only (some prior to version-2 switch).
451    
452    checkpoint64l (2013/08/05)
453    o model/src:
454      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
455      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
456        when using TAF but only if using OpenAD.
457    o pkg/mom_common+fluxform+vecinv:
458      - always set horiz. viscosity arrays to background value before calling
459        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
460        only when using variable horiz. viscosity (useVariableVisc=T);
461      - simplify mom_vecinv.F (only 1 block for momViscosity).
462    o pkg/mom_common: variable horiz. viscosity in NH code
463      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
464        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
465      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
466        useBiharmonicVisc & useVariableVisc.
467      - fix old bug (already in 1rst implementation of variable horizontal viscosity
468        in calc_gw.F, version 1.27, 2006/06/20):
469        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
470        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
471      - change background horiz viscosity in vertical momentum (gW) to always be
472        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
473        any type of variable viscosity, e.g., viscAh/4Grid)
474      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
475        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
476        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
477        default viscAh,viscA4 is zero).
478    o model/src:
479      - extend length of drC & recip_drC from Nr to Nr+1.
480    o Divided Adjoint (DIVA) with MPI:
481      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
482      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
483        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
484    
485    checkpoint64k (2013/07/23)
486    o tools/OAD_support:
487      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
488        and remove it from genmake2.
489    o tools/build_options:
490      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
491        MPI_HEADER_FILES list (let genmake2 find the missing headers)
492    o verification/halfpipe_streamice:
493      - change to driving stress formulation; update both Fwd & AD output.
494    o tools/genmake2 and Divided Adjoint with MPI:
495      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
496      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
497      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
498        Makefile, which is set by genmake2, and check which mpi-headers are needed.
499        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
500      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
501    o testreport:
502      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
503        perform additional runs (number of additional runs is "add_DIVA_runs" taken
504        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
505    o verification/lab_sea (AD test):
506      - change to test Divided Adjoint Run in this set-up (both standard AD test
507        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
508    o pkg atm_ & ocn_compon_interf:
509      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
510        staggerTimeStep implementation) and disable (retired) corresponding
511        parameter.
512    o pkg/offline:
513      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
514      - add S/R OFFLINE_CHECK to print offline parameter summary
515        and stop if loading a file that is not used;
516      - enable to calculate GMRedi tensor, KPP mixing and convective index
517        when the corresponding file(s) is/are not specified (but pkg is used).
518      - comment out resetting of monitorFreq (to endTime) since it still useful
519        for monitoring CFL numbers and checking offline fields.
520    o OpenAD:
521      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
522        smaller standard output) and generate new (smaller) output (on baudelaire
523        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
524    o model/src:
525      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
526        (where external_forcing_adjust was called) and change list of arguments;
527      - merge external_forcing_adjust.F into external_forcing_surf.F
528      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
529        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
530        previously in file "balance_relax.F", now removed); remove corresponding
531        arrays in FFIELDS.h.
532      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
533        a hack for getting back surfaceForcingS (loaded from file) when using
534        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
535      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
536        (was getting only 11 digits for AD-grad, due to different truncation
537         error in AD code).
538    
539    checkpoint64j (2013/07/04)
540    o pkg/offline:
541      - to enable the use of other features with pkg offline (e.g., obcs),
542        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
543      - comment out "allowFreezing" (now active) in 2 offline testing exp.
544    o pkg/exf ALLOW_RUNOFTEMP
545      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
546      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
547      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
548    o pkg/atm_phys:
549      - allows to add some damping on uVel,vVel (strength only function of k).
550    o verification, ad-tests:
551      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
552        global_ocean_ebm and offline_exf_seaice.thsice.
553    o verification/halfpipe_streamice:
554      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
555        flux input boundary conditions to be ignored; a fix for this bug changed
556        verification results for forward test.
557      - add adjoint test.
558    o pkg/ptracers:
559      - allow to restart without SOM pickup (resetting SOM to zero).
560    o pkg/gmredi:
561      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
562      - It uses mixing length theory and suppression by steering level effects to
563        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
564        to JPO, for more details).
565      - It also uses the diffusivity to calculate an eddy induced streamfunction
566        based on a PV closure (rather than a buoyancy closure as in GM).
567      - New files added to pkg/gmredi:
568        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
569          induced overturning streamfunction (called from gmredi_calc_tensor)
570        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
571          for use in gmredi_k3d
572        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
573          the eddy diffusivity
574    
575  checkpoint64i (2013/06/18)  checkpoint64i (2013/06/18)
576  o pkg/cheapaml:  o pkg/cheapaml:
# Line 40  o pkg/cfc: Line 607  o pkg/cfc:
607      atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.      atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
608    - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf    - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
609    - new routine to print summary of CFC params and check for consistency.    - new routine to print summary of CFC params and check for consistency.
610    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
611      similar to thsice_advdiff.
612      Note that for the B-grid case the routine parameters uc/vc are overwritten.
613  o pkg/cfc:  o pkg/cfc:
614    - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);    - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
615      update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.      update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
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