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revision 1.1767 by jmc, Mon Nov 12 15:48:35 2012 UTC revision 1.2002 by jmc, Wed May 28 23:14:38 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 model/src & most packages:
8      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
9      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
10        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
11        "data.{pkg}" exist ; and leave the S/R (return) just after.
12      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
13        + call LAND_READPARMS from packages_readparms.F
14    o pkg/seaice:
15      - remove code that resets useThSice in S/R seaice_readparms and
16        replace by a warning in S/R seaice_check
17      - remove parameter MULTDIM, replace with nITD and runtime
18        parameter SEAICE_multDim (still hard-wired to nITD if
19        SEAICE_ITD is defined)
20    
21    checkpoint64x (2014/05/24)
22    o verification/lab_sea:
23      - update adjoint and TLM output following changes to pkg/salt_plume
24      - un-do the update after putting back local recip_Cp in few places.
25    o pkg/salt_plume: modifications by An Nguyen:
26      - add capability to do brine rejection (salt-plume) as function of
27        volume+tracers (instead of only salinity tracer).
28      - conserve volume by exchanging volume from each kLev to above to
29        accommodate in-coming brine volume
30      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
31      - switch KPP surf buoyancy due to brine forcing to 3-d
32        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
33      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
34      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
35        in East/West Arctic.
36    o pkg/sbo:
37      - incorporate modifications from Katherine Quinn to enable the use of sbo
38        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
39        output for future testreport verification (unfinished).
40    o pkg/atm_phys:
41      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
42        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
43        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
44    o pkg/seaice
45      seaice_calc_ice_strength.F: modify expression to avoid divisions
46        (affects truncation)
47      seaice_do_ridging.F: clean up the insectarium
48      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
49      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
50      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
51      - add some debugging information and error messages (warnings)
52    o model/src: modifications relatd to atmosphere p*:
53      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
54      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
55        of vertical profile tRef in geopotential background and anomaly.
56      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
57        and pkg/atm_phys.
58      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
59        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
60    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
61    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
62        not used right now, but can be used in BGC packages to fix conservation.
63    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
64        other packages too.
65    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
66        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
67    o model/src:
68      - since we have several heat capacity (even in model/src), define "recip_Cp"
69        as local variable (no longer in common block) to avoid any confusion.
70      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
71    o pkg/exf:
72      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
73        air density as function of air Temp, Humidity and atm pressure.
74    
75    checkpoint64w (2014/05/02)
76    o verification:
77      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
78        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
79        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
80        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
81        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
82    o model/src: for atmosphere in p* coords:
83      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
84      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
85        but not yet activated.
86    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
87      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
88      - this changes the results (but not for any verification experiment, because
89        none tests this), but avoids having an extra field in the restart files
90    o pkg/seaice: remove global variable TICE (not needed)
91      - replace by TICES or local variable where necessary (cost_seaice_test,
92        seaice_diagnostics_state)
93      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
94      - use specific read/write routines for reading and writing individual leves
95        of a multilevel field
96    o pkg/ctrl & model/inc:
97      - move additional anomaly fields of control vars (related to options:
98         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
99        from DYNVARS.h into new header file: CTRL_FIELDS.h
100    o pkg/seaice: some small modifications to the ridging code
101      - make fw2ObyRidge a global variable and add the freshwater flux to
102        seaice_growth
103      - pass actual thickness from seaice_prepare_ridging, so that it is
104        computed only in one place and compute it in the same way as in
105        seaice_growth
106      - initialise more fields in seaice_do_ridging that where cause floating
107        point exceptions over land
108    o pkg/seaice: preparations for ridging code and first real ridging code
109      - move most of "PART 1" of S/R seaice_growth into a new and separate
110        S/R seaice_reg_ridge that will both regularize the state variable after
111        advection call the actual ridging routine;
112      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
113        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
114      - remove ridging code from seaice_advdiff
115      - clean up remaining part 1 of seaice_growth in an attempt to make it
116        more readable (this is probably subjective)
117      - call seaice_itd_redist once in the initialisation phase to have the initial
118        conditions in the correct category
119      - finally: add new ridging routine for ITD code
120    
121    checkpoint64v (2014/04/11)
122    o pkg/ecco:
123      - add runtime parameters mdt[start,end]date[1,2]
124      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
125    o pkg/seaice:
126      - make deltaC a global variable, so that it can be used in ridging code
127      - first step towards ridging: introduce new routines that compute
128        ice strength based on ridging parameters
129      - add diagnostic for HSNOWITD
130      - add opnWtrFrac as a global variable (required for ridging scheme)
131    o pkg/salt_plume + pkg/seaice/seaice_growth.F
132      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
133        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
134    o verification/hs94.1x64x5:
135      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
136      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
137    o autodiff:
138      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
139        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
140        For now, only in pkgs used in verification/hs94.1x64x5.
141      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
142        which are specific to TAF/TAMC).
143      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
144        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
145        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
146      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
147        building mitgcmuv_ad (make adAll).
148    o pkg/ecco:
149      - cost_gencost_seaicev4.F:
150         reformulate proxy cost as function of sst and local param SEAICE_freeze
151         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
152      - add stop statement if old names siv4-[sst,vol] are used
153      - add snapshots + cost reports for atmospheric longwave
154      - remove factor 0.1 in front of wtau[u,v]
155      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
156         ALLOW_TMI_SST_COST_CONTRIBUTION
157    o pkg/atm_phys:
158      - add some diagnostics for Short-wave and for convection S/R.
159    o pkg/seaice/seaice_growth:
160      - fix a bug in the lateral melt parameterization for SEAICE_ITD
161        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
162      - rearrange loop order for better vector code in the same code block
163      - rewrite the floeDiameter formula to have fewer divisions
164      -  (miraculously) none of this changes the results of seaice_itd
165    o pkg/smooth:
166      - move param smooth2Ddiffnbt to pkg/ecco
167    o pkg/salt_plume:
168      - salt_plume_frac.F:
169         clean up local param names
170         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
171    o pkg/rw:
172      - add RS version of S/R READ_MFLDS_LEV.
173    o pkg/streamice:
174      - fix the restart test by writing/reading pickup_streamice files.
175    o pkg/seaice:
176      - refine checks for jfnk-related parameters
177      - comment out if statement with SEAICEuseIMEX parameter as long as there
178        is no IMEX code to avoid confusion and surprises
179    
180    checkpoint64u (2014/03/07)
181    o verification/MLAdjust:
182      - rename secondary test suffix:
183         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
184         0.leithD -> AhFlxF  + switch to flux-form
185         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
186         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
187    o pkg/mom_vecinv:
188      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
189        to be before mom_calc_visc.F)
190      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
191      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
192        this is simpler for the adjoint and for diagnostics.
193    o model/src + pkg/momentum:
194      - add input files for  2-D additional Western and Southern cell-edge wall
195         (e.g., to add "thin-wall" where it is =1).
196      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
197        using 2nd hFacZ that is computed from initial (fix domain) hFac
198      - known limitations of thin wall implementation: not yet coded for sigma
199        coords; not working with CD-scheme neither.
200    o pkg/seaice:
201      - rename recently introduced parameters from (wrong name) AB to
202        BDF (backward difference time discretisation)
203      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
204    o tools/adjoint_options:
205      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
206    
207    checkpoint64t (2014/02/01)
208    o pkg/ecco
209      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
210        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
211      - replace hard-coded record number and period which only work for monthly
212        with read-in runtime param that works for other periods (month,day,year)
213    o pkg/thsice
214      - corrected store directive fixes thsice adjoint gradient checks
215    o genmake2 & testreport:
216      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
217        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
218        Update testreport accordingly. No need to set "export OPENAD=true"
219        in adjoint_options/adjoint_oad anymore (will be removed later).
220    o pkg/shelfice:
221      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
222        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
223        so that surface forcing applies to k=kSurf if using pkg/shelfice.
224    o pkg/ctrl, pkg/grdchk, pkg/ecco:
225      - Changes to make GENARR more modular (i.e. invisible if not used)
226    o model/src/temp_integrate.F and salt_integrate.F
227      - re-include store directives that were removed on Dec 27th.
228    o model/src/external_forcing_surf.F
229      - add storage directives for EmPmR and PmEpR to avoid recomputation of
230        seaice_model in the adjoint that is problematic when seaice_model is
231        turned off in the adjoint. The resolved issue dated back to July when
232        EXTERNAL_FORCING_SURF call was moved.
233        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
234    o pkg/exf/exf_check.F
235      - fix a small bug again (originally found by Wentao Liu, now found again)
236      - streamline error output
237    o pkg/streamice and aim_v23:
238      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
239        Apple's /usr/bin/cpp knows what to do:
240        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
241        Target: x86_64-apple-darwin13.0.0
242    
243    checkpoint64s (2014/01/05)
244    o tools/adjoint_options:
245      - switch to fastopt.net TAF server (instead of default fastopt.de) for
246        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
247    o model/src:
248      - remove some unnecessary TAF storage directives in forward_step.F and
249        in dynamics.F (note: not always removed by TAF, e.g., double storage
250        of kappaRU,kappaRV in former version of dynamics.F).
251    o model/src & pkg/ptracers:
252      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
253        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
254        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
255      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
256      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
257      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
258    o useSingleCpuInput separates single-CPU input from single-CPU output;
259        for now only implemented for in exf_interp_read.F
260    o verification/advect_xy:
261      - fix missing EXCH call in local version of ini_salt.F and update output.
262    o momentum diagnostics:
263      - fix which deltaT is used in Total-Tendency diagnostics.
264      - fix typo in diagnostics for momentum tendency from AB.
265    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
266        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
267    
268    checkpoint64r (2013/12/08)
269    o verification/*/results:
270      - Update reference output of experiments that were passing with just 13 digits
271         (make it easier to detect future changes in results)
272    o model/src & pkg/ptracers:
273      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
274        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
275        to inside ptracers_integrate.F ; remove ptracers_advection.F
276    o coupling interface pkgs:
277        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
278      - change the config check to test the agreement of Ocean Depth
279        with ATM land/sea mask (instead of ATM orography);
280      - send to coupler the number of coupler time-steps to do for this run:
281        this allows to check for consistency and don't need anymore to be
282        specified in parameter file "data";
283      in coupler:
284      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
285      - improve report to log-file of config setting (pass log-file unit to few S/R)
286    o pkg/compon_communic:
287      - add coupling send/receive for non-tiled integer vector;
288      - add S/R to check and stop if any proc has an error (similar to
289        eesupp/src/stop_if_error.F but single thread and across Comm_World).
290    o pkg/exch2:
291      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
292        through list of all tiles my proc owns.
293    o model/src:
294      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
295        from rTrans) to simplify dependencies (no need to store rTrans anymore in
296        calling S/R); this affects AD results at machine truncation level:
297        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
298        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
299    o tools/build_options:
300      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
301    o coupling interface pkgs:
302        [compon_communic, atm_compon_interf & ocn_compon_interf]
303      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
304        to each S/R that needs it; remove un-used variables.
305      - change component tile registration (cpl_register.F in both compon_interf
306        and mitcomponent_tile_register.F) to pass the full list of tiles
307        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
308      - with pkg/exch2: adopt the same convention used for I/O to define mapping
309        towards coupler global array (unless W2_useE2ioLayOut=F):
310         a) can now use different tiling between atm & ocn comp.
311         b) no needs to modify the run-Off map when changing tiling (was needed
312            even if using the same tiling between atm & ocn).
313         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
314            full land tiles); not yet tested.
315      - check for valid mapping from comp. tile to coupler global array
316      - improve report of tile registration results to log file.
317    o pkg/exch2:
318      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
319        tile-registration (CPL_REGISTER);
320      - activate (un-comment) definition and setting of "W2_tileIndex" list to
321        store the local bi,bj indices of each tile;
322      - also print bi,bj in local report to log file;
323      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
324        Jun 2009 modif of pkg/exch2).
325    o testing on baudelaire:
326      - run 2 tests at a time: no significant slow down (since enough cpu) and
327        get the full set of test done earlier
328      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
329    o model/src/thermodynamics.F and routines called from it:
330      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
331        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
332        velocity (outp) by adding bolus velocity.
333      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
334        mass transport from velocity + lateral grid cell area
335      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
336      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
337     in thermodynamics.F
338      - remove k from thermodynamics.F and move it to temp_integrate.F
339        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
340        loop).
341      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
342        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
343        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
344        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
345      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
346        global_ocean.90x40x15, tutorial_global_oce_biogeo and
347        tutorial_tracer_adjsens (+ TLM output).
348    o tools/OAD_support and (verification/*/) code_oad:
349      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
350        module conversion ; remove unneeded CPP_EEOPTIONS.h.
351      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
352        version (closer to model/inc/CPP_OPTIONS.h).
353    o model/src:
354      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
355        retired list of parameters (routine FREEZE has been replace by surface
356        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
357    o pkg/gmredi:
358      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
359        velocity (same scheme but affects machine truncation) for GM_AdvForm.
360      - update output of FWD experiments: front_relax.bvp,
361        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
362    
363    checkpoint64q (2013/11/17)
364    o verification:
365      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
366        tutorial_global_oce_biogeo and global_ocean.90x40x15.
367      - generate new output (growth & melt) for seaice_itd experiment after
368        updating the input pickup_seaice files (previously wrong).
369    o pkg/cost:
370      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
371        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
372        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
373          cannot be applied to var in common block).
374        o allows to get results independent of tile-per-proc setting (if using
375          slower GLOBAL_SUM_SEND_RECV option).
376      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
377        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
378        forward gradients: update output).
379      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
380        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
381    o pkg/mom_common:
382      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
383        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
384        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
385        ensure that all field value that are used are set.
386    o tutorial_deep_convection (smag3d):
387      - add missing scaling in mom_calc_smag_3d.F;
388      - set smag3D_coeff in input.smag3d such that results do not change.
389    o pkg/dic:
390      - change dic_cost.F to compute cost on each tile first and then apply
391        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
392        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
393      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
394    o eesupp/src & pkg/mdsio:
395      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
396        (from pkg/mdsio) since they are no longer used for tape IO.
397      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
398        (+ keep a copy in pkg/atm_ocn_coupler).
399    o verification/isomip:
400      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
401    o tools/build_options:
402      - optfile linux_amd64_ifort11, fast (no ieee) case:
403        to get a working restart for all experiments, add "-fp-model source"
404        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
405    
406    checkpoint64p (2013/10/20)
407    o pkg/autodiff:
408      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
409        criteria, return to simple (default) tape IO format.
410    o pkg/mdsio (+ eesupp/src):
411      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
412        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
413      - fix globalFile and singleCpuIO options using simpler global mapping.
414      - new pairs of scatter/gather vector S/R (one for each type, generated from
415        template) corresponding to simpler global mapping.
416      - adread_write.F: switch to new S/R (but leave old calls commented) and write
417        to globalFile when parameter globalFiles is set to True.
418      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
419    o pkg/autodiff:
420      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
421        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
422        missing, just add a STOP if array type do not match.
423    o pkg/exf:
424      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
425         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
426         and rename array obsSIce to exf_iceFraction.
427    o tutorial_deep_convection:
428      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
429        for now all in this exp. code dir.
430      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
431        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
432    o eesupp/src:
433      - added SINGLE_DISK_IO option because reading of parameter files on
434        very large number of processors did not work with existing set-up
435    
436    checkpoint64o (2013/09/25)
437    o pkg/atm_phys & atm_compon_interf:
438      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
439    o tools/build_options:
440      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
441        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
442        remove CPP setting (was identical to genmake2 default).
443    o pkg/gmredi & model/src: Some updating and work done on the residual model.
444      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
445      - fixed up the calculation of the eddy stress and how it is added to the
446        external forcing via taueddy_external_forcing.F
447      - at the moment, it is very experimental and only works with the variable eddy
448        diffusivity calculated in gmredi_k3d.F
449    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
450        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
451    o testreport (& tools/do_tst_2+2):
452      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
453    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
454      - remove CPP='cpp -traditional -P' (this is genmake2 default)
455      - add switch (for big setups) to use 'medium' memory-model (but leave it
456        commented out for now). Note: needed with FC 19 to compile big setups.
457    o pkg/atm_compon_interf:
458      - regroup per field origin (model & pkgs) the coupling storage routines
459         (which accumalate in time each coupling field)
460      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
461        update accordingly + simplify aim_do_physics.F
462    
463    checkpoint64n (2013/08/26)
464    o pkg/bbl:
465      - update formulation to reduce dispersion of tracer properties in bbl
466      - replaced horizontal and vertical transport parameters with velocities
467      - changes results for verification/global_with_exf.yearly
468    o verification/halfpipe_streamice:
469      - change to matrix construction; update both Fwd & AD output.
470    o verification/tutorial_tracer_adjsens:
471      - OpenAD test: switch to vector-invariant momentum since fluxform with
472        rStar causes problems with OpenAD; update output.
473    o tools:
474      - genmake2: define a common prefix for all temp-file names ; move them
475        to local /tmp disk (but would be easy to move them back);
476      - xmakedepend: apply the same switch for temp-files.
477    o pkg/offline:
478      - changes for use with rStar (NLFS): assume that we continue to provide
479        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
480        output files) and apply r* scaling at each time-step (function of the time
481        varying Eta field); use normal pickup files (needed for restart with NLFS).
482    o adjoint with OpenAD:
483      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
484        package openad.  This package has to be compiled for all runs with OpenAD
485        instead of specifying code_oad_all as a modification directory.
486      - link the fortran templates from tools/OAD_support to the build directory
487        for preprocessing to avoid conflicts between different setups compiled
488        simultaneously and simplify cleanup.
489    o pkg/exf:
490      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
491        main model or other pkgs are exchanged in EXF_MAPFIELDS).
492    o model/src:
493      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
494        (similar to do_fields_blocking_exchanges.F).
495    o tools/genmake2:
496      - remove TAF output src code just before calling staf (when not doing a fresh
497        built, will stop if things go wrong with staf).
498      - fix target "adobj" (left from TAF version-2 transition)
499    o pkg/diagnostics:
500      - add a parameter to track the status of pkg/diagnostics activation;
501        this replace/extend the use of logical param "settingDiags" (to check
502        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
503        New S/R to print error message and stop when pkgStatus is not right.
504      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
505    
506    checkpoint64m (2013/08/13)
507    o model/inc:
508      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
509        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
510    o pkg/kpp & aim_v23:
511      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
512    o pkg/seaice:
513      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
514        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
515      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
516    o eesupp/src:
517      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
518        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
519    o switch to TAF version-2:
520      - add flow directives to "freeze" naming convention for ad-routines that
521        are used in I/O routines of adjoint state and associated common blocks
522        that are used in adcommon.h (backward compatible with version-1)
523      - update all ad-optfiles (in tools/adjoint_options + few local to some
524        verification exp) to switch to latest TAF version (currently 2.5.5);
525        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
526        out except for diva).
527      - the major change with TAF version-2 is that both the differentiated
528        routines and the forward routines (new) are returned as part of the TAF
529        output source code. Update genmake2 accordingly.
530      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
531        with version-2 when compared to TLM or FWD gradient); other experiments
532        output show minor changes (machine truncation level); update the few AD &
533        TLM output with 12 matching digits only (some prior to version-2 switch).
534    
535    checkpoint64l (2013/08/05)
536    o model/src:
537      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
538      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
539        when using TAF but only if using OpenAD.
540    o pkg/mom_common+fluxform+vecinv:
541      - always set horiz. viscosity arrays to background value before calling
542        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
543        only when using variable horiz. viscosity (useVariableVisc=T);
544      - simplify mom_vecinv.F (only 1 block for momViscosity).
545    o pkg/mom_common: variable horiz. viscosity in NH code
546      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
547        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
548      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
549        useBiharmonicVisc & useVariableVisc.
550      - fix old bug (already in 1rst implementation of variable horizontal viscosity
551        in calc_gw.F, version 1.27, 2006/06/20):
552        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
553        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
554      - change background horiz viscosity in vertical momentum (gW) to always be
555        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
556        any type of variable viscosity, e.g., viscAh/4Grid)
557      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
558        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
559        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
560        default viscAh,viscA4 is zero).
561    o model/src:
562      - extend length of drC & recip_drC from Nr to Nr+1.
563    o Divided Adjoint (DIVA) with MPI:
564      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
565      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
566        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
567    
568    checkpoint64k (2013/07/23)
569    o tools/OAD_support:
570      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
571        and remove it from genmake2.
572    o tools/build_options:
573      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
574        MPI_HEADER_FILES list (let genmake2 find the missing headers)
575    o verification/halfpipe_streamice:
576      - change to driving stress formulation; update both Fwd & AD output.
577    o tools/genmake2 and Divided Adjoint with MPI:
578      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
579      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
580      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
581        Makefile, which is set by genmake2, and check which mpi-headers are needed.
582        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
583      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
584    o testreport:
585      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
586        perform additional runs (number of additional runs is "add_DIVA_runs" taken
587        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
588    o verification/lab_sea (AD test):
589      - change to test Divided Adjoint Run in this set-up (both standard AD test
590        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
591    o pkg atm_ & ocn_compon_interf:
592      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
593        staggerTimeStep implementation) and disable (retired) corresponding
594        parameter.
595    o pkg/offline:
596      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
597      - add S/R OFFLINE_CHECK to print offline parameter summary
598        and stop if loading a file that is not used;
599      - enable to calculate GMRedi tensor, KPP mixing and convective index
600        when the corresponding file(s) is/are not specified (but pkg is used).
601      - comment out resetting of monitorFreq (to endTime) since it still useful
602        for monitoring CFL numbers and checking offline fields.
603    o OpenAD:
604      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
605        smaller standard output) and generate new (smaller) output (on baudelaire
606        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
607    o model/src:
608      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
609        (where external_forcing_adjust was called) and change list of arguments;
610      - merge external_forcing_adjust.F into external_forcing_surf.F
611      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
612        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
613        previously in file "balance_relax.F", now removed); remove corresponding
614        arrays in FFIELDS.h.
615      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
616        a hack for getting back surfaceForcingS (loaded from file) when using
617        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
618      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
619        (was getting only 11 digits for AD-grad, due to different truncation
620         error in AD code).
621    
622    checkpoint64j (2013/07/04)
623    o pkg/offline:
624      - to enable the use of other features with pkg offline (e.g., obcs),
625        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
626      - comment out "allowFreezing" (now active) in 2 offline testing exp.
627    o pkg/exf ALLOW_RUNOFTEMP
628      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
629      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
630      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
631    o pkg/atm_phys:
632      - allows to add some damping on uVel,vVel (strength only function of k).
633    o verification, ad-tests:
634      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
635        global_ocean_ebm and offline_exf_seaice.thsice.
636    o verification/halfpipe_streamice:
637      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
638        flux input boundary conditions to be ignored; a fix for this bug changed
639        verification results for forward test.
640      - add adjoint test.
641    o pkg/ptracers:
642      - allow to restart without SOM pickup (resetting SOM to zero).
643    o pkg/gmredi:
644      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
645      - It uses mixing length theory and suppression by steering level effects to
646        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
647        to JPO, for more details).
648      - It also uses the diffusivity to calculate an eddy induced streamfunction
649        based on a PV closure (rather than a buoyancy closure as in GM).
650      - New files added to pkg/gmredi:
651        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
652          induced overturning streamfunction (called from gmredi_calc_tensor)
653        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
654          for use in gmredi_k3d
655        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
656          the eddy diffusivity
657    
658    checkpoint64i (2013/06/18)
659    o pkg/cheapaml:
660      - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
661        that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
662        with pkg/cheapaml.
663    o utils/python: add subpackage for cubed sphere function, first example is
664        simple cs.pcol to plot 2D fields on a map
665    o pkg/streamice:
666      - This is a new package in MITgcm, which solves dynamic equations for ice
667         sheets and ice streams
668      - At the moment it is independent of atmosphere/ocean dynamics, or any
669        other physical packages in MITgcm, even ShelfIce (although it is anticipat-
670        ed that this will change)
671      - There is a new verification exercise that tests it, halfpipe_streamice,
672        evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
673        rectangular embayment
674      - halfpipe_streamice is forward-only for now, will have TAF test soon
675      - for questions, email dgoldber@mit.edu
676    o pkg/thsice:
677      - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
678        of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
679      - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
680         call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
681      - allow precip from pkg/cheapaml to make snow over seaice.
682    o pkg/cfc:
683      - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
684      - remove atmos CFC 2-D arrays from common bloc (now local variables)
685      - change some hard-coded constant to run time parameter for reading and
686        and interpolating atmospheric CFC ; keep same default as previously.
687      - more flexible reading of Atmos CFC (number of records no longer hard-coded)
688      - put arguments in standard order: myTime, myIter, myThid
689      - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
690        atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
691      - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
692      - new routine to print summary of CFC params and check for consistency.
693    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
694      similar to thsice_advdiff.
695      Note that for the B-grid case the routine parameters uc/vc are overwritten.
696    o pkg/cfc:
697      - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
698        update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
699      - fix interpolation of atmphspheric CFC between Sorthern and Northern
700        hemisphere value.
701    o pkg/seaice:
702      - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
703    o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
704                  so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
705      - requires an additional time level that is stored in the pickup
706      - you can start with AB2 from a pickup without this time level with
707        pickupStrictlyMatch = .false.
708    
709    checkpoint64h (2013/05/26)
710    o pkg/cheapaml:
711      - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
712        affect machine truncation (but exp cheapAML_box still pass with 13 digits).
713      - consistent treatment of uWind,vWind location: assume everywhere in
714        pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
715        (Note: was already the case for Tair,Qair advection);
716        add option (INCONSISTENT_WIND_LOCATION) to recover old results.
717      - compute diabatic forcing only in the interior (excluding overlap regions)
718      - fill in array "Qsw" (for short-wave heating);
719      - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
720        before any update (consistent with MITgcm state var diagnostics);
721      - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
722        non periodic ; + adjusted for uWind,vWind (C-grid).
723    o pkg/seaice:
724      - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
725        add explicitly pkg/exf in experiments that currently use pkg/seaice.
726      - allows to compile pkg/seaice without pkg/exf.
727    o tools/OAD_support:
728      - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
729        of array "ourStepOf" in function rvNextAction (revolve.F90).
730    o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
731      - change pkg name (to be used with other atmospheric physics pkg)
732        but by-pass CVS when making the new pkg so that we keep the CVS history.
733    o pkg/offline:
734      - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
735        (previously called from pkg/dic_surfforcing_init.F)
736    o model/src:
737      - re-order sequence of calls within packages_init_variables.F, using
738        standard order, except for:
739         DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
740         CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
741    o new pkg: atm_phys
742      - add entry point and source code (previously in contrib
743          verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
744        (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
745      - re-order sequence of calls within packages_readparms.F,
746         packages_init_fixed.F and packages_write_pickup.F
747        (but skip packages_init_variables.F because of TAF issues).
748      - update contrib/*/atm_gray/ experiment.
749    o pkg/seaice (ITD code):
750      - simplify and fix the writing of pickup-files for ITD case
751    o pkg/seaice (ITD code):
752      - introduce floe size dependent lateral melt for ITD case;
753      - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
754      - update seaice_itd experiment main output.
755    o pkg/thsice:
756      - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
757        declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
758        changed accordingly pkg/atm2d.
759    
760    checkpoint64g (2013/05/01)
761    o pkg/exf ALLOW_RUNOFTEMP
762      - if defined,  river and glacier runoff temperature can be read-in from
763        runoftempfile; runoftempfile needs to have same format as runofffile
764    o pkg/thsice (& pkg/bulk_force):
765      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
766        for energy content of Precip + RunOff & Evap (like with pkg/exf).
767      - change computation domain to always be the interior (without overlap).
768      - fix bug (wrong overlap) when using EXF and stressReduction > 0.
769    o verification/tutorial_global_oce_biogeo:
770      - add preliminary OpenAD setup (still has problems)
771    o pkg/seaice:
772      - turn some parameters for choosing the convergence criterion of
773        the inexact Newton method (JFNK) into runtime parameters for convenience
774      - clean up seaice_calc_viscosities.F: remove/retire two options for
775        SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
776        the results of lab_sea/input because a division has been replaced by
777        a multiplication with the reciprocal (sumNorm)
778      - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
779        convergence of solver (changes results, of course), and to test some
780        new features
781    o model/src:
782      - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
783      - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
784      - move forcing adjustment (balancing surface forcing) in specific S/R
785        where might also be applied exchanges (if needed) to forcing arrays.
786    o pkg/shelfice:
787      - allow to specify the Ice-Shelf mass per unit area (instead of
788        shelficeLoadAnomaly) and do the conversion from one to the other
789      - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
790        to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
791        (b) will be loaded in time (before calling INI_PRESSURE) in case it is
792        needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
793      - update isomip experiment forward output (get machine truncation error
794        from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
795    o verification/offline_exf_seaice:
796      revise data.seaice in input.thermo and input_ad and update results accordingly
797        HO = 0.2, SEAICE_areaLossFormula = 2,
798        SEAICE_growMeltByConv = .TRUE.,
799        SEAICE_doOpenWaterMelt = .TRUE.,
800      Improve consistency with input.thsice and fix the spurious 500m ice corners
801    o verification/global_ocean.cs32x15:
802      - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
803        in icedyn (thsice+seaice-dyn) test and update output.
804    o verification/offline_exf_seaice:
805      - adjust list of tested variables (with testreport) and update
806        standard test output with better slection of monitored fields.
807    o pkg/cd_code:
808      - swtich off Adams-Bashforth on the 1rst iteration. Update output of
809        experiment lab_sea.hb87
810    o tools/genmake2:
811      - change default makedepend from the system default to tools/xmakedepend:
812        When no makedepend is specified, select tools/xmakedepend it the test pass,
813        otherwise select the system default (if exist and pass the test) or
814        try to build cyrus-makedepend ; stop if none of the 3 works.
815    o pkg/exf & pkg/thsice:
816      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
817        for energy content of Precip + RunOff & Evap. Assumes:
818       1) Rain has same temp as Air.
819       2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
820       3) Run-Off comes at the temp of surface water (with same Cp)
821       4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
822        put directly into Latent Heat flux & should use water-vapor heat capacity.
823       5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
824        with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
825    o pkg/seaice: simplify the use of CPP flags in JFNK-related files
826        (compile when SEAICE_ALLOW_JFNK is defined)
827    o pkg/thsice:
828      - fix oceanic flux diagnostics & timeave (left from new sequence of calls
829        implementation): move THSICE_AVE call after the advection (called directly
830        from thsice_do_advect.F).
831    o verification/global_ocean.90x40x15 and OpenAD:
832      New experiment for OpenAD is identical to the one in input_ad except that
833        multiDimAdvection=.FALSE.,
834      There is still an issue with this.
835    o pkg/thsice:
836      - account for ice velocity (ocean relative velocity) in turbulent heat flux
837        at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
838        and offline_exf_seaice (main test).
839    
840    checkpoint64f (2013/03/31)
841    o verification/OpenAD:
842      - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
843    o verification/isomip, pkg/shelfice and OpenAD:
844      - add OpenAD setup to this exp and make shelfice package work with OpenAD
845    o verification/tutorial_global_oce_biogeo:
846      - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
847    o verification/offline_exf_seaice:
848      - replace adjoint experiment (now similar to fwd input.thermo/ setup).
849    o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
850      - add OpenAD setup to this exp and make ptracers package work with OpenAD
851    o pkg/seaice/seaice_evp.F:
852       mask the asymmetric contribution of the ice-ocean stress (when
853       the turningAngle is non-zero) over open water to avoid stripes
854       in the EVP-solutions after many EVP-substeps. This does not change
855       the verification experiment (because turningAngle=0 in that experiment),
856       but will affect other EVP solutions with turningAngle.ne.0
857    o verification, AD & TLM output:
858      - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
859        additions and multiplications which affect results at machine truncation
860        level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
861        lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
862        (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
863        digits of matching.
864    o pkg/seaice:
865       modify lsr-algorithm so that it vectorizes AND converges by using a
866       "zebra" method: split vector loop into two with step size 2; this
867       solves a general convergence problem for the JFNK solver on a vector
868       computer. It has the potential to even improve convergence for
869       non-vector machines, but it does change the results so it is turned
870       off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
871       SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
872    
873    checkpoint64e (2013/03/05)
874    o pkg/ecco and several verification experiments:
875       Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
876       from ecco package, and revert to unified routine in model/src/
877       Adjust verification experiments accordingly, especially gloal_oce_llc90
878       Should conclude long-standing work by Gael to reconsile the_main_loop with
879       ECCO and will enable OpenAD's revolve loop in ECCO setup.
880    o pkg/generic_advdiff:
881      - implement compressible flow method for multi-dim advection (similar to
882        gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
883        TAF generates many recomputations) to use it; no yet coded with implicit
884        vertical advection.
885      - change experiment advect_cs (new output) and advect_xy (same output)
886        to test compressible flow multi-dim advection.
887    o pkg/generic_advdiff:
888      - fix SOM advection for unusual cases (linear Free-Surf in r*, other
889        cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
890    o pkg/seaice:
891      - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
892        bug affects two verification experiments (lab_sea and lab_sea.hb87),
893        recover old (wrong) results by setting noSlipFac = 2. in
894        seaice_calc_strainrates.F;
895      - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
896      - add runtime parameter SEAICE_JFNKepsilon for that finite difference
897        gradient in the Jacobian times vector operation (s/r seaice_jacvec)
898      - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
899    o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
900      - new subroutines seaice_lsr_tridiagu/v
901      - introduce loop bounds i/jmin/max to be able to use a restricted
902        additive Schwarz method, but not used for now.
903      - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
904      - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
905    o OpenAD support
906       Reorganize S/R call for overall time-stepping loop to facilitate
907       OpenAD revolve loop replacement
908       (new S/R main_do_loop.F)
909    o model/src:
910      - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
911      - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
912        ADAMS_BASHFORTH2.
913    o pkg/cheapaml:
914      - add new parameter (default=F, same as before) to disable full domain
915        (including land) periodicity in X & Y dir.
916      - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
917        prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
918        into single S/R CHEAPAML_TIMESTEP.
919    
920    checkpoint64d (2013/02/17)
921    o pkg/monitor (angular momentum):
922      - do not add Eta contribution to the total AM if using rigid-lid;
923      - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
924      - horizontal discretisation: compute Zonal wind contribution separately for
925        each component (instead of from cell centered averaged) and use the 4
926        grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
927      - Check that AM is conserved with linear dynamics (momAdvection=F and linear
928        FreeSurf) if using vectorInvariant momentum.
929    o model/src (horizontal grid):
930      - move initialisation of all horizontal grid arrays to null value
931        from specific horizontal grid S/R to main S/R INI_GRID;
932      - add 2 new arrays to project model C-grid velocity on to zonal direction
933        (similar to AngleCosC & -AngleSinC but at U and V point location) and
934        compute them in S/R CALC_GRID_ANGLES.
935    o pkg/seaice: replace a hard coded parameter by a runtime parameter
936        SEAICE_JFNK_tolIter
937    o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
938        preconditioner for JFNK (run LSR into the overlaps as far as possible,
939        i.e OLx/y-2, but overwrite the solution in the overlaps)
940      - extend loop range in seaice_calc_viscosity
941      - add new parameters SEAICE_OLx/y (default = OLx/y-2)
942      - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
943      - slightly modify loops in tridiagonal solver lsr-preconditioner
944      - by default remove the extra exchange in seaice_preconditioner with a
945        replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
946      - modify offline_exf_seaice so that old results without RAS are reproduced
947        for output.dyn_jfnk.txt
948      in seaice_fgmres.F (unrelated to RAS)
949      - add a cpp-flag option for a re-ordered mapping (potentially more
950        efficient), but because this changes the results, turn it off by
951        default
952      - replace the save statement by local common blocks
953    o utils/matlab:
954      - fix tile-offset in rdmnc.m when output was produced using EXCH2.
955      - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
956        instead of local script "load_cs.m".
957    o pkg/seaice:
958      - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
959        to the scalarProductMetric and the unrolling. By chance this does not
960        change the verification experiment, because of the particular domain
961        decomposition
962    o pkg/diagnostics:
963      - change default missing_value from UNSET_RL to -999.
964    o pkg/layers: improve vectorization of layers_fluxcalc.F
965      - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
966        time spent in this routine by more than a factor of 3 on an NEC-SX8
967      - step 2: replace search algorithm by a bisection algorithm found in
968        Press et al. Numerical Recipes in Fortran. This algorithm can be
969        vectorized and finds the correct bin in approx. log2(Nlayers) steps.
970        For now, use this algorithm only for TARGET_NEC_SX defined.
971      - moved the search algorithm into a separate subroutine, that is kept
972        within the same file for automatic inlining.
973      - modified catching potential errors
974    o pkg/ecco:
975      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
976    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
977      - modifications for ALLOW_GENTIM2D_CONTROL
978      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
979      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
980      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
981      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
982    o model/src:
983      - account for moist thermodynamics in (dry) potential temperature equation;
984        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
985        and cpl_aim+ocn.
986      - also switch to standard compiler (gfortran, was using ifort previously)
987        for fizhi-cs experiments reference output.
988    o pkg/ctrl:
989      - 1st step toward generic time-varying control variable (2D) via CPP option
990        ALLOW_GENTIM2D_CONTROL
991      - note new namelist ctrl_nml_genarr in data.ctrl
992    o verification/global_ocean.cs32x15:
993      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
994        thsice calling sequence and update "output.icedyn.txt" output file.
995    o pkg/ptracers:
996      - from Ryan A.: code to allow to restart a tracer at regular time interval
997        specifying a reset frequency and a reset-phase (for each tracers).
998    o pkg/thsice:
999      - implement new sequence of calls for thsice+seaice:
1000          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
1001          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
1002      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
1003        in CPP_OPTIONS.h) to recover old sequence;
1004      - update diagnostics for Intermediate State thsice diagnostics: now filled
1005        just before advection (instead of just after advection in old sequence);
1006      - update output of experiment offline_exf_seaice (standard test);
1007      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
1008        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
1009    o pkg/aim_v23:
1010      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
1011      - use standard pkg/mdsio routines to read & write CO2 pickup file;
1012      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
1013      - Implement new sequence of calls for seaice advection (with thsice and
1014        seaice diffusion): do ice advection after ice-Thermodynamic (previously
1015        was done before); change aim_do_physics.F (split the bi,bj loops block);
1016      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
1017    o pkg/thsice:
1018      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
1019        where just seaice diffusion is used without seaice-dynamics.
1020    
1021    checkpoint64c (2013/01/18)
1022    o pkg/seaice:
1023      - add a parameter JFNKres_tFac that can replace JFNKres_t
1024        (= JFNKres_tFac*JFNKresidual before JFNK solver)
1025      - add a line search option to the JFNK solver
1026      - move update of u/vIce and computation of initial residual into a separate
1027        routine (same file); makes the code a little easier to read (?)
1028      - the line search requires computation of the residual and for some reason
1029        I cannot do the update of u/vIce at the beginning of the Newton loop
1030        without changing the results, so we move computation of the new residual
1031        also to the end of the Newton loop, even without the line search
1032    o pkg/mdsio:
1033      - write missing value (corresponding to undefined array value) to meta files;
1034        skip this if missing value is one (UNSET_RL would be a better value for the
1035        case of undefined missing value but it's current the default missing-value);
1036        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
1037    o pkg/exf & thsice:
1038      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
1039        diagnostics) even when SHORTWAVE_HEATING is #undef;
1040    o verification/cfc_example:
1041      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
1042        illustrate how to use it).
1043    o verification/offline_exf_seaice:
1044      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
1045        files to only one time-record.
1046      in input.thermo: narrow the 2 bands of low initial ice-concentration near
1047        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
1048        snapshot output; same mcPheePiston value as in thsice with
1049        surf-current=0.2m/s.
1050      in input.thsice: similar set-up as in input.thermo (channel with same seaice
1051        initial conditions).
1052    o verification/cfc_example:
1053      - update file "data" with more standard choice (default rotationPeriod,
1054        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
1055        set deltaTFreeSurf to deltaTtracer) and update the output.
1056    o pkg/layers:
1057      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
1058      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
1059    o verification/offline_exf_seaice:
1060      - set all {field}period to zero for constant-in-time forcing (not tested
1061        anywhere else).
1062    o verification/offline_exf_seaice:
1063      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
1064      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
1065    o model/src:
1066      - implement Finite-Volume method for (hydrostatic) presure gradient
1067        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
1068    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
1069      - In order to be compatible with the default EVP code, this requires changing
1070        the EVP code around a little; and because any small change immediately
1071        breaks the lab_sea.hb87 verification experiment, the reference output is
1072        updated two times (each time the remaining aggrement was only 2 digits):
1073        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
1074        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
1075        The adjoint test lab_sea.evp also needed to be updated.
1076      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
1077        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
1078        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
1079        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
1080        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
1081        kept obscure, because I need to test it a little more.
1082    o pkg/cheapaml:
1083      - fix few incorrect type (_RL/_RS) in subroutine calls.
1084    o pkg/seaice:
1085      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
1086        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
1087    o model/src:
1088      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
1089        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
1090        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
1091    o pkg/cheapaml:
1092      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
1093        update output of experiment cheapAML_box.
1094      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
1095        and set them only in one place (cheapaml_readparms.F).
1096      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
1097      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
1098        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
1099    o model/src/the_main_loop.F:
1100      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
1101    o pkg/seaice:
1102      - remove legacy branch code.
1103      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
1104    o verification/*/code*/SEAICE_OPTIONS.h:
1105      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
1106        SEAICE_CAP_HEFF).
1107    o pkg/cheapaml:
1108      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
1109        to load new forcing fields.
1110      - add missing "_d 0" where it's needed; + some editing (improve indentation).
1111      - remove switch to "-r8" compiler option (no longer needed) in verification
1112        cheapAML_box, keep same output (small trucation error differences).
1113    o verification/offline_exf_seaice:
1114      - add thermodynamics only test.
1115    o verification/cheapAML_box:
1116      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
1117        keep same output (same 14 digits for cg2d).
1118      - switch on "-r8" compiler option (some numerical values are missing
1119        the "_d 0") and update output (only 6 digits for cg2d were preserved).
1120    
1121    checkpoint64b (2012/12/24)
1122    o pkg/cheapaml:
1123      - remove un-used variables (Qnet,EmPmR) from pickup files.
1124      - store tendency of advected variables into cheapaml pickup file
1125        and fix the AB-2 restart.
1126    o verification/offline_exf_seaice and lab_sea adjoint:
1127      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
1128      - switch to 4 time steps in offline, consistent with lab_sea.
1129      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
1130      - update results after change of experiment seaice.
1131    o pkg/seaice:
1132      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
1133        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
1134        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
1135        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
1136    o model/src:
1137      - add run-time parameter to select CG2D solver minimum-residual solution
1138        (in case of a poor convergence).
1139    o pkg/seaice/seaice_lsr.F
1140      - move calculation of matrix coefficients into new
1141        S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
1142        file; the main purpose of this change is to be able to reuse the code
1143        in S/R SEAICE_PRECONDITIONER
1144      - modify the computation of the residual so that the mass of sea-ice
1145        is not used twice; this simplifies the calculations, but since
1146        the residual is never used except when LSR_mixIniGuess.ge.4---and this is
1147        not tested in testreport---this does not affect the testreport results.
1148    o verification/seaice_obcs:
1149      - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
1150        verification/lab_sea/input.salt_plume; changes results/output.txt*
1151    o model/src:
1152      - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
1153    o pkg/seaice:
1154      - improve description of parameters in seaice_fgmres.F and start
1155        cleaning up the code
1156      - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
1157        second argument
1158      - add a metric based on grid cell area to SEAICE_SCALPROD; update
1159        results of offline_exf_seaice.dyn_jfnk
1160      - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
1161    o pkg/aim_v23:
1162      - fix an other bug in dissipation heating (grid-cell area was missing).
1163    o model/src + pkg/seaice:
1164      - add global (multi-tile) linear solver for pair of tri-diagonal system
1165        along X and Y lines, respectively for U and V component.
1166        Note: 1) MPI and cube-exchange not yet coded.
1167            2) probably not accurate for poorly conditioned / large size problem.
1168      - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
1169        default: not compiled and not used.
1170    o pkg/seaice:
1171      - first attempt at a multi-threaded fgmres solver for the JFNK solver:
1172        introduce bi/bj loops and use global_sum_tile_rl instead of
1173        mpi_allreduce in seaice_fgmres.F
1174      - improve diagnostics output for fgmres solver (seaice_fgmres.F)
1175      - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
1176      - add a verification experiment for JFNK in offline_exf_seaice
1177    o verification:
1178      - change (for now, only fwd test) offline_exf_seaice experiment:
1179        use a re-entrant channel with idealized coastline (trapezoidal shape)
1180        at southern boundary to explore seaice dynamics and thermodynamics
1181        with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
1182        secondary test (input.thsice) use thermodynamics only with SST relaxation.
1183      - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
1184    o pkg/exf:
1185      - disable "sstExtrapol" when Nr=1
1186    o verification:
1187      - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
1188        to test pkg/cheapaml.
1189    o pkg/aim_v23 & pkg/shap_filt:
1190      - fix dissipation heating (erroneous gravity multiplication factor).
1191    o pkg/seaice:
1192      - remove unused field pressPre from jfnk solver
1193      - rename two subroutines in seaice_preconditioner.F
1194    o eesupp/src:
1195       - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
1196    o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
1197       - remove wrong parts of the rhs and the lhs (were in there
1198         because I did not understand the concept of this preconditioner)
1199       - add an exchange between u- and v-sweep. This increases communication
1200         by a factor of two but improves the convergence of jfnk. Ideally,
1201         one would like the u- and v-sweep to be independent. So far within
1202         undocumented ifdefs
1203       - reorganize the extra computations for printing the residuals
1204    o tools/genmake2:
1205      - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
1206        since it's not necessary (and was preventing to use MNC in some cases).
1207    
1208    checkpoint64a (2012/11/16)
1209    o pkg/autodiff:
1210      - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
1211        autodiff_readparms.F no longer depends on calling order (within
1212        packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
1213        rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
1214        and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
1215    o pkg/obcs:
1216      - adding tidal velocity forcing capability to obcs
1217        for usage example, see verification/seaice_obcs/input.tides
1218    o pkg/seaice:
1219      - turn the LSR-relaxation parameters WFAU/V into runtime parameters
1220        SEAICE_LSRrelaxU/V
1221      - introduce runtime parameter SEAICEetaZmethod (=0 by default)
1222  o pkg/aim_v23:  o pkg/aim_v23:
1223    - implement heating from friction (bottom friction and stratospheric drag).    - implement heating from friction (bottom friction and stratospheric drag).
1224  o pkg/shap_filt:  o pkg/shap_filt:
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