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revision 1.1860 by mlosch, Wed May 1 09:20:10 2013 UTC revision 1.2012 by mlosch, Fri Jun 27 14:37:03 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
8      - remove unnecessary u/vTmp from subroutine call of
9        seaice_lsr_tridiagu/v
10      - remove some store directives and add new ones in an effort to get
11        finally rid off the recomputation warnings. This is successful
12        for SEAICE_VECTORIZE_LSR defined (i.e. no extensive recomputation
13        warnings left), but there are still too many recomputations on the
14        solver iteration level
15      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
16        SEAICE_SIZE.h
17      - add a store directive in S/R seaice_calc_viscosities
18    o pkg/seaice (ITD code):
19      - fix definition of Hlimit for multi-threaded case
20      - use double precision arithmetic to compute Hlimit: this affects results;
21        update output of experiment seaice_itd.
22    o replace content of verification/seaice_itd
23      - instead of a 1D column use the configuration of offline_exf_seaice
24        to test the ice thickness distribution code with ridging
25      - this is a first shot at this experiment
26      - change of some defaults of ridging parameters SEAICEhStar (from
27        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
28        and lot of new comments.
29    
30    checkpoint64y (2014/06/20)
31    o pkg/seaice/seaice_reg_ridge.F:
32      - modify the regularization of very small volumes of ice; only check
33        total volume HEFF, and do not apply correction to individual ice
34        classes because that leads to funny patterns in the heat and fw-fluxes
35        into the ocean. Adjust seaice_itd/results/output.txt
36      - replace nITD by SEAICE_multDim in loop-ranges
37    o pkg/exf:
38      - add code to process the case field period = -12. with UV interpolation.
39      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
40        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
41    o verification/global_with_exf:
42      - switch all fields period to -12. (was previously untested) in input/data.exf
43        (but keep secondary test ".yearly" unchanged); update the reference output.
44    o pkg/cal:
45      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
46    o pkg/exf:
47      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
48        to replace logical switch "exf_verbose"
49      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
50    o pkg/sbo:
51      - update from Katherine Quinn: evaluate mass directly from density and SSH
52        (budget using Finite Volume method) instead of from bottom pressure.
53      - allow testreport to collect few selected SBO output ; tested in exp.
54        global_ocean.90x40x15 (after updating the results, to include SBO output).
55      - fix some multi-threading issues (in output part).
56    o model/src & most packages:
57      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
58      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
59        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
60        "data.{pkg}" exist ; and leave the S/R (return) just after.
61      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
62        + call LAND_READPARMS from packages_readparms.F
63    o pkg/seaice:
64      - remove code that resets useThSice in S/R seaice_readparms and
65        replace it by a warning in S/R seaice_check
66      - remove parameter MULTDIM, replace with nITD and runtime
67        parameter SEAICE_multDim (still hard-wired to nITD if
68        SEAICE_ITD is defined)
69    
70    checkpoint64x (2014/05/24)
71    o verification/lab_sea:
72      - update adjoint and TLM output following changes to pkg/salt_plume
73      - un-do the update after putting back local recip_Cp in few places.
74    o pkg/salt_plume: modifications by An Nguyen:
75      - add capability to do brine rejection (salt-plume) as function of
76        volume+tracers (instead of only salinity tracer).
77      - conserve volume by exchanging volume from each kLev to above to
78        accommodate in-coming brine volume
79      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
80      - switch KPP surf buoyancy due to brine forcing to 3-d
81        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
82      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
83      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
84        in East/West Arctic.
85    o pkg/sbo:
86      - incorporate modifications from Katherine Quinn to enable the use of sbo
87        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
88        output for future testreport verification (unfinished).
89    o pkg/atm_phys:
90      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
91        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
92        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
93    o pkg/seaice
94      seaice_calc_ice_strength.F: modify expression to avoid divisions
95        (affects truncation)
96      seaice_do_ridging.F: clean up the insectarium
97      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
98      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
99      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
100      - add some debugging information and error messages (warnings)
101    o model/src: modifications relatd to atmosphere p*:
102      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
103      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
104        of vertical profile tRef in geopotential background and anomaly.
105      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
106        and pkg/atm_phys.
107      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
108        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
109    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
110    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
111        not used right now, but can be used in BGC packages to fix conservation.
112    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
113        other packages too.
114    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
115        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
116    o model/src:
117      - since we have several heat capacity (even in model/src), define "recip_Cp"
118        as local variable (no longer in common block) to avoid any confusion.
119      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
120    o pkg/exf:
121      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
122        air density as function of air Temp, Humidity and atm pressure.
123    
124    checkpoint64w (2014/05/02)
125    o verification:
126      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
127        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
128        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
129        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
130        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
131    o model/src: for atmosphere in p* coords:
132      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
133      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
134        but not yet activated.
135    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
136      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
137      - this changes the results (but not for any verification experiment, because
138        none tests this), but avoids having an extra field in the restart files
139    o pkg/seaice: remove global variable TICE (not needed)
140      - replace by TICES or local variable where necessary (cost_seaice_test,
141        seaice_diagnostics_state)
142      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
143      - use specific read/write routines for reading and writing individual leves
144        of a multilevel field
145    o pkg/ctrl & model/inc:
146      - move additional anomaly fields of control vars (related to options:
147         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
148        from DYNVARS.h into new header file: CTRL_FIELDS.h
149    o pkg/seaice: some small modifications to the ridging code
150      - make fw2ObyRidge a global variable and add the freshwater flux to
151        seaice_growth
152      - pass actual thickness from seaice_prepare_ridging, so that it is
153        computed only in one place and compute it in the same way as in
154        seaice_growth
155      - initialise more fields in seaice_do_ridging that where cause floating
156        point exceptions over land
157    o pkg/seaice: preparations for ridging code and first real ridging code
158      - move most of "PART 1" of S/R seaice_growth into a new and separate
159        S/R seaice_reg_ridge that will both regularize the state variable after
160        advection call the actual ridging routine;
161      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
162        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
163      - remove ridging code from seaice_advdiff
164      - clean up remaining part 1 of seaice_growth in an attempt to make it
165        more readable (this is probably subjective)
166      - call seaice_itd_redist once in the initialisation phase to have the initial
167        conditions in the correct category
168      - finally: add new ridging routine for ITD code
169    
170    checkpoint64v (2014/04/11)
171    o pkg/ecco:
172      - add runtime parameters mdt[start,end]date[1,2]
173      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
174    o pkg/seaice:
175      - make deltaC a global variable, so that it can be used in ridging code
176      - first step towards ridging: introduce new routines that compute
177        ice strength based on ridging parameters
178      - add diagnostic for HSNOWITD
179      - add opnWtrFrac as a global variable (required for ridging scheme)
180    o pkg/salt_plume + pkg/seaice/seaice_growth.F
181      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
182        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
183    o verification/hs94.1x64x5:
184      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
185      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
186    o autodiff:
187      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
188        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
189        For now, only in pkgs used in verification/hs94.1x64x5.
190      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
191        which are specific to TAF/TAMC).
192      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
193        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
194        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
195      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
196        building mitgcmuv_ad (make adAll).
197    o pkg/ecco:
198      - cost_gencost_seaicev4.F:
199         reformulate proxy cost as function of sst and local param SEAICE_freeze
200         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
201      - add stop statement if old names siv4-[sst,vol] are used
202      - add snapshots + cost reports for atmospheric longwave
203      - remove factor 0.1 in front of wtau[u,v]
204      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
205         ALLOW_TMI_SST_COST_CONTRIBUTION
206    o pkg/atm_phys:
207      - add some diagnostics for Short-wave and for convection S/R.
208    o pkg/seaice/seaice_growth:
209      - fix a bug in the lateral melt parameterization for SEAICE_ITD
210        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
211      - rearrange loop order for better vector code in the same code block
212      - rewrite the floeDiameter formula to have fewer divisions
213      -  (miraculously) none of this changes the results of seaice_itd
214    o pkg/smooth:
215      - move param smooth2Ddiffnbt to pkg/ecco
216    o pkg/salt_plume:
217      - salt_plume_frac.F:
218         clean up local param names
219         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
220    o pkg/rw:
221      - add RS version of S/R READ_MFLDS_LEV.
222    o pkg/streamice:
223      - fix the restart test by writing/reading pickup_streamice files.
224    o pkg/seaice:
225      - refine checks for jfnk-related parameters
226      - comment out if statement with SEAICEuseIMEX parameter as long as there
227        is no IMEX code to avoid confusion and surprises
228    
229    checkpoint64u (2014/03/07)
230    o verification/MLAdjust:
231      - rename secondary test suffix:
232         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
233         0.leithD -> AhFlxF  + switch to flux-form
234         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
235         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
236    o pkg/mom_vecinv:
237      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
238        to be before mom_calc_visc.F)
239      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
240      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
241        this is simpler for the adjoint and for diagnostics.
242    o model/src + pkg/momentum:
243      - add input files for  2-D additional Western and Southern cell-edge wall
244         (e.g., to add "thin-wall" where it is =1).
245      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
246        using 2nd hFacZ that is computed from initial (fix domain) hFac
247      - known limitations of thin wall implementation: not yet coded for sigma
248        coords; not working with CD-scheme neither.
249    o pkg/seaice:
250      - rename recently introduced parameters from (wrong name) AB to
251        BDF (backward difference time discretisation)
252      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
253    o tools/adjoint_options:
254      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
255    
256    checkpoint64t (2014/02/01)
257    o pkg/ecco
258      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
259        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
260      - replace hard-coded record number and period which only work for monthly
261        with read-in runtime param that works for other periods (month,day,year)
262    o pkg/thsice
263      - corrected store directive fixes thsice adjoint gradient checks
264    o genmake2 & testreport:
265      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
266        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
267        Update testreport accordingly. No need to set "export OPENAD=true"
268        in adjoint_options/adjoint_oad anymore (will be removed later).
269    o pkg/shelfice:
270      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
271        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
272        so that surface forcing applies to k=kSurf if using pkg/shelfice.
273    o pkg/ctrl, pkg/grdchk, pkg/ecco:
274      - Changes to make GENARR more modular (i.e. invisible if not used)
275    o model/src/temp_integrate.F and salt_integrate.F
276      - re-include store directives that were removed on Dec 27th.
277    o model/src/external_forcing_surf.F
278      - add storage directives for EmPmR and PmEpR to avoid recomputation of
279        seaice_model in the adjoint that is problematic when seaice_model is
280        turned off in the adjoint. The resolved issue dated back to July when
281        EXTERNAL_FORCING_SURF call was moved.
282        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
283    o pkg/exf/exf_check.F
284      - fix a small bug again (originally found by Wentao Liu, now found again)
285      - streamline error output
286    o pkg/streamice and aim_v23:
287      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
288        Apple's /usr/bin/cpp knows what to do:
289        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
290        Target: x86_64-apple-darwin13.0.0
291    
292    checkpoint64s (2014/01/05)
293    o tools/adjoint_options:
294      - switch to fastopt.net TAF server (instead of default fastopt.de) for
295        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
296    o model/src:
297      - remove some unnecessary TAF storage directives in forward_step.F and
298        in dynamics.F (note: not always removed by TAF, e.g., double storage
299        of kappaRU,kappaRV in former version of dynamics.F).
300    o model/src & pkg/ptracers:
301      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
302        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
303        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
304      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
305      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
306      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
307    o useSingleCpuInput separates single-CPU input from single-CPU output;
308        for now only implemented for in exf_interp_read.F
309    o verification/advect_xy:
310      - fix missing EXCH call in local version of ini_salt.F and update output.
311    o momentum diagnostics:
312      - fix which deltaT is used in Total-Tendency diagnostics.
313      - fix typo in diagnostics for momentum tendency from AB.
314    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
315        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
316    
317    checkpoint64r (2013/12/08)
318    o verification/*/results:
319      - Update reference output of experiments that were passing with just 13 digits
320         (make it easier to detect future changes in results)
321    o model/src & pkg/ptracers:
322      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
323        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
324        to inside ptracers_integrate.F ; remove ptracers_advection.F
325    o coupling interface pkgs:
326        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
327      - change the config check to test the agreement of Ocean Depth
328        with ATM land/sea mask (instead of ATM orography);
329      - send to coupler the number of coupler time-steps to do for this run:
330        this allows to check for consistency and don't need anymore to be
331        specified in parameter file "data";
332      in coupler:
333      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
334      - improve report to log-file of config setting (pass log-file unit to few S/R)
335    o pkg/compon_communic:
336      - add coupling send/receive for non-tiled integer vector;
337      - add S/R to check and stop if any proc has an error (similar to
338        eesupp/src/stop_if_error.F but single thread and across Comm_World).
339    o pkg/exch2:
340      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
341        through list of all tiles my proc owns.
342    o model/src:
343      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
344        from rTrans) to simplify dependencies (no need to store rTrans anymore in
345        calling S/R); this affects AD results at machine truncation level:
346        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
347        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
348    o tools/build_options:
349      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
350    o coupling interface pkgs:
351        [compon_communic, atm_compon_interf & ocn_compon_interf]
352      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
353        to each S/R that needs it; remove un-used variables.
354      - change component tile registration (cpl_register.F in both compon_interf
355        and mitcomponent_tile_register.F) to pass the full list of tiles
356        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
357      - with pkg/exch2: adopt the same convention used for I/O to define mapping
358        towards coupler global array (unless W2_useE2ioLayOut=F):
359         a) can now use different tiling between atm & ocn comp.
360         b) no needs to modify the run-Off map when changing tiling (was needed
361            even if using the same tiling between atm & ocn).
362         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
363            full land tiles); not yet tested.
364      - check for valid mapping from comp. tile to coupler global array
365      - improve report of tile registration results to log file.
366    o pkg/exch2:
367      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
368        tile-registration (CPL_REGISTER);
369      - activate (un-comment) definition and setting of "W2_tileIndex" list to
370        store the local bi,bj indices of each tile;
371      - also print bi,bj in local report to log file;
372      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
373        Jun 2009 modif of pkg/exch2).
374    o testing on baudelaire:
375      - run 2 tests at a time: no significant slow down (since enough cpu) and
376        get the full set of test done earlier
377      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
378    o model/src/thermodynamics.F and routines called from it:
379      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
380        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
381        velocity (outp) by adding bolus velocity.
382      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
383        mass transport from velocity + lateral grid cell area
384      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
385      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
386     in thermodynamics.F
387      - remove k from thermodynamics.F and move it to temp_integrate.F
388        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
389        loop).
390      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
391        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
392        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
393        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
394      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
395        global_ocean.90x40x15, tutorial_global_oce_biogeo and
396        tutorial_tracer_adjsens (+ TLM output).
397    o tools/OAD_support and (verification/*/) code_oad:
398      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
399        module conversion ; remove unneeded CPP_EEOPTIONS.h.
400      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
401        version (closer to model/inc/CPP_OPTIONS.h).
402    o model/src:
403      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
404        retired list of parameters (routine FREEZE has been replace by surface
405        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
406    o pkg/gmredi:
407      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
408        velocity (same scheme but affects machine truncation) for GM_AdvForm.
409      - update output of FWD experiments: front_relax.bvp,
410        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
411    
412    checkpoint64q (2013/11/17)
413    o verification:
414      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
415        tutorial_global_oce_biogeo and global_ocean.90x40x15.
416      - generate new output (growth & melt) for seaice_itd experiment after
417        updating the input pickup_seaice files (previously wrong).
418    o pkg/cost:
419      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
420        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
421        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
422          cannot be applied to var in common block).
423        o allows to get results independent of tile-per-proc setting (if using
424          slower GLOBAL_SUM_SEND_RECV option).
425      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
426        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
427        forward gradients: update output).
428      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
429        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
430    o pkg/mom_common:
431      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
432        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
433        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
434        ensure that all field value that are used are set.
435    o tutorial_deep_convection (smag3d):
436      - add missing scaling in mom_calc_smag_3d.F;
437      - set smag3D_coeff in input.smag3d such that results do not change.
438    o pkg/dic:
439      - change dic_cost.F to compute cost on each tile first and then apply
440        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
441        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
442      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
443    o eesupp/src & pkg/mdsio:
444      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
445        (from pkg/mdsio) since they are no longer used for tape IO.
446      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
447        (+ keep a copy in pkg/atm_ocn_coupler).
448    o verification/isomip:
449      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
450    o tools/build_options:
451      - optfile linux_amd64_ifort11, fast (no ieee) case:
452        to get a working restart for all experiments, add "-fp-model source"
453        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
454    
455    checkpoint64p (2013/10/20)
456    o pkg/autodiff:
457      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
458        criteria, return to simple (default) tape IO format.
459    o pkg/mdsio (+ eesupp/src):
460      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
461        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
462      - fix globalFile and singleCpuIO options using simpler global mapping.
463      - new pairs of scatter/gather vector S/R (one for each type, generated from
464        template) corresponding to simpler global mapping.
465      - adread_write.F: switch to new S/R (but leave old calls commented) and write
466        to globalFile when parameter globalFiles is set to True.
467      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
468    o pkg/autodiff:
469      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
470        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
471        missing, just add a STOP if array type do not match.
472    o pkg/exf:
473      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
474         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
475         and rename array obsSIce to exf_iceFraction.
476    o tutorial_deep_convection:
477      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
478        for now all in this exp. code dir.
479      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
480        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
481    o eesupp/src:
482      - added SINGLE_DISK_IO option because reading of parameter files on
483        very large number of processors did not work with existing set-up
484    
485    checkpoint64o (2013/09/25)
486    o pkg/atm_phys & atm_compon_interf:
487      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
488    o tools/build_options:
489      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
490        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
491        remove CPP setting (was identical to genmake2 default).
492    o pkg/gmredi & model/src: Some updating and work done on the residual model.
493      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
494      - fixed up the calculation of the eddy stress and how it is added to the
495        external forcing via taueddy_external_forcing.F
496      - at the moment, it is very experimental and only works with the variable eddy
497        diffusivity calculated in gmredi_k3d.F
498    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
499        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
500    o testreport (& tools/do_tst_2+2):
501      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
502    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
503      - remove CPP='cpp -traditional -P' (this is genmake2 default)
504      - add switch (for big setups) to use 'medium' memory-model (but leave it
505        commented out for now). Note: needed with FC 19 to compile big setups.
506    o pkg/atm_compon_interf:
507      - regroup per field origin (model & pkgs) the coupling storage routines
508         (which accumalate in time each coupling field)
509      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
510        update accordingly + simplify aim_do_physics.F
511    
512    checkpoint64n (2013/08/26)
513    o pkg/bbl:
514      - update formulation to reduce dispersion of tracer properties in bbl
515      - replaced horizontal and vertical transport parameters with velocities
516      - changes results for verification/global_with_exf.yearly
517    o verification/halfpipe_streamice:
518      - change to matrix construction; update both Fwd & AD output.
519    o verification/tutorial_tracer_adjsens:
520      - OpenAD test: switch to vector-invariant momentum since fluxform with
521        rStar causes problems with OpenAD; update output.
522    o tools:
523      - genmake2: define a common prefix for all temp-file names ; move them
524        to local /tmp disk (but would be easy to move them back);
525      - xmakedepend: apply the same switch for temp-files.
526    o pkg/offline:
527      - changes for use with rStar (NLFS): assume that we continue to provide
528        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
529        output files) and apply r* scaling at each time-step (function of the time
530        varying Eta field); use normal pickup files (needed for restart with NLFS).
531    o adjoint with OpenAD:
532      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
533        package openad.  This package has to be compiled for all runs with OpenAD
534        instead of specifying code_oad_all as a modification directory.
535      - link the fortran templates from tools/OAD_support to the build directory
536        for preprocessing to avoid conflicts between different setups compiled
537        simultaneously and simplify cleanup.
538    o pkg/exf:
539      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
540        main model or other pkgs are exchanged in EXF_MAPFIELDS).
541    o model/src:
542      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
543        (similar to do_fields_blocking_exchanges.F).
544    o tools/genmake2:
545      - remove TAF output src code just before calling staf (when not doing a fresh
546        built, will stop if things go wrong with staf).
547      - fix target "adobj" (left from TAF version-2 transition)
548    o pkg/diagnostics:
549      - add a parameter to track the status of pkg/diagnostics activation;
550        this replace/extend the use of logical param "settingDiags" (to check
551        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
552        New S/R to print error message and stop when pkgStatus is not right.
553      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
554    
555    checkpoint64m (2013/08/13)
556    o model/inc:
557      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
558        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
559    o pkg/kpp & aim_v23:
560      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
561    o pkg/seaice:
562      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
563        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
564      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
565    o eesupp/src:
566      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
567        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
568    o switch to TAF version-2:
569      - add flow directives to "freeze" naming convention for ad-routines that
570        are used in I/O routines of adjoint state and associated common blocks
571        that are used in adcommon.h (backward compatible with version-1)
572      - update all ad-optfiles (in tools/adjoint_options + few local to some
573        verification exp) to switch to latest TAF version (currently 2.5.5);
574        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
575        out except for diva).
576      - the major change with TAF version-2 is that both the differentiated
577        routines and the forward routines (new) are returned as part of the TAF
578        output source code. Update genmake2 accordingly.
579      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
580        with version-2 when compared to TLM or FWD gradient); other experiments
581        output show minor changes (machine truncation level); update the few AD &
582        TLM output with 12 matching digits only (some prior to version-2 switch).
583    
584    checkpoint64l (2013/08/05)
585    o model/src:
586      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
587      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
588        when using TAF but only if using OpenAD.
589    o pkg/mom_common+fluxform+vecinv:
590      - always set horiz. viscosity arrays to background value before calling
591        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
592        only when using variable horiz. viscosity (useVariableVisc=T);
593      - simplify mom_vecinv.F (only 1 block for momViscosity).
594    o pkg/mom_common: variable horiz. viscosity in NH code
595      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
596        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
597      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
598        useBiharmonicVisc & useVariableVisc.
599      - fix old bug (already in 1rst implementation of variable horizontal viscosity
600        in calc_gw.F, version 1.27, 2006/06/20):
601        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
602        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
603      - change background horiz viscosity in vertical momentum (gW) to always be
604        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
605        any type of variable viscosity, e.g., viscAh/4Grid)
606      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
607        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
608        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
609        default viscAh,viscA4 is zero).
610    o model/src:
611      - extend length of drC & recip_drC from Nr to Nr+1.
612    o Divided Adjoint (DIVA) with MPI:
613      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
614      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
615        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
616    
617    checkpoint64k (2013/07/23)
618    o tools/OAD_support:
619      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
620        and remove it from genmake2.
621    o tools/build_options:
622      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
623        MPI_HEADER_FILES list (let genmake2 find the missing headers)
624    o verification/halfpipe_streamice:
625      - change to driving stress formulation; update both Fwd & AD output.
626    o tools/genmake2 and Divided Adjoint with MPI:
627      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
628      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
629      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
630        Makefile, which is set by genmake2, and check which mpi-headers are needed.
631        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
632      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
633    o testreport:
634      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
635        perform additional runs (number of additional runs is "add_DIVA_runs" taken
636        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
637    o verification/lab_sea (AD test):
638      - change to test Divided Adjoint Run in this set-up (both standard AD test
639        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
640    o pkg atm_ & ocn_compon_interf:
641      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
642        staggerTimeStep implementation) and disable (retired) corresponding
643        parameter.
644    o pkg/offline:
645      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
646      - add S/R OFFLINE_CHECK to print offline parameter summary
647        and stop if loading a file that is not used;
648      - enable to calculate GMRedi tensor, KPP mixing and convective index
649        when the corresponding file(s) is/are not specified (but pkg is used).
650      - comment out resetting of monitorFreq (to endTime) since it still useful
651        for monitoring CFL numbers and checking offline fields.
652    o OpenAD:
653      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
654        smaller standard output) and generate new (smaller) output (on baudelaire
655        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
656    o model/src:
657      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
658        (where external_forcing_adjust was called) and change list of arguments;
659      - merge external_forcing_adjust.F into external_forcing_surf.F
660      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
661        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
662        previously in file "balance_relax.F", now removed); remove corresponding
663        arrays in FFIELDS.h.
664      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
665        a hack for getting back surfaceForcingS (loaded from file) when using
666        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
667      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
668        (was getting only 11 digits for AD-grad, due to different truncation
669         error in AD code).
670    
671    checkpoint64j (2013/07/04)
672    o pkg/offline:
673      - to enable the use of other features with pkg offline (e.g., obcs),
674        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
675      - comment out "allowFreezing" (now active) in 2 offline testing exp.
676    o pkg/exf ALLOW_RUNOFTEMP
677      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
678      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
679      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
680    o pkg/atm_phys:
681      - allows to add some damping on uVel,vVel (strength only function of k).
682    o verification, ad-tests:
683      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
684        global_ocean_ebm and offline_exf_seaice.thsice.
685    o verification/halfpipe_streamice:
686      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
687        flux input boundary conditions to be ignored; a fix for this bug changed
688        verification results for forward test.
689      - add adjoint test.
690    o pkg/ptracers:
691      - allow to restart without SOM pickup (resetting SOM to zero).
692    o pkg/gmredi:
693      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
694      - It uses mixing length theory and suppression by steering level effects to
695        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
696        to JPO, for more details).
697      - It also uses the diffusivity to calculate an eddy induced streamfunction
698        based on a PV closure (rather than a buoyancy closure as in GM).
699      - New files added to pkg/gmredi:
700        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
701          induced overturning streamfunction (called from gmredi_calc_tensor)
702        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
703          for use in gmredi_k3d
704        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
705          the eddy diffusivity
706    
707    checkpoint64i (2013/06/18)
708    o pkg/cheapaml:
709      - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
710        that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
711        with pkg/cheapaml.
712    o utils/python: add subpackage for cubed sphere function, first example is
713        simple cs.pcol to plot 2D fields on a map
714    o pkg/streamice:
715      - This is a new package in MITgcm, which solves dynamic equations for ice
716         sheets and ice streams
717      - At the moment it is independent of atmosphere/ocean dynamics, or any
718        other physical packages in MITgcm, even ShelfIce (although it is anticipat-
719        ed that this will change)
720      - There is a new verification exercise that tests it, halfpipe_streamice,
721        evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
722        rectangular embayment
723      - halfpipe_streamice is forward-only for now, will have TAF test soon
724      - for questions, email dgoldber@mit.edu
725    o pkg/thsice:
726      - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
727        of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
728      - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
729         call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
730      - allow precip from pkg/cheapaml to make snow over seaice.
731    o pkg/cfc:
732      - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
733      - remove atmos CFC 2-D arrays from common bloc (now local variables)
734      - change some hard-coded constant to run time parameter for reading and
735        and interpolating atmospheric CFC ; keep same default as previously.
736      - more flexible reading of Atmos CFC (number of records no longer hard-coded)
737      - put arguments in standard order: myTime, myIter, myThid
738      - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
739        atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
740      - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
741      - new routine to print summary of CFC params and check for consistency.
742    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
743      similar to thsice_advdiff.
744      Note that for the B-grid case the routine parameters uc/vc are overwritten.
745    o pkg/cfc:
746      - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
747        update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
748      - fix interpolation of atmphspheric CFC between Sorthern and Northern
749        hemisphere value.
750    o pkg/seaice:
751      - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
752    o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
753                  so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
754      - requires an additional time level that is stored in the pickup
755      - you can start with AB2 from a pickup without this time level with
756        pickupStrictlyMatch = .false.
757    
758    checkpoint64h (2013/05/26)
759    o pkg/cheapaml:
760      - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
761        affect machine truncation (but exp cheapAML_box still pass with 13 digits).
762      - consistent treatment of uWind,vWind location: assume everywhere in
763        pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
764        (Note: was already the case for Tair,Qair advection);
765        add option (INCONSISTENT_WIND_LOCATION) to recover old results.
766      - compute diabatic forcing only in the interior (excluding overlap regions)
767      - fill in array "Qsw" (for short-wave heating);
768      - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
769        before any update (consistent with MITgcm state var diagnostics);
770      - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
771        non periodic ; + adjusted for uWind,vWind (C-grid).
772    o pkg/seaice:
773      - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
774        add explicitly pkg/exf in experiments that currently use pkg/seaice.
775      - allows to compile pkg/seaice without pkg/exf.
776    o tools/OAD_support:
777      - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
778        of array "ourStepOf" in function rvNextAction (revolve.F90).
779    o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
780      - change pkg name (to be used with other atmospheric physics pkg)
781        but by-pass CVS when making the new pkg so that we keep the CVS history.
782    o pkg/offline:
783      - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
784        (previously called from pkg/dic_surfforcing_init.F)
785    o model/src:
786      - re-order sequence of calls within packages_init_variables.F, using
787        standard order, except for:
788         DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
789         CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
790    o new pkg: atm_phys
791      - add entry point and source code (previously in contrib
792          verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
793        (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
794      - re-order sequence of calls within packages_readparms.F,
795         packages_init_fixed.F and packages_write_pickup.F
796        (but skip packages_init_variables.F because of TAF issues).
797      - update contrib/*/atm_gray/ experiment.
798    o pkg/seaice (ITD code):
799      - simplify and fix the writing of pickup-files for ITD case
800    o pkg/seaice (ITD code):
801      - introduce floe size dependent lateral melt for ITD case;
802      - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
803      - update seaice_itd experiment main output.
804    o pkg/thsice:
805      - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
806        declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
807        changed accordingly pkg/atm2d.
808    
809    checkpoint64g (2013/05/01)
810  o pkg/exf ALLOW_RUNOFTEMP  o pkg/exf ALLOW_RUNOFTEMP
811    - if defined,  river and glacier runoff temperature can be read-in from    - if defined,  river and glacier runoff temperature can be read-in from
812      runoftempfile; runoftempfile needs to have same format as runofffile      runoftempfile; runoftempfile needs to have same format as runofffile
# Line 14  o pkg/thsice (& pkg/bulk_force): Line 817  o pkg/thsice (& pkg/bulk_force):
817    - fix bug (wrong overlap) when using EXF and stressReduction > 0.    - fix bug (wrong overlap) when using EXF and stressReduction > 0.
818  o verification/tutorial_global_oce_biogeo:  o verification/tutorial_global_oce_biogeo:
819    - add preliminary OpenAD setup (still has problems)    - add preliminary OpenAD setup (still has problems)
820  o pkg/seaice:  o pkg/seaice:
821    - turn some parameters for choosing the convergence criterion of    - turn some parameters for choosing the convergence criterion of
822      the inexact Newton method (JFNK) into runtime parameters for convenience      the inexact Newton method (JFNK) into runtime parameters for convenience
823    - clean up seaice_calc_viscosities.F: remove/retire two options for    - clean up seaice_calc_viscosities.F: remove/retire two options for
824      SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes      SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
825      the results of lab_sea/input because a division has been replaced by      the results of lab_sea/input because a division has been replaced by
826      a multiplication with the reciprocal (sumNorm)      a multiplication with the reciprocal (sumNorm)
827    - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve    - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
828      convergence of solver (changes results, of course), and to test some      convergence of solver (changes results, of course), and to test some
829      new features      new features
830  o model/src:  o model/src:
831    - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.    - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
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