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revision 1.1726 by jmc, Tue Aug 28 21:13:08 2012 UTC revision 1.1851 by jmc, Fri Apr 5 21:29:21 2013 UTC
# Line 5  $Name$ Line 5  $Name$
5      ==============================      ==============================
6    
7  o tools/genmake2:  o tools/genmake2:
8      - change default makedepend from the system default to tools/xmakedepend:
9        When no makedepend is specified, select tools/xmakedepend it the test pass,
10        otherwise select the system default (if exist and pass the test) or
11        try to build cyrus-makedepend ; stop if none of the 3 works.
12    o pkg/exf & pkg/thsice:
13      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
14        for energy content of Precip + RunOff & Evap. Assumes:
15       1) Rain has same temp as Air.
16       2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
17       3) Run-Off comes at the temp of surface water (with same Cp)
18       4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
19        put directly into Latent Heat flux & should use water-vapor heat capacity.
20       5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
21        with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
22    o pkg/seaice: simplify the use of CPP flags in JFNK-related files
23        (compile when SEAICE_ALLOW_JFNK is defined)
24    o pkg/thsice:
25      - fix oceanic flux diagnostics & timeave (left from new sequence of calls
26        implementation): move THSICE_AVE call after the advection (called directly
27        from thsice_do_advect.F).
28    o verification/global_ocean.90x40x15 and OpenAD:
29      New experiment for OpenAD is identical to the one in input_ad except that
30        multiDimAdvection=.FALSE.,
31      There is still an issue with this.
32    o pkg/thsice:
33      - account for ice velocity (ocean relative velocity) in turbulent heat flux
34        at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
35        and offline_exf_seaice (main test).
36    
37    checkpoint64f (2013/03/31)
38    o verification/OpenAD:
39      - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
40    o verification/isomip, pkg/shelfice and OpenAD:
41      - add OpenAD setup to this exp and make shelfice package work with OpenAD
42    o verification/tutorial_global_oce_biogeo:
43      - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
44    o verification/offline_exf_seaice:
45      - replace adjoint experiment (now similar to fwd input.thermo/ setup).
46    o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
47      - add OpenAD setup to this exp and make ptracers package work with OpenAD
48    o pkg/seaice/seaice_evp.F:
49       mask the asymmetric contribution of the ice-ocean stress (when
50       the turningAngle is non-zero) over open water to avoid stripes
51       in the EVP-solutions after many EVP-substeps. This does not change
52       the verification experiment (because turningAngle=0 in that experiment),
53       but will affect other EVP solutions with turningAngle.ne.0
54    o verification, AD & TLM output:
55      - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
56        additions and multiplications which affect results at machine truncation
57        level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
58        lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
59        (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
60        digits of matching.
61    o pkg/seaice:
62       modify lsr-algorithm so that it vectorizes AND converges by using a
63       "zebra" method: split vector loop into two with step size 2; this
64       solves a general convergence problem for the JFNK solver on a vector
65       computer. It has the potential to even improve convergence for
66       non-vector machines, but it does change the results so it is turned
67       off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
68       SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
69    
70    checkpoint64e (2013/03/05)
71    o pkg/ecco and several verification experiments:
72       Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
73       from ecco package, and revert to unified routine in model/src/
74       Adjust verification experiments accordingly, especially gloal_oce_llc90
75       Should conclude long-standing work by Gael to reconsile the_main_loop with
76       ECCO and will enable OpenAD's revolve loop in ECCO setup.
77    o pkg/generic_advdiff:
78      - implement compressible flow method for multi-dim advection (similar to
79        gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
80        TAF generates many recomputations) to use it; no yet coded with implicit
81        vertical advection.
82      - change experiment advect_cs (new output) and advect_xy (same output)
83        to test compressible flow multi-dim advection.
84    o pkg/generic_advdiff:
85      - fix SOM advection for unusual cases (linear Free-Surf in r*, other
86        cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
87    o pkg/seaice:
88      - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
89        bug affects two verification experiments (lab_sea and lab_sea.hb87),
90        recover old (wrong) results by setting noSlipFac = 2. in
91        seaice_calc_strainrates.F;
92      - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
93      - add runtime parameter SEAICE_JFNKepsilon for that finite difference
94        gradient in the Jacobian times vector operation (s/r seaice_jacvec)
95      - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
96    o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
97      - new subroutines seaice_lsr_tridiagu/v
98      - introduce loop bounds i/jmin/max to be able to use a restricted
99        additive Schwarz method, but not used for now.
100      - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
101      - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
102    o OpenAD support
103       Reorganize S/R call for overall time-stepping loop to facilitate
104       OpenAD revolve loop replacement
105       (new S/R main_do_loop.F)
106    o model/src:
107      - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
108      - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
109        ADAMS_BASHFORTH2.
110    o pkg/cheapaml:
111      - add new parameter (default=F, same as before) to disable full domain
112        (including land) periodicity in X & Y dir.
113      - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
114        prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
115        into single S/R CHEAPAML_TIMESTEP.
116    
117    checkpoint64d (2013/02/17)
118    o pkg/monitor (angular momentum):
119      - do not add Eta contribution to the total AM if using rigid-lid;
120      - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
121      - horizontal discretisation: compute Zonal wind contribution separately for
122        each component (instead of from cell centered averaged) and use the 4
123        grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
124      - Check that AM is conserved with linear dynamics (momAdvection=F and linear
125        FreeSurf) if using vectorInvariant momentum.
126    o model/src (horizontal grid):
127      - move initialisation of all horizontal grid arrays to null value
128        from specific horizontal grid S/R to main S/R INI_GRID;
129      - add 2 new arrays to project model C-grid velocity on to zonal direction
130        (similar to AngleCosC & -AngleSinC but at U and V point location) and
131        compute them in S/R CALC_GRID_ANGLES.
132    o pkg/seaice: replace a hard coded parameter by a runtime parameter
133        SEAICE_JFNK_tolIter
134    o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
135        preconditioner for JFNK (run LSR into the overlaps as far as possible,
136        i.e OLx/y-2, but overwrite the solution in the overlaps)
137      - extend loop range in seaice_calc_viscosity
138      - add new parameters SEAICE_OLx/y (default = OLx/y-2)
139      - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
140      - slightly modify loops in tridiagonal solver lsr-preconditioner
141      - by default remove the extra exchange in seaice_preconditioner with a
142        replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
143      - modify offline_exf_seaice so that old results without RAS are reproduced
144        for output.dyn_jfnk.txt
145      in seaice_fgmres.F (unrelated to RAS)
146      - add a cpp-flag option for a re-ordered mapping (potentially more
147        efficient), but because this changes the results, turn it off by
148        default
149      - replace the save statement by local common blocks
150    o utils/matlab:
151      - fix tile-offset in rdmnc.m when output was produced using EXCH2.
152      - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
153        instead of local script "load_cs.m".
154    o pkg/seaice:
155      - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
156        to the scalarProductMetric and the unrolling. By chance this does not
157        change the verification experiment, because of the particular domain
158        decomposition
159    o pkg/diagnostics:
160      - change default missing_value from UNSET_RL to -999.
161    o pkg/layers: improve vectorization of layers_fluxcalc.F
162      - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
163        time spent in this routine by more than a factor of 3 on an NEC-SX8
164      - step 2: replace search algorithm by a bisection algorithm found in
165        Press et al. Numerical Recipes in Fortran. This algorithm can be
166        vectorized and finds the correct bin in approx. log2(Nlayers) steps.
167        For now, use this algorithm only for TARGET_NEC_SX defined.
168      - moved the search algorithm into a separate subroutine, that is kept
169        within the same file for automatic inlining.
170      - modified catching potential errors
171    o pkg/ecco:
172      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
173    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
174      - modifications for ALLOW_GENTIM2D_CONTROL
175      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
176      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
177      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
178      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
179    o model/src:
180      - account for moist thermodynamics in (dry) potential temperature equation;
181        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
182        and cpl_aim+ocn.
183      - also switch to standard compiler (gfortran, was using ifort previously)
184        for fizhi-cs experiments reference output.
185    o pkg/ctrl:
186      - 1st step toward generic time-varying control variable (2D) via CPP option
187        ALLOW_GENTIM2D_CONTROL
188      - note new namelist ctrl_nml_genarr in data.ctrl
189    o verification/global_ocean.cs32x15:
190      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
191        thsice calling sequence and update "output.icedyn.txt" output file.
192    o pkg/ptracers:
193      - from Ryan A.: code to allow to restart a tracer at regular time interval
194        specifying a reset frequency and a reset-phase (for each tracers).
195    o pkg/thsice:
196      - implement new sequence of calls for thsice+seaice:
197          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
198          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
199      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
200        in CPP_OPTIONS.h) to recover old sequence;
201      - update diagnostics for Intermediate State thsice diagnostics: now filled
202        just before advection (instead of just after advection in old sequence);
203      - update output of experiment offline_exf_seaice (standard test);
204      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
205        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
206    o pkg/aim_v23:
207      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
208      - use standard pkg/mdsio routines to read & write CO2 pickup file;
209      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
210      - Implement new sequence of calls for seaice advection (with thsice and
211        seaice diffusion): do ice advection after ice-Thermodynamic (previously
212        was done before); change aim_do_physics.F (split the bi,bj loops block);
213      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
214    o pkg/thsice:
215      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
216        where just seaice diffusion is used without seaice-dynamics.
217    
218    checkpoint64c (2013/01/18)
219    o pkg/seaice:
220      - add a parameter JFNKres_tFac that can replace JFNKres_t
221        (= JFNKres_tFac*JFNKresidual before JFNK solver)
222      - add a line search option to the JFNK solver
223      - move update of u/vIce and computation of initial residual into a separate
224        routine (same file); makes the code a little easier to read (?)
225      - the line search requires computation of the residual and for some reason
226        I cannot do the update of u/vIce at the beginning of the Newton loop
227        without changing the results, so we move computation of the new residual
228        also to the end of the Newton loop, even without the line search
229    o pkg/mdsio:
230      - write missing value (corresponding to undefined array value) to meta files;
231        skip this if missing value is one (UNSET_RL would be a better value for the
232        case of undefined missing value but it's current the default missing-value);
233        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
234    o pkg/exf & thsice:
235      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
236        diagnostics) even when SHORTWAVE_HEATING is #undef;
237    o verification/cfc_example:
238      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
239        illustrate how to use it).
240    o verification/offline_exf_seaice:
241      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
242        files to only one time-record.
243      in input.thermo: narrow the 2 bands of low initial ice-concentration near
244        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
245        snapshot output; same mcPheePiston value as in thsice with
246        surf-current=0.2m/s.
247      in input.thsice: similar set-up as in input.thermo (channel with same seaice
248        initial conditions).
249    o verification/cfc_example:
250      - update file "data" with more standard choice (default rotationPeriod,
251        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
252        set deltaTFreeSurf to deltaTtracer) and update the output.
253    o pkg/layers:
254      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
255      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
256    o verification/offline_exf_seaice:
257      - set all {field}period to zero for constant-in-time forcing (not tested
258        anywhere else).
259    o verification/offline_exf_seaice:
260      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
261      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
262    o model/src:
263      - implement Finite-Volume method for (hydrostatic) presure gradient
264        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
265    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
266      - In order to be compatible with the default EVP code, this requires changing
267        the EVP code around a little; and because any small change immediately
268        breaks the lab_sea.hb87 verification experiment, the reference output is
269        updated two times (each time the remaining aggrement was only 2 digits):
270        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
271        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
272        The adjoint test lab_sea.evp also needed to be updated.
273      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
274        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
275        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
276        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
277        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
278        kept obscure, because I need to test it a little more.
279    o pkg/cheapaml:
280      - fix few incorrect type (_RL/_RS) in subroutine calls.
281    o pkg/seaice:
282      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
283        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
284    o model/src:
285      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
286        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
287        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
288    o pkg/cheapaml:
289      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
290        update output of experiment cheapAML_box.
291      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
292        and set them only in one place (cheapaml_readparms.F).
293      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
294      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
295        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
296    o model/src/the_main_loop.F:
297      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
298    o pkg/seaice:
299      - remove legacy branch code.
300      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
301    o verification/*/code*/SEAICE_OPTIONS.h:
302      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
303        SEAICE_CAP_HEFF).
304    o pkg/cheapaml:
305      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
306        to load new forcing fields.
307      - add missing "_d 0" where it's needed; + some editing (improve indentation).
308      - remove switch to "-r8" compiler option (no longer needed) in verification
309        cheapAML_box, keep same output (small trucation error differences).
310    o verification/offline_exf_seaice:
311      - add thermodynamics only test.
312    o verification/cheapAML_box:
313      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
314        keep same output (same 14 digits for cg2d).
315      - switch on "-r8" compiler option (some numerical values are missing
316        the "_d 0") and update output (only 6 digits for cg2d were preserved).
317    
318    checkpoint64b (2012/12/24)
319    o pkg/cheapaml:
320      - remove un-used variables (Qnet,EmPmR) from pickup files.
321      - store tendency of advected variables into cheapaml pickup file
322        and fix the AB-2 restart.
323    o verification/offline_exf_seaice and lab_sea adjoint:
324      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
325      - switch to 4 time steps in offline, consistent with lab_sea.
326      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
327      - update results after change of experiment seaice.
328    o pkg/seaice:
329      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
330        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
331        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
332        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
333    o model/src:
334      - add run-time parameter to select CG2D solver minimum-residual solution
335        (in case of a poor convergence).
336    o pkg/seaice/seaice_lsr.F
337      - move calculation of matrix coefficients into new
338        S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
339        file; the main purpose of this change is to be able to reuse the code
340        in S/R SEAICE_PRECONDITIONER
341      - modify the computation of the residual so that the mass of sea-ice
342        is not used twice; this simplifies the calculations, but since
343        the residual is never used except when LSR_mixIniGuess.ge.4---and this is
344        not tested in testreport---this does not affect the testreport results.
345    o verification/seaice_obcs:
346      - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
347        verification/lab_sea/input.salt_plume; changes results/output.txt*
348    o model/src:
349      - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
350    o pkg/seaice:
351      - improve description of parameters in seaice_fgmres.F and start
352        cleaning up the code
353      - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
354        second argument
355      - add a metric based on grid cell area to SEAICE_SCALPROD; update
356        results of offline_exf_seaice.dyn_jfnk
357      - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
358    o pkg/aim_v23:
359      - fix an other bug in dissipation heating (grid-cell area was missing).
360    o model/src + pkg/seaice:
361      - add global (multi-tile) linear solver for pair of tri-diagonal system
362        along X and Y lines, respectively for U and V component.
363        Note: 1) MPI and cube-exchange not yet coded.
364            2) probably not accurate for poorly conditioned / large size problem.
365      - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
366        default: not compiled and not used.
367    o pkg/seaice:
368      - first attempt at a multi-threaded fgmres solver for the JFNK solver:
369        introduce bi/bj loops and use global_sum_tile_rl instead of
370        mpi_allreduce in seaice_fgmres.F
371      - improve diagnostics output for fgmres solver (seaice_fgmres.F)
372      - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
373      - add a verification experiment for JFNK in offline_exf_seaice
374    o verification:
375      - change (for now, only fwd test) offline_exf_seaice experiment:
376        use a re-entrant channel with idealized coastline (trapezoidal shape)
377        at southern boundary to explore seaice dynamics and thermodynamics
378        with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
379        secondary test (input.thsice) use thermodynamics only with SST relaxation.
380      - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
381    o pkg/exf:
382      - disable "sstExtrapol" when Nr=1
383    o verification:
384      - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
385        to test pkg/cheapaml.
386    o pkg/aim_v23 & pkg/shap_filt:
387      - fix dissipation heating (erroneous gravity multiplication factor).
388    o pkg/seaice:
389      - remove unused field pressPre from jfnk solver
390      - rename two subroutines in seaice_preconditioner.F
391    o eesupp/src:
392       - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
393    o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
394       - remove wrong parts of the rhs and the lhs (were in there
395         because I did not understand the concept of this preconditioner)
396       - add an exchange between u- and v-sweep. This increases communication
397         by a factor of two but improves the convergence of jfnk. Ideally,
398         one would like the u- and v-sweep to be independent. So far within
399         undocumented ifdefs
400       - reorganize the extra computations for printing the residuals
401    o tools/genmake2:
402      - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
403        since it's not necessary (and was preventing to use MNC in some cases).
404    
405    checkpoint64a (2012/11/16)
406    o pkg/autodiff:
407      - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
408        autodiff_readparms.F no longer depends on calling order (within
409        packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
410        rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
411        and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
412    o pkg/obcs:
413      - adding tidal velocity forcing capability to obcs
414        for usage example, see verification/seaice_obcs/input.tides
415    o pkg/seaice:
416      - turn the LSR-relaxation parameters WFAU/V into runtime parameters
417        SEAICE_LSRrelaxU/V
418      - introduce runtime parameter SEAICEetaZmethod (=0 by default)
419    o pkg/aim_v23:
420      - implement heating from friction (bottom friction and stratospheric drag).
421    o pkg/shap_filt:
422      - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
423        dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
424    o model/src:
425      - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
426        time-constant addMass field from file (addMassFile);
427      - support for heating due to friction (and Kinetic Energy dissipation):
428        add option, run-time switch and 3-D field array + support code ; each pkg
429        or S/R can add heating contribution (if there is a sink of KE); the sum is
430        accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
431    o pkg/seaice:
432      - complete merge of ITD code into seaice_growth.F
433        from MITgcm_contrib/torge/itd/code/
434        no verification so far, but Torge Martin tested
435        "1-D test case and Beaufort set up;
436        deliver okay results after 1 model year."
437      - complete merge of SEAICE_SIZE.h into all relevant routines
438      - move computation of eta at Z-points into calc_viscosities
439        + introduce global field etaZ
440        + add different methods for computing etaZ, for now the old
441          method (simple averages of eta to Z-points) is hardwired
442        + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
443          seaice_preconditioner
444      - simplify computations for SEAICE_ZETA_SMOOTHREG
445      - seaice_preconditioner:
446        + replace one remaining press by pressLoc (mistake)
447        + adjust printing of residuals
448      - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
449        + add (SEAICE.h) and rename some counters (initiliased in
450          seaice_init_fixed.F)
451        + add _BEGIN/END_MASTER (myThid)  around print statements
452        + print total number of iterations and failures over SEAICE_monFreq
453          interval to STDOUT
454      - move control over output-messages by fgmres to seaice_jfnk to save
455        some operations
456      - move resetting initial guess for fgmres outside of seaice_fgmres_driver
457        in order to make restarts with sol .ne. zero (fgmres with restarts)
458        (seaice_jfnk.F, seaice_fgmres.F)
459      - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
460        a serious convergence problem when open boundaries are involved
461    o pkg/ggl90: fix computation of control volumes for the case of
462      ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
463      up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
464    o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
465    o pkg/autodiff
466      - Add inAdMode switch for SEAICEuseDYNAMICS:
467        SEAICEuseDYNAMICSinAdMode
468        (extend logic in ADAUTODIFF_INADMODE_SET)
469    o pkg/seaice
470      - Step 1 of merging ice-thickness distribution (ITD) code from
471        MITgcm_contrib/torge/itd/ (author: Torge Martin)
472        The code implements concept laid out in Thorndike et al. (1975);
473        code is enabled via CPP flag SEAICE_ITD
474        nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
475        code is not complete yet!!
476      - SEAICE_SIZE.h now included in almost all seaice routines
477    o verification (using seaice):
478      - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
479        global_ocean.cs32x15.seaice ; update results.
480      - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
481      - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
482        offline_exf_seaice (previously compiling B-grid).
483    o pkg/exf:
484      - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
485        to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
486        forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
487    o pkg/layers (adjust changes from Sept 19):
488      - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
489        this allows to remove "layers_maxNum" dimension from all layers arrays.
490    o pkg/layers (adjust changes from Sept 19):
491      - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
492      - snap-shot extended to all type of layers (not just the 1rst type);
493      - remove layers variables when corresponding CPP option is undef.
494    o pkg/layers:
495      - rename pkg/layers variable and add new output (layer exist & un-weighted
496        velocity in layer)
497    o pkg/seaice:
498      - simplify (?) ocean-drag coefficent computations by using
499        the same routine in all three solvers (saves some code lines)
500      - remove global fields DRAGA and DRAGS from C-grid code and
501        declare them locally in lsr.F (the only place where they are
502        still used)
503      - update AD output of lab_sea.evp (very sensitive anyway).
504    o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
505      (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
506      and SEAICEuseJFNK=.true. A few things to note:
507      - involves a FGMRES, that is parallel but very inefficient,
508        because of many scalar products (global sums) in the Gram-Schmidt
509        orthogonalization method. Needs to be replaced. Original code
510        from J.-F. Lemieux
511      - preconditioner for FGMRES is a stripped down version of LSOR
512      - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
513        preconditioner. For the preconditioner, the default is set to 10.
514      - Jacobian times vector is computed with finite differences
515      - marginally related to JFNK-solver: add a smooth regularization for
516        zeta with tanh that will improve convergence (Lemieux and Tremblay,
517        2009) for any implicit solver (not implemented for EVP because EVP
518        does not need this regularization in the first place). Define
519        SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
520    o eesupp/src:
521      - check in genmake2 that intrinsic S/R flush is available.
522      - add S/R to flush IO unit (if intrinsic S/R flush is available)
523      - flush standard & error msg unit before MPI termination
524      - if debugMode, flush IO unit after printing msg
525    o pkg/ctrl:
526      - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
527        to ctrl_set_unpack_xyz.
528    
529    checkpoint64 (2012/10/09)
530    o pkg/shelfice
531      - in mom_fluxform.F, mom_vecinv.F:
532        CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
533        Bug fix KappaRU -> KappaRV
534        does not change verification/isomip but may change other setups
535        (presumably constant KappaRU=KappaRV)
536      - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
537    o pkg/obcs:
538      - fixed some indexing bugs in obcs_seaice_sponge.F
539      - added obcs relaxation subroutines for HSALT and HSNOW
540      - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
541    o pkg/seaice:
542      - add "multicategory" parameterization for snow in analogy to ice,
543        default is off for now.
544    o pkg/obcs:
545      - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
546        see verification/seaice_obcs/input.seaiceSponge for example application.
547      - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
548        index setting by master-thread. This fix multi-threads Pb in previous modifs.
549    o pkg/layers :
550      - add diagnostics to pkg/layers
551      - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
552        (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
553    o pkg/generic_advdiff/gad_implicit_r.F :
554      - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
555    o pkg/seaice/seaice_growth.F:
556      - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
557    o pkg/obcs:
558      - change default setting of OBCS_UVICE_OLD from defined to undef;
559      - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
560        in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
561      - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
562      - change OB null index value (OB_indexNone) to -99 ; this fix the problem
563        with Southern & Western OB at a tile edge (at least in a simple set-up).
564    o pkg/obcs:
565      - change settings of OB index in case OB coincides with tile edge (shared by
566        2 tiles), so that common OB location is registered by both tiles (instead of
567        only 1). However, for Southern and Western OB, index value = 0 is not
568        recognized as valid OB index (=default null value) and needs to be fixed.
569      - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
570      - new parameter "OB_indexNone" for null index value (for now, still zero)
571        to replace hard-coded null index value of zero.
572    o pkg/exch2:
573      - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
574        always check buffer-size (but outside the loop); move checking for valid
575        index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
576        print each tile and point connection only if |W2_printMsg|>= 2 and 3.
577    o pkg/ctrl (pack & unpack):
578      - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
579        (locally defined) for different variables (+ remove the variable-specific
580        file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
581        (to be extended to other local file names in ctrl.h).
582    o pkg/flt:
583      - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
584    o pkg/mdsio:
585      - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
586    o tools/genmake2:
587      - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
588        (added by Alistair in version 1.51 for building without make depend);
589      - remove Header files list (H_SRC_FILES) from the dependence of targets
590         ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
591        place in version 1.23): this save going through staf when unrelated header
592        file has been modified.
593       Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
594        "make depend" step, still need to do "make links" before "make adtaf".
595    o eesupp/src (+ few pkg src files) & genmake2:
596      - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
597      - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
598      - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
599         upper/lower case ; account for space between "#" and undef/define)
600    o pkg/flt (with exch2):
601      - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
602      - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
603    
604    checkpoint63s (2012/09/05)
605    o pkg/ecco:
606      - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
607      - add more relevant #ifdef ALLOW_SMOOTH ones.
608      - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
609    o pkg/ctrl:
610      - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
611        ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
612      - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
613        doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
614        ctrlSmoothCorrel3D (new).
615        The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
616      - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
617      - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
618        controls when useAtmWind, and vice versa.
619      - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
620      - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
621          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
622      - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
623          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
624      - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
625        replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
626    o pkg/smooth:
627      - remove un-necessary includes.
628      - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
629        Those CPP options were never defined, and not necessary.
630    o model/src:
631      - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
632      - standard treatment of useSMOOTH.
633    o pkg/autodiff:
634      - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
635        useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
636    o pkg/exch2:
637      - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
638        + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
639      - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
640        and tiles to process mapping.
641      - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
642        moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
643        rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
644        from w2_eeboot.F to w2_readparms.F.
645    o eesupp/src:
646      - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
647        ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
648        also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
649      - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
650        is defined (remove condition on usingMPI) to match cases where MPI_INIT
651        has been called.
652      - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
653      - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
654        (so that on 1 proc, get same myPid independently of usingMPI)
655      - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
656        useCubedSphereExchange with EXCH-1 (safer).
657      - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
658    o pkg/ggl90:
659      - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
660        used in ALLOW_GGL90_SMOOTH code.
661    o pkg/flt:
662      - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
663        floats at the Southern end of the domain).
664    o eesupp/inc:
665      - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
666        but not used (and not to be used) anywhere, just for documentation.
667    o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
668      - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
669        a) can damage previously written records in any other multi-record files.
670        b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
671    o tools/genmake2:
672    - define variable MAKE within Makefile and use it in place of 'make';    - define variable MAKE within Makefile and use it in place of 'make';
673    - update AD_CONFIG.h (if needed) before building any of the executable    - update AD_CONFIG.h (if needed) before building any of the executable
674      (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;      (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
675      and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;      and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
676    - always print usual warning comment 'this file is automatically generated'    - always print usual warning comment 'this file is automatically generated'
677      from script convert_cpp_cmd2defines (+ remove this warning from genmake2).      from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
678    o pkg/cheapaml:
679      - updated to correspond to the code used in accepted paper (Nico Wienders).
680  o pkg/exf:  o pkg/exf:
681      added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.      added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
682      ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)      ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
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