/[MITgcm]/MITgcm/doc/tag-index
ViewVC logotype

Diff of /MITgcm/doc/tag-index

Parent Directory Parent Directory | Revision Log Revision Log | View Revision Graph Revision Graph | View Patch Patch

revision 1.1664 by jmc, Mon Jun 4 21:05:46 2012 UTC revision 1.1808 by mlosch, Thu Jan 17 09:00:32 2013 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/seaice: add a line search option to the JFNK solver
8      - move update of u/vIce and computation of initial residual into a separate
9        routine (same file); makes the code a little easier to read (?)
10      - the line search requires computation of the residual and for some reason
11        I cannot do the update of u/vIce at the beginning of the Newton loop
12        without changing the results, so we move computation of the new residual
13        also to the end of the Newton loop, even without the line search
14    o pkg/mdsio:
15      - write missing value (corresponding to undefined array value) to meta files;
16        skip this if missing value is one (UNSET_RL would be a better value for the
17        case of undefined missing value but it's current the default missing-value);
18        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
19    o pkg/exf & thsice:
20      - for diagnostics purpose, fill-up and update Qsw array (+ fill the diagnostics)
21        even when SHORTWAVE_HEATING is #undef;
22    o verification/cfc_example:
23      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to illustrate
24        how to use it).
25    o verification/offline_exf_seaice:
26      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
27        files to only one time-record.
28      in input.thermo: narrow the 2 bands of low initial ice-concentration near
29        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
30        snapshot output; same mcPheePiston value as in thsice with surf-current=0.2m/s.
31      in input.thsice: similar set-up as in input.thermo (channel with same seaice
32        initial conditions).
33    o verification/cfc_example:
34      - update file "data" with more standard choice (default rotationPeriod,
35        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
36        set deltaTFreeSurf to deltaTtracer) and update the output.
37    o pkg/layers:
38      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
39      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
40    o verification/offline_exf_seaice:
41      - set all {field}period to zero for constant-in-time forcing (not tested
42        anywhere else).
43    o verification/offline_exf_seaice:
44      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
45      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
46    o model/src:
47      - implement Finite-Volume method for (hydrostatic) presure gradient
48        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
49    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
50      - In order to be compatible with the default EVP code, this requires changing
51        the EVP code around a little; and because any small change immediately
52        breaks the lab_sea.hb87 verification experiment, the reference output is
53        updated two times (each time the remaining aggrement was only 2 digits):
54        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
55        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
56        The adjoint test lab_sea.evp also needed to be updated.
57      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
58        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
59        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
60        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
61        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
62        kept obscure, because I need to test it a little more.
63    o pkg/cheapaml:
64      - fix few incorrect type (_RL/_RS) in subroutine calls.
65    o pkg/seaice:
66      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
67        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
68    o model/src:
69      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
70        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
71        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
72    o pkg/cheapaml:
73      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
74        update output of experiment cheapAML_box.
75      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
76        and set them only in one place (cheapaml_readparms.F).
77      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
78      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
79        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
80    o model/src/the_main_loop.F:
81      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
82    o pkg/seaice:
83      - remove legacy branch code.
84      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
85    o verification/*/code*/SEAICE_OPTIONS.h:
86      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
87        SEAICE_CAP_HEFF).
88    o pkg/cheapaml:
89      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
90        to load new forcing fields.
91      - add missing "_d 0" where it's needed; + some editing (improve indentation).
92      - remove switch to "-r8" compiler option (no longer needed) in verification
93        cheapAML_box, keep same output (small trucation error differences).
94    o verification/offline_exf_seaice:
95      - add thermodynamics only test.
96    o verification/cheapAML_box:
97      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
98        keep same output (same 14 digits for cg2d).
99      - switch on "-r8" compiler option (some numerical values are missing
100        the "_d 0") and update output (only 6 digits for cg2d were preserved).
101    
102    checkpoint64b (2012/12/24)
103    o pkg/cheapaml:
104      - remove un-used variables (Qnet,EmPmR) from pickup files.
105      - store tendency of advected variables into cheapaml pickup file
106        and fix the AB-2 restart.
107    o verification/offline_exf_seaice and lab_sea adjoint:
108      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
109      - switch to 4 time steps in offline, consistent with lab_sea.
110      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
111      - update results after change of experiment seaice.
112    o pkg/seaice:
113      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
114        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
115        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
116        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
117    o model/src:
118      - add run-time parameter to select CG2D solver minimum-residual solution
119        (in case of a poor convergence).
120    o pkg/seaice/seaice_lsr.F
121      - move calculation of matrix coefficients into new
122        S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
123        file; the main purpose of this change is to be able to reuse the code
124        in S/R SEAICE_PRECONDITIONER
125      - modify the computation of the residual so that the mass of sea-ice
126        is not used twice; this simplifies the calculations, but since
127        the residual is never used except when LSR_mixIniGuess.ge.4---and this is
128        not tested in testreport---this does not affect the testreport results.
129    o verification/seaice_obcs:
130      - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
131        verification/lab_sea/input.salt_plume; changes results/output.txt*
132    o model/src:
133      - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
134    o pkg/seaice:
135      - improve description of parameters in seaice_fgmres.F and start
136        cleaning up the code
137      - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
138        second argument
139      - add a metric based on grid cell area to SEAICE_SCALPROD; update
140        results of offline_exf_seaice.dyn_jfnk
141      - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
142    o pkg/aim_v23:
143      - fix an other bug in dissipation heating (grid-cell area was missing).
144    o model/src + pkg/seaice:
145      - add global (multi-tile) linear solver for pair of tri-diagonal system
146        along X and Y lines, respectively for U and V component.
147        Note: 1) MPI and cube-exchange not yet coded.
148            2) probably not accurate for poorly conditioned / large size problem.
149      - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
150        default: not compiled and not used.
151    o pkg/seaice:
152      - first attempt at a multi-threaded fgmres solver for the JFNK solver:
153        introduce bi/bj loops and use global_sum_tile_rl instead of
154        mpi_allreduce in seaice_fgmres.F
155      - improve diagnostics output for fgmres solver (seaice_fgmres.F)
156      - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
157      - add a verification experiment for JFNK in offline_exf_seaice
158    o verification:
159      - change (for now, only fwd test) offline_exf_seaice experiment:
160        use a re-entrant channel with idealized coastline (trapezoidal shape)
161        at southern boundary to explore seaice dynamics and thermodynamics
162        with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
163        secondary test (input.thsice) use thermodynamics only with SST relaxation.
164      - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
165    o pkg/exf:
166      - disable "sstExtrapol" when Nr=1
167    o verification:
168      - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
169        to test pkg/cheapaml.
170    o pkg/aim_v23 & pkg/shap_filt:
171      - fix dissipation heating (erroneous gravity multiplication factor).
172    o pkg/seaice:
173      - remove unused field pressPre from jfnk solver
174      - rename two subroutines in seaice_preconditioner.F
175    o eesupp/src:
176       - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
177    o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
178       - remove wrong parts of the rhs and the lhs (were in there
179         because I did not understand the concept of this preconditioner)
180       - add an exchange between u- and v-sweep. This increases communication
181         by a factor of two but improves the convergence of jfnk. Ideally,
182         one would like the u- and v-sweep to be independent. So far within
183         undocumented ifdefs
184       - reorganize the extra computations for printing the residuals
185    o tools/genmake2:
186      - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
187        since it's not necessary (and was preventing to use MNC in some cases).
188    
189    checkpoint64a (2012/11/16)
190    o pkg/autodiff:
191      - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
192        autodiff_readparms.F no longer depends on calling order (within
193        packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
194        rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
195        and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
196    o pkg/obcs:
197      - adding tidal velocity forcing capability to obcs
198        for usage example, see verification/seaice_obcs/input.tides
199    o pkg/seaice:
200      - turn the LSR-relaxation parameters WFAU/V into runtime parameters
201        SEAICE_LSRrelaxU/V
202      - introduce runtime parameter SEAICEetaZmethod (=0 by default)
203    o pkg/aim_v23:
204      - implement heating from friction (bottom friction and stratospheric drag).
205    o pkg/shap_filt:
206      - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
207        dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
208    o model/src:
209      - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
210        time-constant addMass field from file (addMassFile);
211      - support for heating due to friction (and Kinetic Energy dissipation):
212        add option, run-time switch and 3-D field array + support code ; each pkg
213        or S/R can add heating contribution (if there is a sink of KE); the sum is
214        accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
215    o pkg/seaice:
216      - complete merge of ITD code into seaice_growth.F
217        from MITgcm_contrib/torge/itd/code/
218        no verification so far, but Torge Martin tested
219        "1-D test case and Beaufort set up;
220        deliver okay results after 1 model year."
221      - complete merge of SEAICE_SIZE.h into all relevant routines
222      - move computation of eta at Z-points into calc_viscosities
223        + introduce global field etaZ
224        + add different methods for computing etaZ, for now the old
225          method (simple averages of eta to Z-points) is hardwired
226        + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
227          seaice_preconditioner
228      - simplify computations for SEAICE_ZETA_SMOOTHREG
229      - seaice_preconditioner:
230        + replace one remaining press by pressLoc (mistake)
231        + adjust printing of residuals
232      - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
233        + add (SEAICE.h) and rename some counters (initiliased in
234          seaice_init_fixed.F)
235        + add _BEGIN/END_MASTER (myThid)  around print statements
236        + print total number of iterations and failures over SEAICE_monFreq
237          interval to STDOUT
238      - move control over output-messages by fgmres to seaice_jfnk to save
239        some operations
240      - move resetting initial guess for fgmres outside of seaice_fgmres_driver
241        in order to make restarts with sol .ne. zero (fgmres with restarts)
242        (seaice_jfnk.F, seaice_fgmres.F)
243      - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
244        a serious convergence problem when open boundaries are involved
245    o pkg/ggl90: fix computation of control volumes for the case of
246      ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
247      up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
248    o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
249    o pkg/autodiff
250      - Add inAdMode switch for SEAICEuseDYNAMICS:
251        SEAICEuseDYNAMICSinAdMode
252        (extend logic in ADAUTODIFF_INADMODE_SET)
253    o pkg/seaice
254      - Step 1 of merging ice-thickness distribution (ITD) code from
255        MITgcm_contrib/torge/itd/ (author: Torge Martin)
256        The code implements concept laid out in Thorndike et al. (1975);
257        code is enabled via CPP flag SEAICE_ITD
258        nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
259        code is not complete yet!!
260      - SEAICE_SIZE.h now included in almost all seaice routines
261    o verification (using seaice):
262      - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
263        global_ocean.cs32x15.seaice ; update results.
264      - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
265      - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
266        offline_exf_seaice (previously compiling B-grid).
267    o pkg/exf:
268      - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
269        to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
270        forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
271    o pkg/layers (adjust changes from Sept 19):
272      - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
273        this allows to remove "layers_maxNum" dimension from all layers arrays.
274    o pkg/layers (adjust changes from Sept 19):
275      - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
276      - snap-shot extended to all type of layers (not just the 1rst type);
277      - remove layers variables when corresponding CPP option is undef.
278    o pkg/layers:
279      - rename pkg/layers variable and add new output (layer exist & un-weighted
280        velocity in layer)
281    o pkg/seaice:
282      - simplify (?) ocean-drag coefficent computations by using
283        the same routine in all three solvers (saves some code lines)
284      - remove global fields DRAGA and DRAGS from C-grid code and
285        declare them locally in lsr.F (the only place where they are
286        still used)
287      - update AD output of lab_sea.evp (very sensitive anyway).
288    o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
289      (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
290      and SEAICEuseJFNK=.true. A few things to note:
291      - involves a FGMRES, that is parallel but very inefficient,
292        because of many scalar products (global sums) in the Gram-Schmidt
293        orthogonalization method. Needs to be replaced. Original code
294        from J.-F. Lemieux
295      - preconditioner for FGMRES is a stripped down version of LSOR
296      - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
297        preconditioner. For the preconditioner, the default is set to 10.
298      - Jacobian times vector is computed with finite differences
299      - marginally related to JFNK-solver: add a smooth regularization for
300        zeta with tanh that will improve convergence (Lemieux and Tremblay,
301        2009) for any implicit solver (not implemented for EVP because EVP
302        does not need this regularization in the first place). Define
303        SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
304    o eesupp/src:
305      - check in genmake2 that intrinsic S/R flush is available.
306      - add S/R to flush IO unit (if intrinsic S/R flush is available)
307      - flush standard & error msg unit before MPI termination
308      - if debugMode, flush IO unit after printing msg
309    o pkg/ctrl:
310      - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
311        to ctrl_set_unpack_xyz.
312    
313    checkpoint64 (2012/10/09)
314    o pkg/shelfice
315      - in mom_fluxform.F, mom_vecinv.F:
316        CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
317        Bug fix KappaRU -> KappaRV
318        does not change verification/isomip but may change other setups
319        (presumably constant KappaRU=KappaRV)
320      - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
321    o pkg/obcs:
322      - fixed some indexing bugs in obcs_seaice_sponge.F
323      - added obcs relaxation subroutines for HSALT and HSNOW
324      - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
325    o pkg/seaice:
326      - add "multicategory" parameterization for snow in analogy to ice,
327        default is off for now.
328    o pkg/obcs:
329      - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
330        see verification/seaice_obcs/input.seaiceSponge for example application.
331      - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
332        index setting by master-thread. This fix multi-threads Pb in previous modifs.
333    o pkg/layers :
334      - add diagnostics to pkg/layers
335      - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
336        (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
337    o pkg/generic_advdiff/gad_implicit_r.F :
338      - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
339    o pkg/seaice/seaice_growth.F:
340      - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
341    o pkg/obcs:
342      - change default setting of OBCS_UVICE_OLD from defined to undef;
343      - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
344        in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
345      - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
346      - change OB null index value (OB_indexNone) to -99 ; this fix the problem
347        with Southern & Western OB at a tile edge (at least in a simple set-up).
348    o pkg/obcs:
349      - change settings of OB index in case OB coincides with tile edge (shared by
350        2 tiles), so that common OB location is registered by both tiles (instead of
351        only 1). However, for Southern and Western OB, index value = 0 is not
352        recognized as valid OB index (=default null value) and needs to be fixed.
353      - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
354      - new parameter "OB_indexNone" for null index value (for now, still zero)
355        to replace hard-coded null index value of zero.
356    o pkg/exch2:
357      - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
358        always check buffer-size (but outside the loop); move checking for valid
359        index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
360        print each tile and point connection only if |W2_printMsg|>= 2 and 3.
361    o pkg/ctrl (pack & unpack):
362      - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
363        (locally defined) for different variables (+ remove the variable-specific
364        file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
365        (to be extended to other local file names in ctrl.h).
366    o pkg/flt:
367      - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
368    o pkg/mdsio:
369      - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
370    o tools/genmake2:
371      - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
372        (added by Alistair in version 1.51 for building without make depend);
373      - remove Header files list (H_SRC_FILES) from the dependence of targets
374         ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
375        place in version 1.23): this save going through staf when unrelated header
376        file has been modified.
377       Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
378        "make depend" step, still need to do "make links" before "make adtaf".
379    o eesupp/src (+ few pkg src files) & genmake2:
380      - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
381      - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
382      - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
383         upper/lower case ; account for space between "#" and undef/define)
384    o pkg/flt (with exch2):
385      - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
386      - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
387    
388    checkpoint63s (2012/09/05)
389    o pkg/ecco:
390      - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
391      - add more relevant #ifdef ALLOW_SMOOTH ones.
392      - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
393    o pkg/ctrl:
394      - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
395        ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
396      - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
397        doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
398        ctrlSmoothCorrel3D (new).
399        The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
400      - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
401      - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
402        controls when useAtmWind, and vice versa.
403      - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
404      - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
405          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
406      - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
407          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
408      - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
409        replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
410    o pkg/smooth:
411      - remove un-necessary includes.
412      - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
413        Those CPP options were never defined, and not necessary.
414    o model/src:
415      - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
416      - standard treatment of useSMOOTH.
417    o pkg/autodiff:
418      - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
419        useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
420    o pkg/exch2:
421      - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
422        + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
423      - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
424        and tiles to process mapping.
425      - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
426        moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
427        rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
428        from w2_eeboot.F to w2_readparms.F.
429    o eesupp/src:
430      - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
431        ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
432        also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
433      - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
434        is defined (remove condition on usingMPI) to match cases where MPI_INIT
435        has been called.
436      - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
437      - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
438        (so that on 1 proc, get same myPid independently of usingMPI)
439      - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
440        useCubedSphereExchange with EXCH-1 (safer).
441      - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
442    o pkg/ggl90:
443      - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
444        used in ALLOW_GGL90_SMOOTH code.
445    o pkg/flt:
446      - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
447        floats at the Southern end of the domain).
448    o eesupp/inc:
449      - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
450        but not used (and not to be used) anywhere, just for documentation.
451    o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
452      - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
453        a) can damage previously written records in any other multi-record files.
454        b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
455    o tools/genmake2:
456      - define variable MAKE within Makefile and use it in place of 'make';
457      - update AD_CONFIG.h (if needed) before building any of the executable
458        (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
459        and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
460      - always print usual warning comment 'this file is automatically generated'
461        from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
462    o pkg/cheapaml:
463      - updated to correspond to the code used in accepted paper (Nico Wienders).
464    o pkg/exf:
465        added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
466        ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
467        and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
468    o pkg/exf, autodiff, ctrl, ecco and seaice:
469        remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
470    o pkg/ctrl, ecco:
471        allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
472        Depending on useAtmWind, one is inactive, and the other is active (see
473        exf_getffields.F/exf_getsurfacefluxes.F).
474    o tools/genmake2:
475      - improve error msg when failing in 2nd test of check_for_broken_Ff
476      - fix option '-makefile' short-name (-mf according to genmake2 -help)
477      - source local config file "genmake_local" just after processing the genmake2
478        command arguments (previously done before processing arg).
479    o pkg/grdchk:
480      - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
481        to this routine from cost_final has been dropped in g_cost_final)
482      - improve printed information (more explicit msg, no longer using "print *,"
483         fix fcpertminus printed value).
484    o model/src:
485      - move call to COST_INIT_VARIA out of packages_init_variables.F directly
486        into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
487        this prevents getting cost-funct reset in adinitialise_varia recomputations.
488    o pkg/dic:
489      - move initialisation of "freefe" array from from dic_biotic_forcing.F to
490        fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
491    o pkg/grdchk:
492      - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
493      - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
494    o pkg/autodiff/ctrl/grdchk :
495      - attempt to sort out what works and what does not,
496        with regard to I/O, and to warn/stop accordingly.
497    o pkg/grdchk:
498      - attempt to fix grdchk in the case of useSingleCpuIO.
499      - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
500       statements were moved from grdchk_main.F and into
501       grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
502      - a global sum is applied to record numbers icvrec/layer
503       out of grdchk_loc so that they be passed to I/O routines.
504    o pkg/smooth:
505      - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
506        smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
507    o verification/testreport:
508      - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
509      - can also use compressed (gzip) reference output file;
510      - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
511        to be easier to collect by testreport.
512      - update existing TLM output (half out-of-date by more than 3 yrs).
513      - report NETCDF & LAPACK settings (from genmake2) in output dir.
514      - report run-time in each individual summary (previously only for AD test);
515        for TLM test, add also TAF version.
516      - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
517    
518    checkpoint63r (2012/08/15)
519    o tools/genmake2:
520      - fix Makefile for target ftlall (+ update files to clean after make ftlall)
521    o pkg/ecco/ecco_cost_final.F :
522      - fix fc print statements (to stdout and costfunction0000) so
523        that the printed value is always after the global sum.
524    o pkg/seaice/seaice_dynsolver.F :
525      - fix ice strength assymptote at SEAICE_area_max<1
526        (no change for the standard case of SEAICE_area_max=1)
527    o some cleaning:
528      - pkg source files: ensure that all *.F files from each pkg included the
529        corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
530        only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
531        code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
532        includes;
533      - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
534      - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
535        is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
536        ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
537      - update option-file CPP_OPTIONS.h of all AD experiments:
538        * no longer include PACKAGES_CONFIG.h ;
539        * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
540        * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
541          including ECCO_CPPOPTIONS.h).
542    o pkg/cost, pkg/ctrl, pkg/ecco option-file:
543      - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
544        separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
545        not necessary accurate).
546      - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
547        pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
548        deliberately break compilation (a remainder that it needs to be customized)
549      - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
550      - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
551      - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
552    o tools/genamke2:
553      - check for lapack.
554    o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
555      - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
556        jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
557        from both packages.
558      - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
559      - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
560      - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
561        of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
562    o pkg/cost : add comments to explain special and/or untested setups.
563    o pkg/exf:
564      - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
565        (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
566    o verification/*/code_ad:
567      mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
568      - reccord when this file is included (define ECCO_CPPOPTIONS_H)
569      - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
570        allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
571    o pkg/seaice :
572      - added possibility to change ice strength/PRESS0 relationship to
573        HEFF, according to the following run time parameters
574        SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
575        SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
576        SEAICEpresH0   :: HEFF threshold for ice strength            (m)
577    o pkg/ggl90 :
578      - added run time flag mxlSurfFlag to include the code that ensure
579        mixing between first and second level (previously included as a comment)
580    o verification/1D_ocean_ice_column/input_ad/data.autodiff :
581      - add test of newly added dumpAdByRec=T option where
582        we write all records to one file per variable.
583    o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
584      - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
585        to check that this code is ok with taf and compiles in adjoint.
586    o pkg/autodiff :
587      - added run time param dumpAdByRec : ad dump format switch.
588        If true then write all records to one file per variable.
589        Else write one file per record (remains the default).
590      - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
591    o pkg/seaice:
592     - Added SEAICEuseTILT run time switch : if set to
593       false then omit the tilt term in seaice dynamics.
594     - Fix free drift calculation.
595    o pkg/shelfice:
596      When initializing SHELFICEDragQuadratic, set default to be
597      consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
598      but retain option to set it independently
599      (inconsistenty spotted by Veronique Dansereau)
600    o eesupp/inc:
601      - in EEPARAMS.h, add real-type constant for some frequently used simple number
602         (0,1,2,1/2), with name explicitly referring to RS/RL type.
603    o model/src:
604      - move balancing of relaxation terms to new S/R balance_relax.F.
605    o pkg/autodiff:
606      re-write active I/O high-level (control) S/R:
607      - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
608      - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
609      - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
610        MDS_READ/WRITE_FIELD); change loops to multi-threads.
611      - update and merge active_file_control_slice.flow into active_file_control.flow
612      - update the calls in lower level S/R (active_file.F, active_file_g.F and
613        active_file_ad.F) keeping the argument list and function unchanged.
614      - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
615        =.TRUE.") and remove high-level (control) _loc version (not called anymore).
616      - new low-level active I/O routines, one for each type (RL/RS), for active var
617        of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
618        fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
619        right type.
620    o autodiff and RS=real*4:
621      - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
622        ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
623      - change argument type of 3-D mask argument to _RS to match type in the call
624        (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
625    o pkg/thsice:
626      - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
627      - option to correct ocean fresh-water flux for imbalance of Atmos+Land
628        fresh-water flux: uniform correction or proportional to local precip.
629    o pkg/ctrl:
630      - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
631      - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
632                            ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
633      - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
634    
635    checkpoint63q (2012/07/30)
636    o pkg/autodiff:
637      note about monitor and snap-shot of ad-variables:
638      a) need to apply ADEXCH before monitor or output of ad-vars to include
639       overlap contributions (was done for adjDump but missing for monitor).
640      b) since ADEXCH implies adding overlap values to interior array, machine
641       truncation error is expected when adding an ADEXCH call in the middle of
642       the time-stepping (although mathematically identical).
643      modifs:
644      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
645        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
646      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
647        apply ADEXCH before monitor or snap-shot of ad-variables:
648           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
649      - implement new method (copy+adexch) for snap-shot and monitor of main model
650        ad-vars (initially not used by default -> output unchanged).
651      - change default (set to 2) to use new method and update few output_adm.txt
652        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
653        and both tutorial_tracer_adjsens tests).
654      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
655        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
656    o pkg/ctrl:
657      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
658      generic control variables via
659      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
660      Only required customization should be S/R ctrl_map_ini_genarr.F
661      (routine in repository contains example)
662    o pkg/exf:
663      - fix and refine checking of surface-relaxation setting when using EXF
664    o verification (adjoint exp):
665      - reduce length of simulation by half for experiment global_ocean.cs32x15
666        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
667    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
668      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
669        of KE that can occur with aggressive optimization
670      + put quadratic bottom drag calculation in separated loops (only done if
671        using bottomDragQuadratic)
672    o model/src: CG2D_NSA
673      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
674         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
675      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
676         change cg2d residual target to be expressed in Wunits (=> do not normalise
677         RHS ; this fix global_max Pb with TAF); update output.
678    o verification/tutorial_tracer_adjsens:
679       improve parameter consistency (and get rid of warnings):
680       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
681       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
682       - use staggerTimeStep (for stability) in som81; use default rotation period.
683    o pkg/exch2:
684      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
685        reset to 0 = 1 long line in X)
686    o pkg/mdsio:
687      - fix reading of dimensions from meta file for large-size domain
688    o model/src:
689      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
690      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
691        Cubed-Sphere Exch with CS-corners inside the domain;
692        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
693        globalArea and to set hasWetCSCorners.
694      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
695        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
696      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
697        useCDscheme and useCubedSphereExchange).
698    o pkg/seaice/seaice_growth.F :
699      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
700        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
701        when the previous code was not correct.
702      - in all cases diagnoze the boundary condition mismatch to SIaaflux
703      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
704        that term to QNET (essentially to set the melt/freeze water to 0degC).
705        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
706    o verification/global_ocean.cs32x15/input.seaice :
707      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
708      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
709      - update results (output.seaice.txt) accordingly.
710    o verification/lab_sea/input/data.seaice :
711      - remove SEAICEheatConsFix, which is now be tested
712        in global_ocean.cs32x15. The presently coded fix
713        is only consistent with real fresh water + nlfs.
714      - update results (output.txt) accordingly.
715    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
716    o AD_CONFIG.h file:
717      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
718      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
719        add it explicitly in each fortran src file where it is needed.
720        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
721        thus introducing potentially wrong dependency; therefore, better to include
722        it only where it's really needed, and after any other included OPTIONS file
723        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
724        or ALLOW_TANGENTLINEAR_RUN).
725    
726    checkpoint63p (2012/07/06)
727    o pkg/autodiff:
728      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
729      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
730        which are now read from new parameter file "data.autodiff" (inAdExact
731        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
732      - add file "data.autodiff" in all verification/*/input_ad/ directories.
733      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
734        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
735    o verification/tutorial_tracer_adjsens/
736      - add extra sub-verification which uses "SOM" advection scheme
737        (2nd Order-Moment Advection Scheme, Prather Limiter) with
738          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
739        and in data:
740          multiDimAdvection=.TRUE.,
741          tempAdvScheme=81,
742          saltAdvScheme=81,
743    o model/src:
744      - introduce ALLOW_BALANCE_RELAX which allow the removal
745       of the global mean of relaxation terms by setting
746       balanceThetaClimRelax and balanceSaltClimRelax
747      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
748       This case is now treated appropriately in seaice_growth.F
749    o pkg/seaice:
750      - do balanceEmPmR and balanceQnet based on the net fluxes
751        (SItflux) that enter the ocean+ice system rather than QNET
752        and EMPMR. Works best in real fresh water.
753      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
754        out of the diagnotics bloc, and stored in global arrays.
755    
756    checkpoint63o (2012/06/29)
757    o vertical mixing schemes:
758      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
759      - replace computation of density (in Function STATE1, opps_calc.F) by a call
760        to S/R FIND_RHO_SCALAR
761      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
762        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
763        affects output (vermix.ggl90) at truncation level.
764    o testreport:
765      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
766        (nSx,nSy) for the number of threads (from eedata.mth)
767    o model/src:
768      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
769        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
770    o verification/tutorial_tracer_adjsens/
771      - compile with ALLOW_CG2D_NSA
772      - run with nonlinFreeSurf=3
773      - update reference output_adm.txt
774    o tools/genmake2:
775      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
776        refine usePROFILES switching off (only when NetCDF is not available).
777    o verification (atmospheric set-up):
778      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
779    o pkg/profiles : refine profiles and files handling.
780    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
781    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
782      - changes to use model/src/the_main_loop.F rather than the ecco version
783        in ecco type adjoint runs.
784    o model/src:
785      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
786      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
787      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
788    o model/src:
789      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
790        update output of test experiment bottom_ctrl_5x5.
791    o pkg/generic_advdiff:
792      - implement vertical bi-harmonic diffusion (for now, only for T & S and
793        only explicitly).
794    o verification/bottom_ctrl_5x5/
795      update reference output (results changed quite some time ago,
796      not sure when; but new reference results look ok in terms of grdchk)
797    o verification/1D_ocean_ice_column/
798      For verification purposes, the exact adjoint rather than an approx.
799      should be used (e.g., to comare against F.D. or TLM).
800      removed autodiff_inadmode*_ad.F routines in code_ad/
801      Update results/ accordingly.
802    o pkg/cal:
803      - change cal_getdate.F so that output date is function of input time only
804        (less ambiguous, not mixed up with input iteration number).
805      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
806    o pkg/diagnostics:
807      - implement calendarDumps also for stats-diags
808      - implement calendarDumps also for snap-shot output (negative freq)
809      - for now, ignores calendarDumps if non-zero phase-lag.
810    
811  checkpoint63n (2012/06/04)  checkpoint63n (2012/06/04)
812  o model/src:  o model/src:
813    - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)    - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
Legend:
Removed from v.1.1664  
changed lines
  Added in v.1.1808
  ViewVC Help
Powered by ViewVC 1.1.22