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revision 1.1716 by jmc, Wed Aug 15 14:44:48 2012 UTC revision 1.1854 by jmc, Thu Apr 11 15:43:30 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 verification/offline_exf_seaice:
8      revise data.seaice in input.thermo and input_ad and update results accordingly
9        HO = 0.2, SEAICE_areaLossFormula = 2,
10        SEAICE_growMeltByConv = .TRUE.,
11        SEAICE_doOpenWaterMelt = .TRUE.,
12      Improve consistency with input.thsice and fix the spurious 500m ice corners
13    o verification/global_ocean.cs32x15:
14      - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
15        in icedyn (thsice+seaice-dyn) test and update output.
16    o verification/offline_exf_seaice:
17      - adjust list of tested variables (with testreport) and update
18        standard test output with better slection of monitored fields.
19    o pkg/cd_code:
20      - swtich off Adams-Bashforth on the 1rst iteration. Update output of
21        experiment lab_sea.hb87
22    o tools/genmake2:
23      - change default makedepend from the system default to tools/xmakedepend:
24        When no makedepend is specified, select tools/xmakedepend it the test pass,
25        otherwise select the system default (if exist and pass the test) or
26        try to build cyrus-makedepend ; stop if none of the 3 works.
27    o pkg/exf & pkg/thsice:
28      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
29        for energy content of Precip + RunOff & Evap. Assumes:
30       1) Rain has same temp as Air.
31       2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
32       3) Run-Off comes at the temp of surface water (with same Cp)
33       4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
34        put directly into Latent Heat flux & should use water-vapor heat capacity.
35       5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
36        with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
37    o pkg/seaice: simplify the use of CPP flags in JFNK-related files
38        (compile when SEAICE_ALLOW_JFNK is defined)
39    o pkg/thsice:
40      - fix oceanic flux diagnostics & timeave (left from new sequence of calls
41        implementation): move THSICE_AVE call after the advection (called directly
42        from thsice_do_advect.F).
43    o verification/global_ocean.90x40x15 and OpenAD:
44      New experiment for OpenAD is identical to the one in input_ad except that
45        multiDimAdvection=.FALSE.,
46      There is still an issue with this.
47    o pkg/thsice:
48      - account for ice velocity (ocean relative velocity) in turbulent heat flux
49        at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
50        and offline_exf_seaice (main test).
51    
52    checkpoint64f (2013/03/31)
53    o verification/OpenAD:
54      - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
55    o verification/isomip, pkg/shelfice and OpenAD:
56      - add OpenAD setup to this exp and make shelfice package work with OpenAD
57    o verification/tutorial_global_oce_biogeo:
58      - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
59    o verification/offline_exf_seaice:
60      - replace adjoint experiment (now similar to fwd input.thermo/ setup).
61    o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
62      - add OpenAD setup to this exp and make ptracers package work with OpenAD
63    o pkg/seaice/seaice_evp.F:
64       mask the asymmetric contribution of the ice-ocean stress (when
65       the turningAngle is non-zero) over open water to avoid stripes
66       in the EVP-solutions after many EVP-substeps. This does not change
67       the verification experiment (because turningAngle=0 in that experiment),
68       but will affect other EVP solutions with turningAngle.ne.0
69    o verification, AD & TLM output:
70      - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
71        additions and multiplications which affect results at machine truncation
72        level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
73        lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
74        (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
75        digits of matching.
76    o pkg/seaice:
77       modify lsr-algorithm so that it vectorizes AND converges by using a
78       "zebra" method: split vector loop into two with step size 2; this
79       solves a general convergence problem for the JFNK solver on a vector
80       computer. It has the potential to even improve convergence for
81       non-vector machines, but it does change the results so it is turned
82       off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
83       SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
84    
85    checkpoint64e (2013/03/05)
86    o pkg/ecco and several verification experiments:
87       Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
88       from ecco package, and revert to unified routine in model/src/
89       Adjust verification experiments accordingly, especially gloal_oce_llc90
90       Should conclude long-standing work by Gael to reconsile the_main_loop with
91       ECCO and will enable OpenAD's revolve loop in ECCO setup.
92    o pkg/generic_advdiff:
93      - implement compressible flow method for multi-dim advection (similar to
94        gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
95        TAF generates many recomputations) to use it; no yet coded with implicit
96        vertical advection.
97      - change experiment advect_cs (new output) and advect_xy (same output)
98        to test compressible flow multi-dim advection.
99    o pkg/generic_advdiff:
100      - fix SOM advection for unusual cases (linear Free-Surf in r*, other
101        cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
102    o pkg/seaice:
103      - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
104        bug affects two verification experiments (lab_sea and lab_sea.hb87),
105        recover old (wrong) results by setting noSlipFac = 2. in
106        seaice_calc_strainrates.F;
107      - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
108      - add runtime parameter SEAICE_JFNKepsilon for that finite difference
109        gradient in the Jacobian times vector operation (s/r seaice_jacvec)
110      - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
111    o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
112      - new subroutines seaice_lsr_tridiagu/v
113      - introduce loop bounds i/jmin/max to be able to use a restricted
114        additive Schwarz method, but not used for now.
115      - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
116      - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
117    o OpenAD support
118       Reorganize S/R call for overall time-stepping loop to facilitate
119       OpenAD revolve loop replacement
120       (new S/R main_do_loop.F)
121    o model/src:
122      - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
123      - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
124        ADAMS_BASHFORTH2.
125    o pkg/cheapaml:
126      - add new parameter (default=F, same as before) to disable full domain
127        (including land) periodicity in X & Y dir.
128      - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
129        prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
130        into single S/R CHEAPAML_TIMESTEP.
131    
132    checkpoint64d (2013/02/17)
133    o pkg/monitor (angular momentum):
134      - do not add Eta contribution to the total AM if using rigid-lid;
135      - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
136      - horizontal discretisation: compute Zonal wind contribution separately for
137        each component (instead of from cell centered averaged) and use the 4
138        grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
139      - Check that AM is conserved with linear dynamics (momAdvection=F and linear
140        FreeSurf) if using vectorInvariant momentum.
141    o model/src (horizontal grid):
142      - move initialisation of all horizontal grid arrays to null value
143        from specific horizontal grid S/R to main S/R INI_GRID;
144      - add 2 new arrays to project model C-grid velocity on to zonal direction
145        (similar to AngleCosC & -AngleSinC but at U and V point location) and
146        compute them in S/R CALC_GRID_ANGLES.
147    o pkg/seaice: replace a hard coded parameter by a runtime parameter
148        SEAICE_JFNK_tolIter
149    o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
150        preconditioner for JFNK (run LSR into the overlaps as far as possible,
151        i.e OLx/y-2, but overwrite the solution in the overlaps)
152      - extend loop range in seaice_calc_viscosity
153      - add new parameters SEAICE_OLx/y (default = OLx/y-2)
154      - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
155      - slightly modify loops in tridiagonal solver lsr-preconditioner
156      - by default remove the extra exchange in seaice_preconditioner with a
157        replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
158      - modify offline_exf_seaice so that old results without RAS are reproduced
159        for output.dyn_jfnk.txt
160      in seaice_fgmres.F (unrelated to RAS)
161      - add a cpp-flag option for a re-ordered mapping (potentially more
162        efficient), but because this changes the results, turn it off by
163        default
164      - replace the save statement by local common blocks
165    o utils/matlab:
166      - fix tile-offset in rdmnc.m when output was produced using EXCH2.
167      - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
168        instead of local script "load_cs.m".
169    o pkg/seaice:
170      - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
171        to the scalarProductMetric and the unrolling. By chance this does not
172        change the verification experiment, because of the particular domain
173        decomposition
174    o pkg/diagnostics:
175      - change default missing_value from UNSET_RL to -999.
176    o pkg/layers: improve vectorization of layers_fluxcalc.F
177      - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
178        time spent in this routine by more than a factor of 3 on an NEC-SX8
179      - step 2: replace search algorithm by a bisection algorithm found in
180        Press et al. Numerical Recipes in Fortran. This algorithm can be
181        vectorized and finds the correct bin in approx. log2(Nlayers) steps.
182        For now, use this algorithm only for TARGET_NEC_SX defined.
183      - moved the search algorithm into a separate subroutine, that is kept
184        within the same file for automatic inlining.
185      - modified catching potential errors
186    o pkg/ecco:
187      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
188    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
189      - modifications for ALLOW_GENTIM2D_CONTROL
190      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
191      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
192      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
193      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
194    o model/src:
195      - account for moist thermodynamics in (dry) potential temperature equation;
196        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
197        and cpl_aim+ocn.
198      - also switch to standard compiler (gfortran, was using ifort previously)
199        for fizhi-cs experiments reference output.
200    o pkg/ctrl:
201      - 1st step toward generic time-varying control variable (2D) via CPP option
202        ALLOW_GENTIM2D_CONTROL
203      - note new namelist ctrl_nml_genarr in data.ctrl
204    o verification/global_ocean.cs32x15:
205      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
206        thsice calling sequence and update "output.icedyn.txt" output file.
207    o pkg/ptracers:
208      - from Ryan A.: code to allow to restart a tracer at regular time interval
209        specifying a reset frequency and a reset-phase (for each tracers).
210    o pkg/thsice:
211      - implement new sequence of calls for thsice+seaice:
212          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
213          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
214      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
215        in CPP_OPTIONS.h) to recover old sequence;
216      - update diagnostics for Intermediate State thsice diagnostics: now filled
217        just before advection (instead of just after advection in old sequence);
218      - update output of experiment offline_exf_seaice (standard test);
219      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
220        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
221    o pkg/aim_v23:
222      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
223      - use standard pkg/mdsio routines to read & write CO2 pickup file;
224      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
225      - Implement new sequence of calls for seaice advection (with thsice and
226        seaice diffusion): do ice advection after ice-Thermodynamic (previously
227        was done before); change aim_do_physics.F (split the bi,bj loops block);
228      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
229    o pkg/thsice:
230      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
231        where just seaice diffusion is used without seaice-dynamics.
232    
233    checkpoint64c (2013/01/18)
234    o pkg/seaice:
235      - add a parameter JFNKres_tFac that can replace JFNKres_t
236        (= JFNKres_tFac*JFNKresidual before JFNK solver)
237      - add a line search option to the JFNK solver
238      - move update of u/vIce and computation of initial residual into a separate
239        routine (same file); makes the code a little easier to read (?)
240      - the line search requires computation of the residual and for some reason
241        I cannot do the update of u/vIce at the beginning of the Newton loop
242        without changing the results, so we move computation of the new residual
243        also to the end of the Newton loop, even without the line search
244    o pkg/mdsio:
245      - write missing value (corresponding to undefined array value) to meta files;
246        skip this if missing value is one (UNSET_RL would be a better value for the
247        case of undefined missing value but it's current the default missing-value);
248        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
249    o pkg/exf & thsice:
250      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
251        diagnostics) even when SHORTWAVE_HEATING is #undef;
252    o verification/cfc_example:
253      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
254        illustrate how to use it).
255    o verification/offline_exf_seaice:
256      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
257        files to only one time-record.
258      in input.thermo: narrow the 2 bands of low initial ice-concentration near
259        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
260        snapshot output; same mcPheePiston value as in thsice with
261        surf-current=0.2m/s.
262      in input.thsice: similar set-up as in input.thermo (channel with same seaice
263        initial conditions).
264    o verification/cfc_example:
265      - update file "data" with more standard choice (default rotationPeriod,
266        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
267        set deltaTFreeSurf to deltaTtracer) and update the output.
268    o pkg/layers:
269      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
270      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
271    o verification/offline_exf_seaice:
272      - set all {field}period to zero for constant-in-time forcing (not tested
273        anywhere else).
274    o verification/offline_exf_seaice:
275      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
276      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
277    o model/src:
278      - implement Finite-Volume method for (hydrostatic) presure gradient
279        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
280    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
281      - In order to be compatible with the default EVP code, this requires changing
282        the EVP code around a little; and because any small change immediately
283        breaks the lab_sea.hb87 verification experiment, the reference output is
284        updated two times (each time the remaining aggrement was only 2 digits):
285        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
286        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
287        The adjoint test lab_sea.evp also needed to be updated.
288      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
289        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
290        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
291        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
292        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
293        kept obscure, because I need to test it a little more.
294    o pkg/cheapaml:
295      - fix few incorrect type (_RL/_RS) in subroutine calls.
296    o pkg/seaice:
297      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
298        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
299    o model/src:
300      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
301        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
302        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
303    o pkg/cheapaml:
304      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
305        update output of experiment cheapAML_box.
306      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
307        and set them only in one place (cheapaml_readparms.F).
308      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
309      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
310        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
311    o model/src/the_main_loop.F:
312      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
313    o pkg/seaice:
314      - remove legacy branch code.
315      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
316    o verification/*/code*/SEAICE_OPTIONS.h:
317      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
318        SEAICE_CAP_HEFF).
319    o pkg/cheapaml:
320      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
321        to load new forcing fields.
322      - add missing "_d 0" where it's needed; + some editing (improve indentation).
323      - remove switch to "-r8" compiler option (no longer needed) in verification
324        cheapAML_box, keep same output (small trucation error differences).
325    o verification/offline_exf_seaice:
326      - add thermodynamics only test.
327    o verification/cheapAML_box:
328      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
329        keep same output (same 14 digits for cg2d).
330      - switch on "-r8" compiler option (some numerical values are missing
331        the "_d 0") and update output (only 6 digits for cg2d were preserved).
332    
333    checkpoint64b (2012/12/24)
334    o pkg/cheapaml:
335      - remove un-used variables (Qnet,EmPmR) from pickup files.
336      - store tendency of advected variables into cheapaml pickup file
337        and fix the AB-2 restart.
338    o verification/offline_exf_seaice and lab_sea adjoint:
339      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
340      - switch to 4 time steps in offline, consistent with lab_sea.
341      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
342      - update results after change of experiment seaice.
343    o pkg/seaice:
344      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
345        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
346        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
347        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
348    o model/src:
349      - add run-time parameter to select CG2D solver minimum-residual solution
350        (in case of a poor convergence).
351    o pkg/seaice/seaice_lsr.F
352      - move calculation of matrix coefficients into new
353        S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
354        file; the main purpose of this change is to be able to reuse the code
355        in S/R SEAICE_PRECONDITIONER
356      - modify the computation of the residual so that the mass of sea-ice
357        is not used twice; this simplifies the calculations, but since
358        the residual is never used except when LSR_mixIniGuess.ge.4---and this is
359        not tested in testreport---this does not affect the testreport results.
360    o verification/seaice_obcs:
361      - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
362        verification/lab_sea/input.salt_plume; changes results/output.txt*
363    o model/src:
364      - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
365    o pkg/seaice:
366      - improve description of parameters in seaice_fgmres.F and start
367        cleaning up the code
368      - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
369        second argument
370      - add a metric based on grid cell area to SEAICE_SCALPROD; update
371        results of offline_exf_seaice.dyn_jfnk
372      - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
373    o pkg/aim_v23:
374      - fix an other bug in dissipation heating (grid-cell area was missing).
375    o model/src + pkg/seaice:
376      - add global (multi-tile) linear solver for pair of tri-diagonal system
377        along X and Y lines, respectively for U and V component.
378        Note: 1) MPI and cube-exchange not yet coded.
379            2) probably not accurate for poorly conditioned / large size problem.
380      - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
381        default: not compiled and not used.
382    o pkg/seaice:
383      - first attempt at a multi-threaded fgmres solver for the JFNK solver:
384        introduce bi/bj loops and use global_sum_tile_rl instead of
385        mpi_allreduce in seaice_fgmres.F
386      - improve diagnostics output for fgmres solver (seaice_fgmres.F)
387      - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
388      - add a verification experiment for JFNK in offline_exf_seaice
389    o verification:
390      - change (for now, only fwd test) offline_exf_seaice experiment:
391        use a re-entrant channel with idealized coastline (trapezoidal shape)
392        at southern boundary to explore seaice dynamics and thermodynamics
393        with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
394        secondary test (input.thsice) use thermodynamics only with SST relaxation.
395      - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
396    o pkg/exf:
397      - disable "sstExtrapol" when Nr=1
398    o verification:
399      - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
400        to test pkg/cheapaml.
401    o pkg/aim_v23 & pkg/shap_filt:
402      - fix dissipation heating (erroneous gravity multiplication factor).
403    o pkg/seaice:
404      - remove unused field pressPre from jfnk solver
405      - rename two subroutines in seaice_preconditioner.F
406    o eesupp/src:
407       - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
408    o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
409       - remove wrong parts of the rhs and the lhs (were in there
410         because I did not understand the concept of this preconditioner)
411       - add an exchange between u- and v-sweep. This increases communication
412         by a factor of two but improves the convergence of jfnk. Ideally,
413         one would like the u- and v-sweep to be independent. So far within
414         undocumented ifdefs
415       - reorganize the extra computations for printing the residuals
416    o tools/genmake2:
417      - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
418        since it's not necessary (and was preventing to use MNC in some cases).
419    
420    checkpoint64a (2012/11/16)
421    o pkg/autodiff:
422      - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
423        autodiff_readparms.F no longer depends on calling order (within
424        packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
425        rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
426        and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
427    o pkg/obcs:
428      - adding tidal velocity forcing capability to obcs
429        for usage example, see verification/seaice_obcs/input.tides
430    o pkg/seaice:
431      - turn the LSR-relaxation parameters WFAU/V into runtime parameters
432        SEAICE_LSRrelaxU/V
433      - introduce runtime parameter SEAICEetaZmethod (=0 by default)
434    o pkg/aim_v23:
435      - implement heating from friction (bottom friction and stratospheric drag).
436    o pkg/shap_filt:
437      - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
438        dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
439    o model/src:
440      - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
441        time-constant addMass field from file (addMassFile);
442      - support for heating due to friction (and Kinetic Energy dissipation):
443        add option, run-time switch and 3-D field array + support code ; each pkg
444        or S/R can add heating contribution (if there is a sink of KE); the sum is
445        accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
446    o pkg/seaice:
447      - complete merge of ITD code into seaice_growth.F
448        from MITgcm_contrib/torge/itd/code/
449        no verification so far, but Torge Martin tested
450        "1-D test case and Beaufort set up;
451        deliver okay results after 1 model year."
452      - complete merge of SEAICE_SIZE.h into all relevant routines
453      - move computation of eta at Z-points into calc_viscosities
454        + introduce global field etaZ
455        + add different methods for computing etaZ, for now the old
456          method (simple averages of eta to Z-points) is hardwired
457        + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
458          seaice_preconditioner
459      - simplify computations for SEAICE_ZETA_SMOOTHREG
460      - seaice_preconditioner:
461        + replace one remaining press by pressLoc (mistake)
462        + adjust printing of residuals
463      - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
464        + add (SEAICE.h) and rename some counters (initiliased in
465          seaice_init_fixed.F)
466        + add _BEGIN/END_MASTER (myThid)  around print statements
467        + print total number of iterations and failures over SEAICE_monFreq
468          interval to STDOUT
469      - move control over output-messages by fgmres to seaice_jfnk to save
470        some operations
471      - move resetting initial guess for fgmres outside of seaice_fgmres_driver
472        in order to make restarts with sol .ne. zero (fgmres with restarts)
473        (seaice_jfnk.F, seaice_fgmres.F)
474      - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
475        a serious convergence problem when open boundaries are involved
476    o pkg/ggl90: fix computation of control volumes for the case of
477      ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
478      up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
479    o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
480    o pkg/autodiff
481      - Add inAdMode switch for SEAICEuseDYNAMICS:
482        SEAICEuseDYNAMICSinAdMode
483        (extend logic in ADAUTODIFF_INADMODE_SET)
484    o pkg/seaice
485      - Step 1 of merging ice-thickness distribution (ITD) code from
486        MITgcm_contrib/torge/itd/ (author: Torge Martin)
487        The code implements concept laid out in Thorndike et al. (1975);
488        code is enabled via CPP flag SEAICE_ITD
489        nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
490        code is not complete yet!!
491      - SEAICE_SIZE.h now included in almost all seaice routines
492    o verification (using seaice):
493      - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
494        global_ocean.cs32x15.seaice ; update results.
495      - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
496      - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
497        offline_exf_seaice (previously compiling B-grid).
498    o pkg/exf:
499      - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
500        to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
501        forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
502    o pkg/layers (adjust changes from Sept 19):
503      - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
504        this allows to remove "layers_maxNum" dimension from all layers arrays.
505    o pkg/layers (adjust changes from Sept 19):
506      - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
507      - snap-shot extended to all type of layers (not just the 1rst type);
508      - remove layers variables when corresponding CPP option is undef.
509    o pkg/layers:
510      - rename pkg/layers variable and add new output (layer exist & un-weighted
511        velocity in layer)
512    o pkg/seaice:
513      - simplify (?) ocean-drag coefficent computations by using
514        the same routine in all three solvers (saves some code lines)
515      - remove global fields DRAGA and DRAGS from C-grid code and
516        declare them locally in lsr.F (the only place where they are
517        still used)
518      - update AD output of lab_sea.evp (very sensitive anyway).
519    o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
520      (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
521      and SEAICEuseJFNK=.true. A few things to note:
522      - involves a FGMRES, that is parallel but very inefficient,
523        because of many scalar products (global sums) in the Gram-Schmidt
524        orthogonalization method. Needs to be replaced. Original code
525        from J.-F. Lemieux
526      - preconditioner for FGMRES is a stripped down version of LSOR
527      - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
528        preconditioner. For the preconditioner, the default is set to 10.
529      - Jacobian times vector is computed with finite differences
530      - marginally related to JFNK-solver: add a smooth regularization for
531        zeta with tanh that will improve convergence (Lemieux and Tremblay,
532        2009) for any implicit solver (not implemented for EVP because EVP
533        does not need this regularization in the first place). Define
534        SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
535    o eesupp/src:
536      - check in genmake2 that intrinsic S/R flush is available.
537      - add S/R to flush IO unit (if intrinsic S/R flush is available)
538      - flush standard & error msg unit before MPI termination
539      - if debugMode, flush IO unit after printing msg
540    o pkg/ctrl:
541      - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
542        to ctrl_set_unpack_xyz.
543    
544    checkpoint64 (2012/10/09)
545    o pkg/shelfice
546      - in mom_fluxform.F, mom_vecinv.F:
547        CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
548        Bug fix KappaRU -> KappaRV
549        does not change verification/isomip but may change other setups
550        (presumably constant KappaRU=KappaRV)
551      - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
552    o pkg/obcs:
553      - fixed some indexing bugs in obcs_seaice_sponge.F
554      - added obcs relaxation subroutines for HSALT and HSNOW
555      - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
556    o pkg/seaice:
557      - add "multicategory" parameterization for snow in analogy to ice,
558        default is off for now.
559    o pkg/obcs:
560      - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
561        see verification/seaice_obcs/input.seaiceSponge for example application.
562      - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
563        index setting by master-thread. This fix multi-threads Pb in previous modifs.
564    o pkg/layers :
565      - add diagnostics to pkg/layers
566      - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
567        (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
568    o pkg/generic_advdiff/gad_implicit_r.F :
569      - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
570    o pkg/seaice/seaice_growth.F:
571      - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
572    o pkg/obcs:
573      - change default setting of OBCS_UVICE_OLD from defined to undef;
574      - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
575        in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
576      - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
577      - change OB null index value (OB_indexNone) to -99 ; this fix the problem
578        with Southern & Western OB at a tile edge (at least in a simple set-up).
579    o pkg/obcs:
580      - change settings of OB index in case OB coincides with tile edge (shared by
581        2 tiles), so that common OB location is registered by both tiles (instead of
582        only 1). However, for Southern and Western OB, index value = 0 is not
583        recognized as valid OB index (=default null value) and needs to be fixed.
584      - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
585      - new parameter "OB_indexNone" for null index value (for now, still zero)
586        to replace hard-coded null index value of zero.
587    o pkg/exch2:
588      - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
589        always check buffer-size (but outside the loop); move checking for valid
590        index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
591        print each tile and point connection only if |W2_printMsg|>= 2 and 3.
592    o pkg/ctrl (pack & unpack):
593      - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
594        (locally defined) for different variables (+ remove the variable-specific
595        file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
596        (to be extended to other local file names in ctrl.h).
597    o pkg/flt:
598      - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
599    o pkg/mdsio:
600      - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
601    o tools/genmake2:
602      - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
603        (added by Alistair in version 1.51 for building without make depend);
604      - remove Header files list (H_SRC_FILES) from the dependence of targets
605         ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
606        place in version 1.23): this save going through staf when unrelated header
607        file has been modified.
608       Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
609        "make depend" step, still need to do "make links" before "make adtaf".
610    o eesupp/src (+ few pkg src files) & genmake2:
611      - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
612      - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
613      - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
614         upper/lower case ; account for space between "#" and undef/define)
615    o pkg/flt (with exch2):
616      - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
617      - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
618    
619    checkpoint63s (2012/09/05)
620    o pkg/ecco:
621      - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
622      - add more relevant #ifdef ALLOW_SMOOTH ones.
623      - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
624    o pkg/ctrl:
625      - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
626        ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
627      - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
628        doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
629        ctrlSmoothCorrel3D (new).
630        The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
631      - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
632      - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
633        controls when useAtmWind, and vice versa.
634      - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
635      - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
636          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
637      - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
638          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
639      - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
640        replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
641    o pkg/smooth:
642      - remove un-necessary includes.
643      - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
644        Those CPP options were never defined, and not necessary.
645    o model/src:
646      - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
647      - standard treatment of useSMOOTH.
648    o pkg/autodiff:
649      - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
650        useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
651    o pkg/exch2:
652      - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
653        + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
654      - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
655        and tiles to process mapping.
656      - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
657        moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
658        rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
659        from w2_eeboot.F to w2_readparms.F.
660    o eesupp/src:
661      - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
662        ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
663        also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
664      - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
665        is defined (remove condition on usingMPI) to match cases where MPI_INIT
666        has been called.
667      - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
668      - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
669        (so that on 1 proc, get same myPid independently of usingMPI)
670      - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
671        useCubedSphereExchange with EXCH-1 (safer).
672      - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
673    o pkg/ggl90:
674      - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
675        used in ALLOW_GGL90_SMOOTH code.
676    o pkg/flt:
677      - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
678        floats at the Southern end of the domain).
679    o eesupp/inc:
680      - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
681        but not used (and not to be used) anywhere, just for documentation.
682    o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
683      - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
684        a) can damage previously written records in any other multi-record files.
685        b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
686    o tools/genmake2:
687      - define variable MAKE within Makefile and use it in place of 'make';
688      - update AD_CONFIG.h (if needed) before building any of the executable
689        (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
690        and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
691      - always print usual warning comment 'this file is automatically generated'
692        from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
693    o pkg/cheapaml:
694      - updated to correspond to the code used in accepted paper (Nico Wienders).
695    o pkg/exf:
696        added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
697        ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
698        and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
699    o pkg/exf, autodiff, ctrl, ecco and seaice:
700        remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
701    o pkg/ctrl, ecco:
702        allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
703        Depending on useAtmWind, one is inactive, and the other is active (see
704        exf_getffields.F/exf_getsurfacefluxes.F).
705    o tools/genmake2:
706      - improve error msg when failing in 2nd test of check_for_broken_Ff
707      - fix option '-makefile' short-name (-mf according to genmake2 -help)
708      - source local config file "genmake_local" just after processing the genmake2
709        command arguments (previously done before processing arg).
710    o pkg/grdchk:
711      - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
712        to this routine from cost_final has been dropped in g_cost_final)
713      - improve printed information (more explicit msg, no longer using "print *,"
714         fix fcpertminus printed value).
715    o model/src:
716      - move call to COST_INIT_VARIA out of packages_init_variables.F directly
717        into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
718        this prevents getting cost-funct reset in adinitialise_varia recomputations.
719    o pkg/dic:
720      - move initialisation of "freefe" array from from dic_biotic_forcing.F to
721        fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
722    o pkg/grdchk:
723      - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
724      - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
725    o pkg/autodiff/ctrl/grdchk :
726      - attempt to sort out what works and what does not,
727        with regard to I/O, and to warn/stop accordingly.
728    o pkg/grdchk:
729      - attempt to fix grdchk in the case of useSingleCpuIO.
730      - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
731       statements were moved from grdchk_main.F and into
732       grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
733      - a global sum is applied to record numbers icvrec/layer
734       out of grdchk_loc so that they be passed to I/O routines.
735    o pkg/smooth:
736      - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
737        smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
738    o verification/testreport:
739      - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
740      - can also use compressed (gzip) reference output file;
741      - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
742        to be easier to collect by testreport.
743      - update existing TLM output (half out-of-date by more than 3 yrs).
744      - report NETCDF & LAPACK settings (from genmake2) in output dir.
745      - report run-time in each individual summary (previously only for AD test);
746        for TLM test, add also TAF version.
747      - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
748    
749  checkpoint63r (2012/08/15)  checkpoint63r (2012/08/15)
750  o tools/genmake2:  o tools/genmake2:
751    - fix Makefile for target ftlall (+ update files to clean after make ftlall)    - fix Makefile for target ftlall (+ update files to clean after make ftlall)
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