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revision 1.1881 by m_bates, Tue Jun 18 21:30:33 2013 UTC revision 1.2006 by jmc, Sat Jun 7 17:54:20 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/exf:
8      - add code to process the case field period = -12. with UV interpolation.
9      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
10        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
11    o verification/global_with_exf:
12      - swith all fields period to -12. (was previously untested) in input/data.exf
13        (but keep secondary test ".yearly" unchanged); update the reference output.
14    o pkg/cal:
15      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
16    o pkg/exf:
17      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
18        to replace logical switch "exf_verbose"
19      - report in STDOUT when loading a new reccord (if exf_debugLev >= 3)
20    o pkg/sbo:
21      - update from Katherine Quinn: evaluate mass directly from density and SSH
22        (budget using Finite Volume method) instead of from bottom pressure.
23      - allow testreport to collect few selected SBO output ; tested in exp.
24        global_ocean.90x40x15 (after updating the results, to include SBO output).
25      - fix some multi-threading issues (in output part).
26    o model/src & most packages:
27      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
28      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
29        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
30        "data.{pkg}" exist ; and leave the S/R (return) just after.
31      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
32        + call LAND_READPARMS from packages_readparms.F
33    o pkg/seaice:
34      - remove code that resets useThSice in S/R seaice_readparms and
35        replace by a warning in S/R seaice_check
36      - remove parameter MULTDIM, replace with nITD and runtime
37        parameter SEAICE_multDim (still hard-wired to nITD if
38        SEAICE_ITD is defined)
39    
40    checkpoint64x (2014/05/24)
41    o verification/lab_sea:
42      - update adjoint and TLM output following changes to pkg/salt_plume
43      - un-do the update after putting back local recip_Cp in few places.
44    o pkg/salt_plume: modifications by An Nguyen:
45      - add capability to do brine rejection (salt-plume) as function of
46        volume+tracers (instead of only salinity tracer).
47      - conserve volume by exchanging volume from each kLev to above to
48        accommodate in-coming brine volume
49      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
50      - switch KPP surf buoyancy due to brine forcing to 3-d
51        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
52      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
53      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
54        in East/West Arctic.
55    o pkg/sbo:
56      - incorporate modifications from Katherine Quinn to enable the use of sbo
57        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
58        output for future testreport verification (unfinished).
59    o pkg/atm_phys:
60      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
61        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
62        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
63    o pkg/seaice
64      seaice_calc_ice_strength.F: modify expression to avoid divisions
65        (affects truncation)
66      seaice_do_ridging.F: clean up the insectarium
67      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
68      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
69      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
70      - add some debugging information and error messages (warnings)
71    o model/src: modifications relatd to atmosphere p*:
72      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
73      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
74        of vertical profile tRef in geopotential background and anomaly.
75      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
76        and pkg/atm_phys.
77      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
78        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
79    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
80    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
81        not used right now, but can be used in BGC packages to fix conservation.
82    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
83        other packages too.
84    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
85        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
86    o model/src:
87      - since we have several heat capacity (even in model/src), define "recip_Cp"
88        as local variable (no longer in common block) to avoid any confusion.
89      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
90    o pkg/exf:
91      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
92        air density as function of air Temp, Humidity and atm pressure.
93    
94    checkpoint64w (2014/05/02)
95    o verification:
96      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
97        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
98        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
99        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
100        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
101    o model/src: for atmosphere in p* coords:
102      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
103      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
104        but not yet activated.
105    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
106      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
107      - this changes the results (but not for any verification experiment, because
108        none tests this), but avoids having an extra field in the restart files
109    o pkg/seaice: remove global variable TICE (not needed)
110      - replace by TICES or local variable where necessary (cost_seaice_test,
111        seaice_diagnostics_state)
112      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
113      - use specific read/write routines for reading and writing individual leves
114        of a multilevel field
115    o pkg/ctrl & model/inc:
116      - move additional anomaly fields of control vars (related to options:
117         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
118        from DYNVARS.h into new header file: CTRL_FIELDS.h
119    o pkg/seaice: some small modifications to the ridging code
120      - make fw2ObyRidge a global variable and add the freshwater flux to
121        seaice_growth
122      - pass actual thickness from seaice_prepare_ridging, so that it is
123        computed only in one place and compute it in the same way as in
124        seaice_growth
125      - initialise more fields in seaice_do_ridging that where cause floating
126        point exceptions over land
127    o pkg/seaice: preparations for ridging code and first real ridging code
128      - move most of "PART 1" of S/R seaice_growth into a new and separate
129        S/R seaice_reg_ridge that will both regularize the state variable after
130        advection call the actual ridging routine;
131      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
132        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
133      - remove ridging code from seaice_advdiff
134      - clean up remaining part 1 of seaice_growth in an attempt to make it
135        more readable (this is probably subjective)
136      - call seaice_itd_redist once in the initialisation phase to have the initial
137        conditions in the correct category
138      - finally: add new ridging routine for ITD code
139    
140    checkpoint64v (2014/04/11)
141    o pkg/ecco:
142      - add runtime parameters mdt[start,end]date[1,2]
143      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
144    o pkg/seaice:
145      - make deltaC a global variable, so that it can be used in ridging code
146      - first step towards ridging: introduce new routines that compute
147        ice strength based on ridging parameters
148      - add diagnostic for HSNOWITD
149      - add opnWtrFrac as a global variable (required for ridging scheme)
150    o pkg/salt_plume + pkg/seaice/seaice_growth.F
151      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
152        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
153    o verification/hs94.1x64x5:
154      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
155      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
156    o autodiff:
157      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
158        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
159        For now, only in pkgs used in verification/hs94.1x64x5.
160      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
161        which are specific to TAF/TAMC).
162      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
163        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
164        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
165      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
166        building mitgcmuv_ad (make adAll).
167    o pkg/ecco:
168      - cost_gencost_seaicev4.F:
169         reformulate proxy cost as function of sst and local param SEAICE_freeze
170         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
171      - add stop statement if old names siv4-[sst,vol] are used
172      - add snapshots + cost reports for atmospheric longwave
173      - remove factor 0.1 in front of wtau[u,v]
174      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
175         ALLOW_TMI_SST_COST_CONTRIBUTION
176    o pkg/atm_phys:
177      - add some diagnostics for Short-wave and for convection S/R.
178    o pkg/seaice/seaice_growth:
179      - fix a bug in the lateral melt parameterization for SEAICE_ITD
180        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
181      - rearrange loop order for better vector code in the same code block
182      - rewrite the floeDiameter formula to have fewer divisions
183      -  (miraculously) none of this changes the results of seaice_itd
184    o pkg/smooth:
185      - move param smooth2Ddiffnbt to pkg/ecco
186    o pkg/salt_plume:
187      - salt_plume_frac.F:
188         clean up local param names
189         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
190    o pkg/rw:
191      - add RS version of S/R READ_MFLDS_LEV.
192    o pkg/streamice:
193      - fix the restart test by writing/reading pickup_streamice files.
194    o pkg/seaice:
195      - refine checks for jfnk-related parameters
196      - comment out if statement with SEAICEuseIMEX parameter as long as there
197        is no IMEX code to avoid confusion and surprises
198    
199    checkpoint64u (2014/03/07)
200    o verification/MLAdjust:
201      - rename secondary test suffix:
202         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
203         0.leithD -> AhFlxF  + switch to flux-form
204         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
205         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
206    o pkg/mom_vecinv:
207      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
208        to be before mom_calc_visc.F)
209      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
210      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
211        this is simpler for the adjoint and for diagnostics.
212    o model/src + pkg/momentum:
213      - add input files for  2-D additional Western and Southern cell-edge wall
214         (e.g., to add "thin-wall" where it is =1).
215      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
216        using 2nd hFacZ that is computed from initial (fix domain) hFac
217      - known limitations of thin wall implementation: not yet coded for sigma
218        coords; not working with CD-scheme neither.
219    o pkg/seaice:
220      - rename recently introduced parameters from (wrong name) AB to
221        BDF (backward difference time discretisation)
222      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
223    o tools/adjoint_options:
224      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
225    
226    checkpoint64t (2014/02/01)
227    o pkg/ecco
228      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
229        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
230      - replace hard-coded record number and period which only work for monthly
231        with read-in runtime param that works for other periods (month,day,year)
232    o pkg/thsice
233      - corrected store directive fixes thsice adjoint gradient checks
234    o genmake2 & testreport:
235      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
236        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
237        Update testreport accordingly. No need to set "export OPENAD=true"
238        in adjoint_options/adjoint_oad anymore (will be removed later).
239    o pkg/shelfice:
240      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
241        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
242        so that surface forcing applies to k=kSurf if using pkg/shelfice.
243    o pkg/ctrl, pkg/grdchk, pkg/ecco:
244      - Changes to make GENARR more modular (i.e. invisible if not used)
245    o model/src/temp_integrate.F and salt_integrate.F
246      - re-include store directives that were removed on Dec 27th.
247    o model/src/external_forcing_surf.F
248      - add storage directives for EmPmR and PmEpR to avoid recomputation of
249        seaice_model in the adjoint that is problematic when seaice_model is
250        turned off in the adjoint. The resolved issue dated back to July when
251        EXTERNAL_FORCING_SURF call was moved.
252        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
253    o pkg/exf/exf_check.F
254      - fix a small bug again (originally found by Wentao Liu, now found again)
255      - streamline error output
256    o pkg/streamice and aim_v23:
257      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
258        Apple's /usr/bin/cpp knows what to do:
259        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
260        Target: x86_64-apple-darwin13.0.0
261    
262    checkpoint64s (2014/01/05)
263    o tools/adjoint_options:
264      - switch to fastopt.net TAF server (instead of default fastopt.de) for
265        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
266    o model/src:
267      - remove some unnecessary TAF storage directives in forward_step.F and
268        in dynamics.F (note: not always removed by TAF, e.g., double storage
269        of kappaRU,kappaRV in former version of dynamics.F).
270    o model/src & pkg/ptracers:
271      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
272        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
273        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
274      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
275      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
276      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
277    o useSingleCpuInput separates single-CPU input from single-CPU output;
278        for now only implemented for in exf_interp_read.F
279    o verification/advect_xy:
280      - fix missing EXCH call in local version of ini_salt.F and update output.
281    o momentum diagnostics:
282      - fix which deltaT is used in Total-Tendency diagnostics.
283      - fix typo in diagnostics for momentum tendency from AB.
284    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
285        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
286    
287    checkpoint64r (2013/12/08)
288    o verification/*/results:
289      - Update reference output of experiments that were passing with just 13 digits
290         (make it easier to detect future changes in results)
291    o model/src & pkg/ptracers:
292      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
293        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
294        to inside ptracers_integrate.F ; remove ptracers_advection.F
295    o coupling interface pkgs:
296        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
297      - change the config check to test the agreement of Ocean Depth
298        with ATM land/sea mask (instead of ATM orography);
299      - send to coupler the number of coupler time-steps to do for this run:
300        this allows to check for consistency and don't need anymore to be
301        specified in parameter file "data";
302      in coupler:
303      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
304      - improve report to log-file of config setting (pass log-file unit to few S/R)
305    o pkg/compon_communic:
306      - add coupling send/receive for non-tiled integer vector;
307      - add S/R to check and stop if any proc has an error (similar to
308        eesupp/src/stop_if_error.F but single thread and across Comm_World).
309    o pkg/exch2:
310      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
311        through list of all tiles my proc owns.
312    o model/src:
313      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
314        from rTrans) to simplify dependencies (no need to store rTrans anymore in
315        calling S/R); this affects AD results at machine truncation level:
316        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
317        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
318    o tools/build_options:
319      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
320    o coupling interface pkgs:
321        [compon_communic, atm_compon_interf & ocn_compon_interf]
322      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
323        to each S/R that needs it; remove un-used variables.
324      - change component tile registration (cpl_register.F in both compon_interf
325        and mitcomponent_tile_register.F) to pass the full list of tiles
326        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
327      - with pkg/exch2: adopt the same convention used for I/O to define mapping
328        towards coupler global array (unless W2_useE2ioLayOut=F):
329         a) can now use different tiling between atm & ocn comp.
330         b) no needs to modify the run-Off map when changing tiling (was needed
331            even if using the same tiling between atm & ocn).
332         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
333            full land tiles); not yet tested.
334      - check for valid mapping from comp. tile to coupler global array
335      - improve report of tile registration results to log file.
336    o pkg/exch2:
337      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
338        tile-registration (CPL_REGISTER);
339      - activate (un-comment) definition and setting of "W2_tileIndex" list to
340        store the local bi,bj indices of each tile;
341      - also print bi,bj in local report to log file;
342      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
343        Jun 2009 modif of pkg/exch2).
344    o testing on baudelaire:
345      - run 2 tests at a time: no significant slow down (since enough cpu) and
346        get the full set of test done earlier
347      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
348    o model/src/thermodynamics.F and routines called from it:
349      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
350        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
351        velocity (outp) by adding bolus velocity.
352      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
353        mass transport from velocity + lateral grid cell area
354      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
355      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
356     in thermodynamics.F
357      - remove k from thermodynamics.F and move it to temp_integrate.F
358        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
359        loop).
360      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
361        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
362        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
363        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
364      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
365        global_ocean.90x40x15, tutorial_global_oce_biogeo and
366        tutorial_tracer_adjsens (+ TLM output).
367    o tools/OAD_support and (verification/*/) code_oad:
368      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
369        module conversion ; remove unneeded CPP_EEOPTIONS.h.
370      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
371        version (closer to model/inc/CPP_OPTIONS.h).
372    o model/src:
373      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
374        retired list of parameters (routine FREEZE has been replace by surface
375        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
376    o pkg/gmredi:
377      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
378        velocity (same scheme but affects machine truncation) for GM_AdvForm.
379      - update output of FWD experiments: front_relax.bvp,
380        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
381    
382    checkpoint64q (2013/11/17)
383    o verification:
384      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
385        tutorial_global_oce_biogeo and global_ocean.90x40x15.
386      - generate new output (growth & melt) for seaice_itd experiment after
387        updating the input pickup_seaice files (previously wrong).
388    o pkg/cost:
389      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
390        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
391        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
392          cannot be applied to var in common block).
393        o allows to get results independent of tile-per-proc setting (if using
394          slower GLOBAL_SUM_SEND_RECV option).
395      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
396        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
397        forward gradients: update output).
398      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
399        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
400    o pkg/mom_common:
401      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
402        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
403        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
404        ensure that all field value that are used are set.
405    o tutorial_deep_convection (smag3d):
406      - add missing scaling in mom_calc_smag_3d.F;
407      - set smag3D_coeff in input.smag3d such that results do not change.
408    o pkg/dic:
409      - change dic_cost.F to compute cost on each tile first and then apply
410        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
411        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
412      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
413    o eesupp/src & pkg/mdsio:
414      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
415        (from pkg/mdsio) since they are no longer used for tape IO.
416      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
417        (+ keep a copy in pkg/atm_ocn_coupler).
418    o verification/isomip:
419      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
420    o tools/build_options:
421      - optfile linux_amd64_ifort11, fast (no ieee) case:
422        to get a working restart for all experiments, add "-fp-model source"
423        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
424    
425    checkpoint64p (2013/10/20)
426    o pkg/autodiff:
427      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
428        criteria, return to simple (default) tape IO format.
429    o pkg/mdsio (+ eesupp/src):
430      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
431        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
432      - fix globalFile and singleCpuIO options using simpler global mapping.
433      - new pairs of scatter/gather vector S/R (one for each type, generated from
434        template) corresponding to simpler global mapping.
435      - adread_write.F: switch to new S/R (but leave old calls commented) and write
436        to globalFile when parameter globalFiles is set to True.
437      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
438    o pkg/autodiff:
439      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
440        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
441        missing, just add a STOP if array type do not match.
442    o pkg/exf:
443      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
444         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
445         and rename array obsSIce to exf_iceFraction.
446    o tutorial_deep_convection:
447      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
448        for now all in this exp. code dir.
449      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
450        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
451    o eesupp/src:
452      - added SINGLE_DISK_IO option because reading of parameter files on
453        very large number of processors did not work with existing set-up
454    
455    checkpoint64o (2013/09/25)
456    o pkg/atm_phys & atm_compon_interf:
457      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
458    o tools/build_options:
459      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
460        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
461        remove CPP setting (was identical to genmake2 default).
462    o pkg/gmredi & model/src: Some updating and work done on the residual model.
463      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
464      - fixed up the calculation of the eddy stress and how it is added to the
465        external forcing via taueddy_external_forcing.F
466      - at the moment, it is very experimental and only works with the variable eddy
467        diffusivity calculated in gmredi_k3d.F
468    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
469        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
470    o testreport (& tools/do_tst_2+2):
471      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
472    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
473      - remove CPP='cpp -traditional -P' (this is genmake2 default)
474      - add switch (for big setups) to use 'medium' memory-model (but leave it
475        commented out for now). Note: needed with FC 19 to compile big setups.
476    o pkg/atm_compon_interf:
477      - regroup per field origin (model & pkgs) the coupling storage routines
478         (which accumalate in time each coupling field)
479      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
480        update accordingly + simplify aim_do_physics.F
481    
482    checkpoint64n (2013/08/26)
483    o pkg/bbl:
484      - update formulation to reduce dispersion of tracer properties in bbl
485      - replaced horizontal and vertical transport parameters with velocities
486      - changes results for verification/global_with_exf.yearly
487    o verification/halfpipe_streamice:
488      - change to matrix construction; update both Fwd & AD output.
489    o verification/tutorial_tracer_adjsens:
490      - OpenAD test: switch to vector-invariant momentum since fluxform with
491        rStar causes problems with OpenAD; update output.
492    o tools:
493      - genmake2: define a common prefix for all temp-file names ; move them
494        to local /tmp disk (but would be easy to move them back);
495      - xmakedepend: apply the same switch for temp-files.
496    o pkg/offline:
497      - changes for use with rStar (NLFS): assume that we continue to provide
498        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
499        output files) and apply r* scaling at each time-step (function of the time
500        varying Eta field); use normal pickup files (needed for restart with NLFS).
501    o adjoint with OpenAD:
502      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
503        package openad.  This package has to be compiled for all runs with OpenAD
504        instead of specifying code_oad_all as a modification directory.
505      - link the fortran templates from tools/OAD_support to the build directory
506        for preprocessing to avoid conflicts between different setups compiled
507        simultaneously and simplify cleanup.
508    o pkg/exf:
509      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
510        main model or other pkgs are exchanged in EXF_MAPFIELDS).
511    o model/src:
512      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
513        (similar to do_fields_blocking_exchanges.F).
514    o tools/genmake2:
515      - remove TAF output src code just before calling staf (when not doing a fresh
516        built, will stop if things go wrong with staf).
517      - fix target "adobj" (left from TAF version-2 transition)
518    o pkg/diagnostics:
519      - add a parameter to track the status of pkg/diagnostics activation;
520        this replace/extend the use of logical param "settingDiags" (to check
521        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
522        New S/R to print error message and stop when pkgStatus is not right.
523      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
524    
525    checkpoint64m (2013/08/13)
526    o model/inc:
527      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
528        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
529    o pkg/kpp & aim_v23:
530      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
531    o pkg/seaice:
532      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
533        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
534      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
535    o eesupp/src:
536      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
537        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
538    o switch to TAF version-2:
539      - add flow directives to "freeze" naming convention for ad-routines that
540        are used in I/O routines of adjoint state and associated common blocks
541        that are used in adcommon.h (backward compatible with version-1)
542      - update all ad-optfiles (in tools/adjoint_options + few local to some
543        verification exp) to switch to latest TAF version (currently 2.5.5);
544        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
545        out except for diva).
546      - the major change with TAF version-2 is that both the differentiated
547        routines and the forward routines (new) are returned as part of the TAF
548        output source code. Update genmake2 accordingly.
549      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
550        with version-2 when compared to TLM or FWD gradient); other experiments
551        output show minor changes (machine truncation level); update the few AD &
552        TLM output with 12 matching digits only (some prior to version-2 switch).
553    
554    checkpoint64l (2013/08/05)
555    o model/src:
556      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
557      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
558        when using TAF but only if using OpenAD.
559    o pkg/mom_common+fluxform+vecinv:
560      - always set horiz. viscosity arrays to background value before calling
561        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
562        only when using variable horiz. viscosity (useVariableVisc=T);
563      - simplify mom_vecinv.F (only 1 block for momViscosity).
564    o pkg/mom_common: variable horiz. viscosity in NH code
565      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
566        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
567      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
568        useBiharmonicVisc & useVariableVisc.
569      - fix old bug (already in 1rst implementation of variable horizontal viscosity
570        in calc_gw.F, version 1.27, 2006/06/20):
571        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
572        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
573      - change background horiz viscosity in vertical momentum (gW) to always be
574        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
575        any type of variable viscosity, e.g., viscAh/4Grid)
576      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
577        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
578        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
579        default viscAh,viscA4 is zero).
580    o model/src:
581      - extend length of drC & recip_drC from Nr to Nr+1.
582    o Divided Adjoint (DIVA) with MPI:
583      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
584      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
585        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
586    
587    checkpoint64k (2013/07/23)
588    o tools/OAD_support:
589      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
590        and remove it from genmake2.
591    o tools/build_options:
592      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
593        MPI_HEADER_FILES list (let genmake2 find the missing headers)
594    o verification/halfpipe_streamice:
595      - change to driving stress formulation; update both Fwd & AD output.
596    o tools/genmake2 and Divided Adjoint with MPI:
597      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
598      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
599      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
600        Makefile, which is set by genmake2, and check which mpi-headers are needed.
601        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
602      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
603    o testreport:
604      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
605        perform additional runs (number of additional runs is "add_DIVA_runs" taken
606        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
607    o verification/lab_sea (AD test):
608      - change to test Divided Adjoint Run in this set-up (both standard AD test
609        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
610    o pkg atm_ & ocn_compon_interf:
611      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
612        staggerTimeStep implementation) and disable (retired) corresponding
613        parameter.
614    o pkg/offline:
615      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
616      - add S/R OFFLINE_CHECK to print offline parameter summary
617        and stop if loading a file that is not used;
618      - enable to calculate GMRedi tensor, KPP mixing and convective index
619        when the corresponding file(s) is/are not specified (but pkg is used).
620      - comment out resetting of monitorFreq (to endTime) since it still useful
621        for monitoring CFL numbers and checking offline fields.
622    o OpenAD:
623      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
624        smaller standard output) and generate new (smaller) output (on baudelaire
625        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
626    o model/src:
627      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
628        (where external_forcing_adjust was called) and change list of arguments;
629      - merge external_forcing_adjust.F into external_forcing_surf.F
630      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
631        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
632        previously in file "balance_relax.F", now removed); remove corresponding
633        arrays in FFIELDS.h.
634      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
635        a hack for getting back surfaceForcingS (loaded from file) when using
636        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
637      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
638        (was getting only 11 digits for AD-grad, due to different truncation
639         error in AD code).
640    
641    checkpoint64j (2013/07/04)
642    o pkg/offline:
643      - to enable the use of other features with pkg offline (e.g., obcs),
644        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
645      - comment out "allowFreezing" (now active) in 2 offline testing exp.
646    o pkg/exf ALLOW_RUNOFTEMP
647      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
648      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
649      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
650    o pkg/atm_phys:
651      - allows to add some damping on uVel,vVel (strength only function of k).
652    o verification, ad-tests:
653      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
654        global_ocean_ebm and offline_exf_seaice.thsice.
655    o verification/halfpipe_streamice:
656      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
657        flux input boundary conditions to be ignored; a fix for this bug changed
658        verification results for forward test.
659      - add adjoint test.
660    o pkg/ptracers:
661      - allow to restart without SOM pickup (resetting SOM to zero).
662    o pkg/gmredi:
663      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
664      - It uses mixing length theory and suppression by steering level effects to
665        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
666        to JPO, for more details).
667      - It also uses the diffusivity to calculate an eddy induced streamfunction
668        based on a PV closure (rather than a buoyancy closure as in GM).
669      - New files added to pkg/gmredi:
670        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
671          induced overturning streamfunction (called from gmredi_calc_tensor)
672        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
673          for use in gmredi_k3d
674        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
675          the eddy diffusivity
676    
677  checkpoint64i (2013/06/18)  checkpoint64i (2013/06/18)
678  o pkg/cheapaml:  o pkg/cheapaml:
# Line 40  o pkg/cfc: Line 709  o pkg/cfc:
709      atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.      atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
710    - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf    - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
711    - new routine to print summary of CFC params and check for consistency.    - new routine to print summary of CFC params and check for consistency.
712    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
713      similar to thsice_advdiff.
714      Note that for the B-grid case the routine parameters uc/vc are overwritten.
715  o pkg/cfc:  o pkg/cfc:
716    - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);    - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
717      update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.      update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
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