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revision 1.1726 by jmc, Tue Aug 28 21:13:08 2012 UTC revision 1.1858 by jmc, Tue Apr 23 16:41:58 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/thsice (& pkg/bulk_force):
8      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
9        for energy content of Precip + RunOff & Evap (like with pkg/exf).
10      - change computation domain to always be the interior (without overlap).
11      - fix bug (wrong overlap) when using EXF and stressReduction > 0.
12    o verification/tutorial_global_oce_biogeo:
13      - add preliminary OpenAD setup (still has problems)
14    o model/src:
15      - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
16      - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
17      - move forcing adjustment (balancing surface forcing) in specific S/R
18        where might also be applied exchanges (if needed) to forcing arrays.
19    o pkg/shelfice:
20      - allow to specify the Ice-Shelf mass per unit area (instead of
21        shelficeLoadAnomaly) and do the conversion from one to the other
22      - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
23        to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
24        (b) will be loaded in time (before calling INI_PRESSURE) in case it is
25        needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
26      - update isomip experiment forward output (get machine truncation error
27        from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
28    o verification/offline_exf_seaice:
29      revise data.seaice in input.thermo and input_ad and update results accordingly
30        HO = 0.2, SEAICE_areaLossFormula = 2,
31        SEAICE_growMeltByConv = .TRUE.,
32        SEAICE_doOpenWaterMelt = .TRUE.,
33      Improve consistency with input.thsice and fix the spurious 500m ice corners
34    o verification/global_ocean.cs32x15:
35      - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
36        in icedyn (thsice+seaice-dyn) test and update output.
37    o verification/offline_exf_seaice:
38      - adjust list of tested variables (with testreport) and update
39        standard test output with better slection of monitored fields.
40    o pkg/cd_code:
41      - swtich off Adams-Bashforth on the 1rst iteration. Update output of
42        experiment lab_sea.hb87
43    o tools/genmake2:
44      - change default makedepend from the system default to tools/xmakedepend:
45        When no makedepend is specified, select tools/xmakedepend it the test pass,
46        otherwise select the system default (if exist and pass the test) or
47        try to build cyrus-makedepend ; stop if none of the 3 works.
48    o pkg/exf & pkg/thsice:
49      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
50        for energy content of Precip + RunOff & Evap. Assumes:
51       1) Rain has same temp as Air.
52       2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
53       3) Run-Off comes at the temp of surface water (with same Cp)
54       4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
55        put directly into Latent Heat flux & should use water-vapor heat capacity.
56       5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
57        with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
58    o pkg/seaice: simplify the use of CPP flags in JFNK-related files
59        (compile when SEAICE_ALLOW_JFNK is defined)
60    o pkg/thsice:
61      - fix oceanic flux diagnostics & timeave (left from new sequence of calls
62        implementation): move THSICE_AVE call after the advection (called directly
63        from thsice_do_advect.F).
64    o verification/global_ocean.90x40x15 and OpenAD:
65      New experiment for OpenAD is identical to the one in input_ad except that
66        multiDimAdvection=.FALSE.,
67      There is still an issue with this.
68    o pkg/thsice:
69      - account for ice velocity (ocean relative velocity) in turbulent heat flux
70        at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
71        and offline_exf_seaice (main test).
72    
73    checkpoint64f (2013/03/31)
74    o verification/OpenAD:
75      - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
76    o verification/isomip, pkg/shelfice and OpenAD:
77      - add OpenAD setup to this exp and make shelfice package work with OpenAD
78    o verification/tutorial_global_oce_biogeo:
79      - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
80    o verification/offline_exf_seaice:
81      - replace adjoint experiment (now similar to fwd input.thermo/ setup).
82    o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
83      - add OpenAD setup to this exp and make ptracers package work with OpenAD
84    o pkg/seaice/seaice_evp.F:
85       mask the asymmetric contribution of the ice-ocean stress (when
86       the turningAngle is non-zero) over open water to avoid stripes
87       in the EVP-solutions after many EVP-substeps. This does not change
88       the verification experiment (because turningAngle=0 in that experiment),
89       but will affect other EVP solutions with turningAngle.ne.0
90    o verification, AD & TLM output:
91      - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
92        additions and multiplications which affect results at machine truncation
93        level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
94        lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
95        (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
96        digits of matching.
97    o pkg/seaice:
98       modify lsr-algorithm so that it vectorizes AND converges by using a
99       "zebra" method: split vector loop into two with step size 2; this
100       solves a general convergence problem for the JFNK solver on a vector
101       computer. It has the potential to even improve convergence for
102       non-vector machines, but it does change the results so it is turned
103       off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
104       SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
105    
106    checkpoint64e (2013/03/05)
107    o pkg/ecco and several verification experiments:
108       Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
109       from ecco package, and revert to unified routine in model/src/
110       Adjust verification experiments accordingly, especially gloal_oce_llc90
111       Should conclude long-standing work by Gael to reconsile the_main_loop with
112       ECCO and will enable OpenAD's revolve loop in ECCO setup.
113    o pkg/generic_advdiff:
114      - implement compressible flow method for multi-dim advection (similar to
115        gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
116        TAF generates many recomputations) to use it; no yet coded with implicit
117        vertical advection.
118      - change experiment advect_cs (new output) and advect_xy (same output)
119        to test compressible flow multi-dim advection.
120    o pkg/generic_advdiff:
121      - fix SOM advection for unusual cases (linear Free-Surf in r*, other
122        cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
123    o pkg/seaice:
124      - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
125        bug affects two verification experiments (lab_sea and lab_sea.hb87),
126        recover old (wrong) results by setting noSlipFac = 2. in
127        seaice_calc_strainrates.F;
128      - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
129      - add runtime parameter SEAICE_JFNKepsilon for that finite difference
130        gradient in the Jacobian times vector operation (s/r seaice_jacvec)
131      - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
132    o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
133      - new subroutines seaice_lsr_tridiagu/v
134      - introduce loop bounds i/jmin/max to be able to use a restricted
135        additive Schwarz method, but not used for now.
136      - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
137      - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
138    o OpenAD support
139       Reorganize S/R call for overall time-stepping loop to facilitate
140       OpenAD revolve loop replacement
141       (new S/R main_do_loop.F)
142    o model/src:
143      - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
144      - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
145        ADAMS_BASHFORTH2.
146    o pkg/cheapaml:
147      - add new parameter (default=F, same as before) to disable full domain
148        (including land) periodicity in X & Y dir.
149      - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
150        prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
151        into single S/R CHEAPAML_TIMESTEP.
152    
153    checkpoint64d (2013/02/17)
154    o pkg/monitor (angular momentum):
155      - do not add Eta contribution to the total AM if using rigid-lid;
156      - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
157      - horizontal discretisation: compute Zonal wind contribution separately for
158        each component (instead of from cell centered averaged) and use the 4
159        grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
160      - Check that AM is conserved with linear dynamics (momAdvection=F and linear
161        FreeSurf) if using vectorInvariant momentum.
162    o model/src (horizontal grid):
163      - move initialisation of all horizontal grid arrays to null value
164        from specific horizontal grid S/R to main S/R INI_GRID;
165      - add 2 new arrays to project model C-grid velocity on to zonal direction
166        (similar to AngleCosC & -AngleSinC but at U and V point location) and
167        compute them in S/R CALC_GRID_ANGLES.
168    o pkg/seaice: replace a hard coded parameter by a runtime parameter
169        SEAICE_JFNK_tolIter
170    o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
171        preconditioner for JFNK (run LSR into the overlaps as far as possible,
172        i.e OLx/y-2, but overwrite the solution in the overlaps)
173      - extend loop range in seaice_calc_viscosity
174      - add new parameters SEAICE_OLx/y (default = OLx/y-2)
175      - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
176      - slightly modify loops in tridiagonal solver lsr-preconditioner
177      - by default remove the extra exchange in seaice_preconditioner with a
178        replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
179      - modify offline_exf_seaice so that old results without RAS are reproduced
180        for output.dyn_jfnk.txt
181      in seaice_fgmres.F (unrelated to RAS)
182      - add a cpp-flag option for a re-ordered mapping (potentially more
183        efficient), but because this changes the results, turn it off by
184        default
185      - replace the save statement by local common blocks
186    o utils/matlab:
187      - fix tile-offset in rdmnc.m when output was produced using EXCH2.
188      - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
189        instead of local script "load_cs.m".
190    o pkg/seaice:
191      - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
192        to the scalarProductMetric and the unrolling. By chance this does not
193        change the verification experiment, because of the particular domain
194        decomposition
195    o pkg/diagnostics:
196      - change default missing_value from UNSET_RL to -999.
197    o pkg/layers: improve vectorization of layers_fluxcalc.F
198      - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
199        time spent in this routine by more than a factor of 3 on an NEC-SX8
200      - step 2: replace search algorithm by a bisection algorithm found in
201        Press et al. Numerical Recipes in Fortran. This algorithm can be
202        vectorized and finds the correct bin in approx. log2(Nlayers) steps.
203        For now, use this algorithm only for TARGET_NEC_SX defined.
204      - moved the search algorithm into a separate subroutine, that is kept
205        within the same file for automatic inlining.
206      - modified catching potential errors
207    o pkg/ecco:
208      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
209    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
210      - modifications for ALLOW_GENTIM2D_CONTROL
211      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
212      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
213      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
214      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
215    o model/src:
216      - account for moist thermodynamics in (dry) potential temperature equation;
217        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
218        and cpl_aim+ocn.
219      - also switch to standard compiler (gfortran, was using ifort previously)
220        for fizhi-cs experiments reference output.
221    o pkg/ctrl:
222      - 1st step toward generic time-varying control variable (2D) via CPP option
223        ALLOW_GENTIM2D_CONTROL
224      - note new namelist ctrl_nml_genarr in data.ctrl
225    o verification/global_ocean.cs32x15:
226      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
227        thsice calling sequence and update "output.icedyn.txt" output file.
228    o pkg/ptracers:
229      - from Ryan A.: code to allow to restart a tracer at regular time interval
230        specifying a reset frequency and a reset-phase (for each tracers).
231    o pkg/thsice:
232      - implement new sequence of calls for thsice+seaice:
233          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
234          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
235      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
236        in CPP_OPTIONS.h) to recover old sequence;
237      - update diagnostics for Intermediate State thsice diagnostics: now filled
238        just before advection (instead of just after advection in old sequence);
239      - update output of experiment offline_exf_seaice (standard test);
240      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
241        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
242    o pkg/aim_v23:
243      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
244      - use standard pkg/mdsio routines to read & write CO2 pickup file;
245      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
246      - Implement new sequence of calls for seaice advection (with thsice and
247        seaice diffusion): do ice advection after ice-Thermodynamic (previously
248        was done before); change aim_do_physics.F (split the bi,bj loops block);
249      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
250    o pkg/thsice:
251      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
252        where just seaice diffusion is used without seaice-dynamics.
253    
254    checkpoint64c (2013/01/18)
255    o pkg/seaice:
256      - add a parameter JFNKres_tFac that can replace JFNKres_t
257        (= JFNKres_tFac*JFNKresidual before JFNK solver)
258      - add a line search option to the JFNK solver
259      - move update of u/vIce and computation of initial residual into a separate
260        routine (same file); makes the code a little easier to read (?)
261      - the line search requires computation of the residual and for some reason
262        I cannot do the update of u/vIce at the beginning of the Newton loop
263        without changing the results, so we move computation of the new residual
264        also to the end of the Newton loop, even without the line search
265    o pkg/mdsio:
266      - write missing value (corresponding to undefined array value) to meta files;
267        skip this if missing value is one (UNSET_RL would be a better value for the
268        case of undefined missing value but it's current the default missing-value);
269        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
270    o pkg/exf & thsice:
271      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
272        diagnostics) even when SHORTWAVE_HEATING is #undef;
273    o verification/cfc_example:
274      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
275        illustrate how to use it).
276    o verification/offline_exf_seaice:
277      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
278        files to only one time-record.
279      in input.thermo: narrow the 2 bands of low initial ice-concentration near
280        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
281        snapshot output; same mcPheePiston value as in thsice with
282        surf-current=0.2m/s.
283      in input.thsice: similar set-up as in input.thermo (channel with same seaice
284        initial conditions).
285    o verification/cfc_example:
286      - update file "data" with more standard choice (default rotationPeriod,
287        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
288        set deltaTFreeSurf to deltaTtracer) and update the output.
289    o pkg/layers:
290      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
291      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
292    o verification/offline_exf_seaice:
293      - set all {field}period to zero for constant-in-time forcing (not tested
294        anywhere else).
295    o verification/offline_exf_seaice:
296      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
297      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
298    o model/src:
299      - implement Finite-Volume method for (hydrostatic) presure gradient
300        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
301    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
302      - In order to be compatible with the default EVP code, this requires changing
303        the EVP code around a little; and because any small change immediately
304        breaks the lab_sea.hb87 verification experiment, the reference output is
305        updated two times (each time the remaining aggrement was only 2 digits):
306        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
307        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
308        The adjoint test lab_sea.evp also needed to be updated.
309      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
310        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
311        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
312        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
313        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
314        kept obscure, because I need to test it a little more.
315    o pkg/cheapaml:
316      - fix few incorrect type (_RL/_RS) in subroutine calls.
317    o pkg/seaice:
318      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
319        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
320    o model/src:
321      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
322        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
323        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
324    o pkg/cheapaml:
325      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
326        update output of experiment cheapAML_box.
327      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
328        and set them only in one place (cheapaml_readparms.F).
329      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
330      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
331        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
332    o model/src/the_main_loop.F:
333      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
334    o pkg/seaice:
335      - remove legacy branch code.
336      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
337    o verification/*/code*/SEAICE_OPTIONS.h:
338      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
339        SEAICE_CAP_HEFF).
340    o pkg/cheapaml:
341      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
342        to load new forcing fields.
343      - add missing "_d 0" where it's needed; + some editing (improve indentation).
344      - remove switch to "-r8" compiler option (no longer needed) in verification
345        cheapAML_box, keep same output (small trucation error differences).
346    o verification/offline_exf_seaice:
347      - add thermodynamics only test.
348    o verification/cheapAML_box:
349      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
350        keep same output (same 14 digits for cg2d).
351      - switch on "-r8" compiler option (some numerical values are missing
352        the "_d 0") and update output (only 6 digits for cg2d were preserved).
353    
354    checkpoint64b (2012/12/24)
355    o pkg/cheapaml:
356      - remove un-used variables (Qnet,EmPmR) from pickup files.
357      - store tendency of advected variables into cheapaml pickup file
358        and fix the AB-2 restart.
359    o verification/offline_exf_seaice and lab_sea adjoint:
360      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
361      - switch to 4 time steps in offline, consistent with lab_sea.
362      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
363      - update results after change of experiment seaice.
364    o pkg/seaice:
365      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
366        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
367        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
368        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
369    o model/src:
370      - add run-time parameter to select CG2D solver minimum-residual solution
371        (in case of a poor convergence).
372    o pkg/seaice/seaice_lsr.F
373      - move calculation of matrix coefficients into new
374        S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
375        file; the main purpose of this change is to be able to reuse the code
376        in S/R SEAICE_PRECONDITIONER
377      - modify the computation of the residual so that the mass of sea-ice
378        is not used twice; this simplifies the calculations, but since
379        the residual is never used except when LSR_mixIniGuess.ge.4---and this is
380        not tested in testreport---this does not affect the testreport results.
381    o verification/seaice_obcs:
382      - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
383        verification/lab_sea/input.salt_plume; changes results/output.txt*
384    o model/src:
385      - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
386    o pkg/seaice:
387      - improve description of parameters in seaice_fgmres.F and start
388        cleaning up the code
389      - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
390        second argument
391      - add a metric based on grid cell area to SEAICE_SCALPROD; update
392        results of offline_exf_seaice.dyn_jfnk
393      - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
394    o pkg/aim_v23:
395      - fix an other bug in dissipation heating (grid-cell area was missing).
396    o model/src + pkg/seaice:
397      - add global (multi-tile) linear solver for pair of tri-diagonal system
398        along X and Y lines, respectively for U and V component.
399        Note: 1) MPI and cube-exchange not yet coded.
400            2) probably not accurate for poorly conditioned / large size problem.
401      - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
402        default: not compiled and not used.
403    o pkg/seaice:
404      - first attempt at a multi-threaded fgmres solver for the JFNK solver:
405        introduce bi/bj loops and use global_sum_tile_rl instead of
406        mpi_allreduce in seaice_fgmres.F
407      - improve diagnostics output for fgmres solver (seaice_fgmres.F)
408      - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
409      - add a verification experiment for JFNK in offline_exf_seaice
410    o verification:
411      - change (for now, only fwd test) offline_exf_seaice experiment:
412        use a re-entrant channel with idealized coastline (trapezoidal shape)
413        at southern boundary to explore seaice dynamics and thermodynamics
414        with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
415        secondary test (input.thsice) use thermodynamics only with SST relaxation.
416      - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
417    o pkg/exf:
418      - disable "sstExtrapol" when Nr=1
419    o verification:
420      - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
421        to test pkg/cheapaml.
422    o pkg/aim_v23 & pkg/shap_filt:
423      - fix dissipation heating (erroneous gravity multiplication factor).
424    o pkg/seaice:
425      - remove unused field pressPre from jfnk solver
426      - rename two subroutines in seaice_preconditioner.F
427    o eesupp/src:
428       - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
429    o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
430       - remove wrong parts of the rhs and the lhs (were in there
431         because I did not understand the concept of this preconditioner)
432       - add an exchange between u- and v-sweep. This increases communication
433         by a factor of two but improves the convergence of jfnk. Ideally,
434         one would like the u- and v-sweep to be independent. So far within
435         undocumented ifdefs
436       - reorganize the extra computations for printing the residuals
437    o tools/genmake2:
438      - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
439        since it's not necessary (and was preventing to use MNC in some cases).
440    
441    checkpoint64a (2012/11/16)
442    o pkg/autodiff:
443      - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
444        autodiff_readparms.F no longer depends on calling order (within
445        packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
446        rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
447        and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
448    o pkg/obcs:
449      - adding tidal velocity forcing capability to obcs
450        for usage example, see verification/seaice_obcs/input.tides
451    o pkg/seaice:
452      - turn the LSR-relaxation parameters WFAU/V into runtime parameters
453        SEAICE_LSRrelaxU/V
454      - introduce runtime parameter SEAICEetaZmethod (=0 by default)
455    o pkg/aim_v23:
456      - implement heating from friction (bottom friction and stratospheric drag).
457    o pkg/shap_filt:
458      - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
459        dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
460    o model/src:
461      - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
462        time-constant addMass field from file (addMassFile);
463      - support for heating due to friction (and Kinetic Energy dissipation):
464        add option, run-time switch and 3-D field array + support code ; each pkg
465        or S/R can add heating contribution (if there is a sink of KE); the sum is
466        accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
467    o pkg/seaice:
468      - complete merge of ITD code into seaice_growth.F
469        from MITgcm_contrib/torge/itd/code/
470        no verification so far, but Torge Martin tested
471        "1-D test case and Beaufort set up;
472        deliver okay results after 1 model year."
473      - complete merge of SEAICE_SIZE.h into all relevant routines
474      - move computation of eta at Z-points into calc_viscosities
475        + introduce global field etaZ
476        + add different methods for computing etaZ, for now the old
477          method (simple averages of eta to Z-points) is hardwired
478        + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
479          seaice_preconditioner
480      - simplify computations for SEAICE_ZETA_SMOOTHREG
481      - seaice_preconditioner:
482        + replace one remaining press by pressLoc (mistake)
483        + adjust printing of residuals
484      - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
485        + add (SEAICE.h) and rename some counters (initiliased in
486          seaice_init_fixed.F)
487        + add _BEGIN/END_MASTER (myThid)  around print statements
488        + print total number of iterations and failures over SEAICE_monFreq
489          interval to STDOUT
490      - move control over output-messages by fgmres to seaice_jfnk to save
491        some operations
492      - move resetting initial guess for fgmres outside of seaice_fgmres_driver
493        in order to make restarts with sol .ne. zero (fgmres with restarts)
494        (seaice_jfnk.F, seaice_fgmres.F)
495      - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
496        a serious convergence problem when open boundaries are involved
497    o pkg/ggl90: fix computation of control volumes for the case of
498      ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
499      up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
500    o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
501    o pkg/autodiff
502      - Add inAdMode switch for SEAICEuseDYNAMICS:
503        SEAICEuseDYNAMICSinAdMode
504        (extend logic in ADAUTODIFF_INADMODE_SET)
505    o pkg/seaice
506      - Step 1 of merging ice-thickness distribution (ITD) code from
507        MITgcm_contrib/torge/itd/ (author: Torge Martin)
508        The code implements concept laid out in Thorndike et al. (1975);
509        code is enabled via CPP flag SEAICE_ITD
510        nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
511        code is not complete yet!!
512      - SEAICE_SIZE.h now included in almost all seaice routines
513    o verification (using seaice):
514      - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
515        global_ocean.cs32x15.seaice ; update results.
516      - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
517      - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
518        offline_exf_seaice (previously compiling B-grid).
519    o pkg/exf:
520      - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
521        to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
522        forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
523    o pkg/layers (adjust changes from Sept 19):
524      - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
525        this allows to remove "layers_maxNum" dimension from all layers arrays.
526    o pkg/layers (adjust changes from Sept 19):
527      - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
528      - snap-shot extended to all type of layers (not just the 1rst type);
529      - remove layers variables when corresponding CPP option is undef.
530    o pkg/layers:
531      - rename pkg/layers variable and add new output (layer exist & un-weighted
532        velocity in layer)
533    o pkg/seaice:
534      - simplify (?) ocean-drag coefficent computations by using
535        the same routine in all three solvers (saves some code lines)
536      - remove global fields DRAGA and DRAGS from C-grid code and
537        declare them locally in lsr.F (the only place where they are
538        still used)
539      - update AD output of lab_sea.evp (very sensitive anyway).
540    o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
541      (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
542      and SEAICEuseJFNK=.true. A few things to note:
543      - involves a FGMRES, that is parallel but very inefficient,
544        because of many scalar products (global sums) in the Gram-Schmidt
545        orthogonalization method. Needs to be replaced. Original code
546        from J.-F. Lemieux
547      - preconditioner for FGMRES is a stripped down version of LSOR
548      - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
549        preconditioner. For the preconditioner, the default is set to 10.
550      - Jacobian times vector is computed with finite differences
551      - marginally related to JFNK-solver: add a smooth regularization for
552        zeta with tanh that will improve convergence (Lemieux and Tremblay,
553        2009) for any implicit solver (not implemented for EVP because EVP
554        does not need this regularization in the first place). Define
555        SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
556    o eesupp/src:
557      - check in genmake2 that intrinsic S/R flush is available.
558      - add S/R to flush IO unit (if intrinsic S/R flush is available)
559      - flush standard & error msg unit before MPI termination
560      - if debugMode, flush IO unit after printing msg
561    o pkg/ctrl:
562      - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
563        to ctrl_set_unpack_xyz.
564    
565    checkpoint64 (2012/10/09)
566    o pkg/shelfice
567      - in mom_fluxform.F, mom_vecinv.F:
568        CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
569        Bug fix KappaRU -> KappaRV
570        does not change verification/isomip but may change other setups
571        (presumably constant KappaRU=KappaRV)
572      - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
573    o pkg/obcs:
574      - fixed some indexing bugs in obcs_seaice_sponge.F
575      - added obcs relaxation subroutines for HSALT and HSNOW
576      - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
577    o pkg/seaice:
578      - add "multicategory" parameterization for snow in analogy to ice,
579        default is off for now.
580    o pkg/obcs:
581      - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
582        see verification/seaice_obcs/input.seaiceSponge for example application.
583      - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
584        index setting by master-thread. This fix multi-threads Pb in previous modifs.
585    o pkg/layers :
586      - add diagnostics to pkg/layers
587      - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
588        (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
589    o pkg/generic_advdiff/gad_implicit_r.F :
590      - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
591    o pkg/seaice/seaice_growth.F:
592      - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
593    o pkg/obcs:
594      - change default setting of OBCS_UVICE_OLD from defined to undef;
595      - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
596        in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
597      - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
598      - change OB null index value (OB_indexNone) to -99 ; this fix the problem
599        with Southern & Western OB at a tile edge (at least in a simple set-up).
600    o pkg/obcs:
601      - change settings of OB index in case OB coincides with tile edge (shared by
602        2 tiles), so that common OB location is registered by both tiles (instead of
603        only 1). However, for Southern and Western OB, index value = 0 is not
604        recognized as valid OB index (=default null value) and needs to be fixed.
605      - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
606      - new parameter "OB_indexNone" for null index value (for now, still zero)
607        to replace hard-coded null index value of zero.
608    o pkg/exch2:
609      - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
610        always check buffer-size (but outside the loop); move checking for valid
611        index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
612        print each tile and point connection only if |W2_printMsg|>= 2 and 3.
613    o pkg/ctrl (pack & unpack):
614      - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
615        (locally defined) for different variables (+ remove the variable-specific
616        file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
617        (to be extended to other local file names in ctrl.h).
618    o pkg/flt:
619      - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
620    o pkg/mdsio:
621      - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
622    o tools/genmake2:
623      - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
624        (added by Alistair in version 1.51 for building without make depend);
625      - remove Header files list (H_SRC_FILES) from the dependence of targets
626         ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
627        place in version 1.23): this save going through staf when unrelated header
628        file has been modified.
629       Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
630        "make depend" step, still need to do "make links" before "make adtaf".
631    o eesupp/src (+ few pkg src files) & genmake2:
632      - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
633      - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
634      - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
635         upper/lower case ; account for space between "#" and undef/define)
636    o pkg/flt (with exch2):
637      - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
638      - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
639    
640    checkpoint63s (2012/09/05)
641    o pkg/ecco:
642      - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
643      - add more relevant #ifdef ALLOW_SMOOTH ones.
644      - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
645    o pkg/ctrl:
646      - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
647        ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
648      - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
649        doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
650        ctrlSmoothCorrel3D (new).
651        The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
652      - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
653      - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
654        controls when useAtmWind, and vice versa.
655      - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
656      - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
657          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
658      - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
659          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
660      - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
661        replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
662    o pkg/smooth:
663      - remove un-necessary includes.
664      - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
665        Those CPP options were never defined, and not necessary.
666    o model/src:
667      - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
668      - standard treatment of useSMOOTH.
669    o pkg/autodiff:
670      - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
671        useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
672    o pkg/exch2:
673      - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
674        + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
675      - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
676        and tiles to process mapping.
677      - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
678        moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
679        rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
680        from w2_eeboot.F to w2_readparms.F.
681    o eesupp/src:
682      - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
683        ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
684        also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
685      - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
686        is defined (remove condition on usingMPI) to match cases where MPI_INIT
687        has been called.
688      - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
689      - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
690        (so that on 1 proc, get same myPid independently of usingMPI)
691      - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
692        useCubedSphereExchange with EXCH-1 (safer).
693      - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
694    o pkg/ggl90:
695      - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
696        used in ALLOW_GGL90_SMOOTH code.
697    o pkg/flt:
698      - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
699        floats at the Southern end of the domain).
700    o eesupp/inc:
701      - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
702        but not used (and not to be used) anywhere, just for documentation.
703    o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
704      - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
705        a) can damage previously written records in any other multi-record files.
706        b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
707  o tools/genmake2:  o tools/genmake2:
708    - define variable MAKE within Makefile and use it in place of 'make';    - define variable MAKE within Makefile and use it in place of 'make';
709    - update AD_CONFIG.h (if needed) before building any of the executable    - update AD_CONFIG.h (if needed) before building any of the executable
# Line 11  o tools/genmake2: Line 711  o tools/genmake2:
711      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;
712    - always print usual warning comment 'this file is automatically generated'    - always print usual warning comment 'this file is automatically generated'
713      from script convert_cpp_cmd2defines (+ remove this warning from genmake2).      from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
714    o pkg/cheapaml:
715      - updated to correspond to the code used in accepted paper (Nico Wienders).
716  o pkg/exf:  o pkg/exf:
717      added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.      added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
718      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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