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revision 1.1726 by jmc, Tue Aug 28 21:13:08 2012 UTC revision 1.1867 by jmc, Fri May 10 20:19:37 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/offline:
8      - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
9        (previously called from pkg/dic_surfforcing_init.F)
10    o model/src:
11      - re-order sequence of calls within packages_init_variables.F, using
12        standard order, except for:
13         DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
14         CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
15    o new pkg: atm_phys
16      - add entry point and source code (previously in contrib
17          verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
18        (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
19      - re-order sequence of calls within packages_readparms.F,
20         packages_init_fixed.F and packages_write_pickup.F
21        (but skip packages_init_variables.F because of TAF issues).
22      - update contrib/*/atm_gray/ experiment.
23    o pkg/seaice (ITD code):
24      - simplify and fix the writing of pickup-files for ITD case
25    o pkg/seaice (ITD code):
26      - introduce floe size dependent lateral melt for ITD case;
27      - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
28      - update seaice_itd experiment main output.
29    o pkg/thsice:
30      - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
31        declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
32        changed accordingly pkg/atm2d.
33    
34    checkpoint64g (2013/05/01)
35    o pkg/exf ALLOW_RUNOFTEMP
36      - if defined,  river and glacier runoff temperature can be read-in from
37        runoftempfile; runoftempfile needs to have same format as runofffile
38    o pkg/thsice (& pkg/bulk_force):
39      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
40        for energy content of Precip + RunOff & Evap (like with pkg/exf).
41      - change computation domain to always be the interior (without overlap).
42      - fix bug (wrong overlap) when using EXF and stressReduction > 0.
43    o verification/tutorial_global_oce_biogeo:
44      - add preliminary OpenAD setup (still has problems)
45    o pkg/seaice:
46      - turn some parameters for choosing the convergence criterion of
47        the inexact Newton method (JFNK) into runtime parameters for convenience
48      - clean up seaice_calc_viscosities.F: remove/retire two options for
49        SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
50        the results of lab_sea/input because a division has been replaced by
51        a multiplication with the reciprocal (sumNorm)
52      - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
53        convergence of solver (changes results, of course), and to test some
54        new features
55    o model/src:
56      - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
57      - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
58      - move forcing adjustment (balancing surface forcing) in specific S/R
59        where might also be applied exchanges (if needed) to forcing arrays.
60    o pkg/shelfice:
61      - allow to specify the Ice-Shelf mass per unit area (instead of
62        shelficeLoadAnomaly) and do the conversion from one to the other
63      - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
64        to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
65        (b) will be loaded in time (before calling INI_PRESSURE) in case it is
66        needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
67      - update isomip experiment forward output (get machine truncation error
68        from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
69    o verification/offline_exf_seaice:
70      revise data.seaice in input.thermo and input_ad and update results accordingly
71        HO = 0.2, SEAICE_areaLossFormula = 2,
72        SEAICE_growMeltByConv = .TRUE.,
73        SEAICE_doOpenWaterMelt = .TRUE.,
74      Improve consistency with input.thsice and fix the spurious 500m ice corners
75    o verification/global_ocean.cs32x15:
76      - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
77        in icedyn (thsice+seaice-dyn) test and update output.
78    o verification/offline_exf_seaice:
79      - adjust list of tested variables (with testreport) and update
80        standard test output with better slection of monitored fields.
81    o pkg/cd_code:
82      - swtich off Adams-Bashforth on the 1rst iteration. Update output of
83        experiment lab_sea.hb87
84    o tools/genmake2:
85      - change default makedepend from the system default to tools/xmakedepend:
86        When no makedepend is specified, select tools/xmakedepend it the test pass,
87        otherwise select the system default (if exist and pass the test) or
88        try to build cyrus-makedepend ; stop if none of the 3 works.
89    o pkg/exf & pkg/thsice:
90      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
91        for energy content of Precip + RunOff & Evap. Assumes:
92       1) Rain has same temp as Air.
93       2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
94       3) Run-Off comes at the temp of surface water (with same Cp)
95       4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
96        put directly into Latent Heat flux & should use water-vapor heat capacity.
97       5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
98        with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
99    o pkg/seaice: simplify the use of CPP flags in JFNK-related files
100        (compile when SEAICE_ALLOW_JFNK is defined)
101    o pkg/thsice:
102      - fix oceanic flux diagnostics & timeave (left from new sequence of calls
103        implementation): move THSICE_AVE call after the advection (called directly
104        from thsice_do_advect.F).
105    o verification/global_ocean.90x40x15 and OpenAD:
106      New experiment for OpenAD is identical to the one in input_ad except that
107        multiDimAdvection=.FALSE.,
108      There is still an issue with this.
109    o pkg/thsice:
110      - account for ice velocity (ocean relative velocity) in turbulent heat flux
111        at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
112        and offline_exf_seaice (main test).
113    
114    checkpoint64f (2013/03/31)
115    o verification/OpenAD:
116      - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
117    o verification/isomip, pkg/shelfice and OpenAD:
118      - add OpenAD setup to this exp and make shelfice package work with OpenAD
119    o verification/tutorial_global_oce_biogeo:
120      - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
121    o verification/offline_exf_seaice:
122      - replace adjoint experiment (now similar to fwd input.thermo/ setup).
123    o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
124      - add OpenAD setup to this exp and make ptracers package work with OpenAD
125    o pkg/seaice/seaice_evp.F:
126       mask the asymmetric contribution of the ice-ocean stress (when
127       the turningAngle is non-zero) over open water to avoid stripes
128       in the EVP-solutions after many EVP-substeps. This does not change
129       the verification experiment (because turningAngle=0 in that experiment),
130       but will affect other EVP solutions with turningAngle.ne.0
131    o verification, AD & TLM output:
132      - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
133        additions and multiplications which affect results at machine truncation
134        level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
135        lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
136        (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
137        digits of matching.
138    o pkg/seaice:
139       modify lsr-algorithm so that it vectorizes AND converges by using a
140       "zebra" method: split vector loop into two with step size 2; this
141       solves a general convergence problem for the JFNK solver on a vector
142       computer. It has the potential to even improve convergence for
143       non-vector machines, but it does change the results so it is turned
144       off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
145       SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
146    
147    checkpoint64e (2013/03/05)
148    o pkg/ecco and several verification experiments:
149       Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
150       from ecco package, and revert to unified routine in model/src/
151       Adjust verification experiments accordingly, especially gloal_oce_llc90
152       Should conclude long-standing work by Gael to reconsile the_main_loop with
153       ECCO and will enable OpenAD's revolve loop in ECCO setup.
154    o pkg/generic_advdiff:
155      - implement compressible flow method for multi-dim advection (similar to
156        gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
157        TAF generates many recomputations) to use it; no yet coded with implicit
158        vertical advection.
159      - change experiment advect_cs (new output) and advect_xy (same output)
160        to test compressible flow multi-dim advection.
161    o pkg/generic_advdiff:
162      - fix SOM advection for unusual cases (linear Free-Surf in r*, other
163        cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
164    o pkg/seaice:
165      - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
166        bug affects two verification experiments (lab_sea and lab_sea.hb87),
167        recover old (wrong) results by setting noSlipFac = 2. in
168        seaice_calc_strainrates.F;
169      - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
170      - add runtime parameter SEAICE_JFNKepsilon for that finite difference
171        gradient in the Jacobian times vector operation (s/r seaice_jacvec)
172      - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
173    o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
174      - new subroutines seaice_lsr_tridiagu/v
175      - introduce loop bounds i/jmin/max to be able to use a restricted
176        additive Schwarz method, but not used for now.
177      - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
178      - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
179    o OpenAD support
180       Reorganize S/R call for overall time-stepping loop to facilitate
181       OpenAD revolve loop replacement
182       (new S/R main_do_loop.F)
183    o model/src:
184      - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
185      - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
186        ADAMS_BASHFORTH2.
187    o pkg/cheapaml:
188      - add new parameter (default=F, same as before) to disable full domain
189        (including land) periodicity in X & Y dir.
190      - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
191        prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
192        into single S/R CHEAPAML_TIMESTEP.
193    
194    checkpoint64d (2013/02/17)
195    o pkg/monitor (angular momentum):
196      - do not add Eta contribution to the total AM if using rigid-lid;
197      - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
198      - horizontal discretisation: compute Zonal wind contribution separately for
199        each component (instead of from cell centered averaged) and use the 4
200        grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
201      - Check that AM is conserved with linear dynamics (momAdvection=F and linear
202        FreeSurf) if using vectorInvariant momentum.
203    o model/src (horizontal grid):
204      - move initialisation of all horizontal grid arrays to null value
205        from specific horizontal grid S/R to main S/R INI_GRID;
206      - add 2 new arrays to project model C-grid velocity on to zonal direction
207        (similar to AngleCosC & -AngleSinC but at U and V point location) and
208        compute them in S/R CALC_GRID_ANGLES.
209    o pkg/seaice: replace a hard coded parameter by a runtime parameter
210        SEAICE_JFNK_tolIter
211    o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
212        preconditioner for JFNK (run LSR into the overlaps as far as possible,
213        i.e OLx/y-2, but overwrite the solution in the overlaps)
214      - extend loop range in seaice_calc_viscosity
215      - add new parameters SEAICE_OLx/y (default = OLx/y-2)
216      - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
217      - slightly modify loops in tridiagonal solver lsr-preconditioner
218      - by default remove the extra exchange in seaice_preconditioner with a
219        replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
220      - modify offline_exf_seaice so that old results without RAS are reproduced
221        for output.dyn_jfnk.txt
222      in seaice_fgmres.F (unrelated to RAS)
223      - add a cpp-flag option for a re-ordered mapping (potentially more
224        efficient), but because this changes the results, turn it off by
225        default
226      - replace the save statement by local common blocks
227    o utils/matlab:
228      - fix tile-offset in rdmnc.m when output was produced using EXCH2.
229      - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
230        instead of local script "load_cs.m".
231    o pkg/seaice:
232      - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
233        to the scalarProductMetric and the unrolling. By chance this does not
234        change the verification experiment, because of the particular domain
235        decomposition
236    o pkg/diagnostics:
237      - change default missing_value from UNSET_RL to -999.
238    o pkg/layers: improve vectorization of layers_fluxcalc.F
239      - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
240        time spent in this routine by more than a factor of 3 on an NEC-SX8
241      - step 2: replace search algorithm by a bisection algorithm found in
242        Press et al. Numerical Recipes in Fortran. This algorithm can be
243        vectorized and finds the correct bin in approx. log2(Nlayers) steps.
244        For now, use this algorithm only for TARGET_NEC_SX defined.
245      - moved the search algorithm into a separate subroutine, that is kept
246        within the same file for automatic inlining.
247      - modified catching potential errors
248    o pkg/ecco:
249      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
250    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
251      - modifications for ALLOW_GENTIM2D_CONTROL
252      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
253      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
254      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
255      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
256    o model/src:
257      - account for moist thermodynamics in (dry) potential temperature equation;
258        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
259        and cpl_aim+ocn.
260      - also switch to standard compiler (gfortran, was using ifort previously)
261        for fizhi-cs experiments reference output.
262    o pkg/ctrl:
263      - 1st step toward generic time-varying control variable (2D) via CPP option
264        ALLOW_GENTIM2D_CONTROL
265      - note new namelist ctrl_nml_genarr in data.ctrl
266    o verification/global_ocean.cs32x15:
267      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
268        thsice calling sequence and update "output.icedyn.txt" output file.
269    o pkg/ptracers:
270      - from Ryan A.: code to allow to restart a tracer at regular time interval
271        specifying a reset frequency and a reset-phase (for each tracers).
272    o pkg/thsice:
273      - implement new sequence of calls for thsice+seaice:
274          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
275          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
276      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
277        in CPP_OPTIONS.h) to recover old sequence;
278      - update diagnostics for Intermediate State thsice diagnostics: now filled
279        just before advection (instead of just after advection in old sequence);
280      - update output of experiment offline_exf_seaice (standard test);
281      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
282        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
283    o pkg/aim_v23:
284      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
285      - use standard pkg/mdsio routines to read & write CO2 pickup file;
286      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
287      - Implement new sequence of calls for seaice advection (with thsice and
288        seaice diffusion): do ice advection after ice-Thermodynamic (previously
289        was done before); change aim_do_physics.F (split the bi,bj loops block);
290      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
291    o pkg/thsice:
292      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
293        where just seaice diffusion is used without seaice-dynamics.
294    
295    checkpoint64c (2013/01/18)
296    o pkg/seaice:
297      - add a parameter JFNKres_tFac that can replace JFNKres_t
298        (= JFNKres_tFac*JFNKresidual before JFNK solver)
299      - add a line search option to the JFNK solver
300      - move update of u/vIce and computation of initial residual into a separate
301        routine (same file); makes the code a little easier to read (?)
302      - the line search requires computation of the residual and for some reason
303        I cannot do the update of u/vIce at the beginning of the Newton loop
304        without changing the results, so we move computation of the new residual
305        also to the end of the Newton loop, even without the line search
306    o pkg/mdsio:
307      - write missing value (corresponding to undefined array value) to meta files;
308        skip this if missing value is one (UNSET_RL would be a better value for the
309        case of undefined missing value but it's current the default missing-value);
310        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
311    o pkg/exf & thsice:
312      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
313        diagnostics) even when SHORTWAVE_HEATING is #undef;
314    o verification/cfc_example:
315      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
316        illustrate how to use it).
317    o verification/offline_exf_seaice:
318      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
319        files to only one time-record.
320      in input.thermo: narrow the 2 bands of low initial ice-concentration near
321        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
322        snapshot output; same mcPheePiston value as in thsice with
323        surf-current=0.2m/s.
324      in input.thsice: similar set-up as in input.thermo (channel with same seaice
325        initial conditions).
326    o verification/cfc_example:
327      - update file "data" with more standard choice (default rotationPeriod,
328        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
329        set deltaTFreeSurf to deltaTtracer) and update the output.
330    o pkg/layers:
331      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
332      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
333    o verification/offline_exf_seaice:
334      - set all {field}period to zero for constant-in-time forcing (not tested
335        anywhere else).
336    o verification/offline_exf_seaice:
337      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
338      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
339    o model/src:
340      - implement Finite-Volume method for (hydrostatic) presure gradient
341        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
342    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
343      - In order to be compatible with the default EVP code, this requires changing
344        the EVP code around a little; and because any small change immediately
345        breaks the lab_sea.hb87 verification experiment, the reference output is
346        updated two times (each time the remaining aggrement was only 2 digits):
347        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
348        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
349        The adjoint test lab_sea.evp also needed to be updated.
350      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
351        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
352        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
353        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
354        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
355        kept obscure, because I need to test it a little more.
356    o pkg/cheapaml:
357      - fix few incorrect type (_RL/_RS) in subroutine calls.
358    o pkg/seaice:
359      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
360        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
361    o model/src:
362      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
363        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
364        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
365    o pkg/cheapaml:
366      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
367        update output of experiment cheapAML_box.
368      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
369        and set them only in one place (cheapaml_readparms.F).
370      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
371      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
372        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
373    o model/src/the_main_loop.F:
374      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
375    o pkg/seaice:
376      - remove legacy branch code.
377      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
378    o verification/*/code*/SEAICE_OPTIONS.h:
379      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
380        SEAICE_CAP_HEFF).
381    o pkg/cheapaml:
382      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
383        to load new forcing fields.
384      - add missing "_d 0" where it's needed; + some editing (improve indentation).
385      - remove switch to "-r8" compiler option (no longer needed) in verification
386        cheapAML_box, keep same output (small trucation error differences).
387    o verification/offline_exf_seaice:
388      - add thermodynamics only test.
389    o verification/cheapAML_box:
390      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
391        keep same output (same 14 digits for cg2d).
392      - switch on "-r8" compiler option (some numerical values are missing
393        the "_d 0") and update output (only 6 digits for cg2d were preserved).
394    
395    checkpoint64b (2012/12/24)
396    o pkg/cheapaml:
397      - remove un-used variables (Qnet,EmPmR) from pickup files.
398      - store tendency of advected variables into cheapaml pickup file
399        and fix the AB-2 restart.
400    o verification/offline_exf_seaice and lab_sea adjoint:
401      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
402      - switch to 4 time steps in offline, consistent with lab_sea.
403      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
404      - update results after change of experiment seaice.
405    o pkg/seaice:
406      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
407        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
408        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
409        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
410    o model/src:
411      - add run-time parameter to select CG2D solver minimum-residual solution
412        (in case of a poor convergence).
413    o pkg/seaice/seaice_lsr.F
414      - move calculation of matrix coefficients into new
415        S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
416        file; the main purpose of this change is to be able to reuse the code
417        in S/R SEAICE_PRECONDITIONER
418      - modify the computation of the residual so that the mass of sea-ice
419        is not used twice; this simplifies the calculations, but since
420        the residual is never used except when LSR_mixIniGuess.ge.4---and this is
421        not tested in testreport---this does not affect the testreport results.
422    o verification/seaice_obcs:
423      - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
424        verification/lab_sea/input.salt_plume; changes results/output.txt*
425    o model/src:
426      - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
427    o pkg/seaice:
428      - improve description of parameters in seaice_fgmres.F and start
429        cleaning up the code
430      - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
431        second argument
432      - add a metric based on grid cell area to SEAICE_SCALPROD; update
433        results of offline_exf_seaice.dyn_jfnk
434      - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
435    o pkg/aim_v23:
436      - fix an other bug in dissipation heating (grid-cell area was missing).
437    o model/src + pkg/seaice:
438      - add global (multi-tile) linear solver for pair of tri-diagonal system
439        along X and Y lines, respectively for U and V component.
440        Note: 1) MPI and cube-exchange not yet coded.
441            2) probably not accurate for poorly conditioned / large size problem.
442      - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
443        default: not compiled and not used.
444    o pkg/seaice:
445      - first attempt at a multi-threaded fgmres solver for the JFNK solver:
446        introduce bi/bj loops and use global_sum_tile_rl instead of
447        mpi_allreduce in seaice_fgmres.F
448      - improve diagnostics output for fgmres solver (seaice_fgmres.F)
449      - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
450      - add a verification experiment for JFNK in offline_exf_seaice
451    o verification:
452      - change (for now, only fwd test) offline_exf_seaice experiment:
453        use a re-entrant channel with idealized coastline (trapezoidal shape)
454        at southern boundary to explore seaice dynamics and thermodynamics
455        with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
456        secondary test (input.thsice) use thermodynamics only with SST relaxation.
457      - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
458    o pkg/exf:
459      - disable "sstExtrapol" when Nr=1
460    o verification:
461      - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
462        to test pkg/cheapaml.
463    o pkg/aim_v23 & pkg/shap_filt:
464      - fix dissipation heating (erroneous gravity multiplication factor).
465    o pkg/seaice:
466      - remove unused field pressPre from jfnk solver
467      - rename two subroutines in seaice_preconditioner.F
468    o eesupp/src:
469       - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
470    o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
471       - remove wrong parts of the rhs and the lhs (were in there
472         because I did not understand the concept of this preconditioner)
473       - add an exchange between u- and v-sweep. This increases communication
474         by a factor of two but improves the convergence of jfnk. Ideally,
475         one would like the u- and v-sweep to be independent. So far within
476         undocumented ifdefs
477       - reorganize the extra computations for printing the residuals
478    o tools/genmake2:
479      - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
480        since it's not necessary (and was preventing to use MNC in some cases).
481    
482    checkpoint64a (2012/11/16)
483    o pkg/autodiff:
484      - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
485        autodiff_readparms.F no longer depends on calling order (within
486        packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
487        rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
488        and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
489    o pkg/obcs:
490      - adding tidal velocity forcing capability to obcs
491        for usage example, see verification/seaice_obcs/input.tides
492    o pkg/seaice:
493      - turn the LSR-relaxation parameters WFAU/V into runtime parameters
494        SEAICE_LSRrelaxU/V
495      - introduce runtime parameter SEAICEetaZmethod (=0 by default)
496    o pkg/aim_v23:
497      - implement heating from friction (bottom friction and stratospheric drag).
498    o pkg/shap_filt:
499      - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
500        dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
501    o model/src:
502      - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
503        time-constant addMass field from file (addMassFile);
504      - support for heating due to friction (and Kinetic Energy dissipation):
505        add option, run-time switch and 3-D field array + support code ; each pkg
506        or S/R can add heating contribution (if there is a sink of KE); the sum is
507        accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
508    o pkg/seaice:
509      - complete merge of ITD code into seaice_growth.F
510        from MITgcm_contrib/torge/itd/code/
511        no verification so far, but Torge Martin tested
512        "1-D test case and Beaufort set up;
513        deliver okay results after 1 model year."
514      - complete merge of SEAICE_SIZE.h into all relevant routines
515      - move computation of eta at Z-points into calc_viscosities
516        + introduce global field etaZ
517        + add different methods for computing etaZ, for now the old
518          method (simple averages of eta to Z-points) is hardwired
519        + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
520          seaice_preconditioner
521      - simplify computations for SEAICE_ZETA_SMOOTHREG
522      - seaice_preconditioner:
523        + replace one remaining press by pressLoc (mistake)
524        + adjust printing of residuals
525      - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
526        + add (SEAICE.h) and rename some counters (initiliased in
527          seaice_init_fixed.F)
528        + add _BEGIN/END_MASTER (myThid)  around print statements
529        + print total number of iterations and failures over SEAICE_monFreq
530          interval to STDOUT
531      - move control over output-messages by fgmres to seaice_jfnk to save
532        some operations
533      - move resetting initial guess for fgmres outside of seaice_fgmres_driver
534        in order to make restarts with sol .ne. zero (fgmres with restarts)
535        (seaice_jfnk.F, seaice_fgmres.F)
536      - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
537        a serious convergence problem when open boundaries are involved
538    o pkg/ggl90: fix computation of control volumes for the case of
539      ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
540      up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
541    o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
542    o pkg/autodiff
543      - Add inAdMode switch for SEAICEuseDYNAMICS:
544        SEAICEuseDYNAMICSinAdMode
545        (extend logic in ADAUTODIFF_INADMODE_SET)
546    o pkg/seaice
547      - Step 1 of merging ice-thickness distribution (ITD) code from
548        MITgcm_contrib/torge/itd/ (author: Torge Martin)
549        The code implements concept laid out in Thorndike et al. (1975);
550        code is enabled via CPP flag SEAICE_ITD
551        nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
552        code is not complete yet!!
553      - SEAICE_SIZE.h now included in almost all seaice routines
554    o verification (using seaice):
555      - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
556        global_ocean.cs32x15.seaice ; update results.
557      - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
558      - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
559        offline_exf_seaice (previously compiling B-grid).
560    o pkg/exf:
561      - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
562        to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
563        forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
564    o pkg/layers (adjust changes from Sept 19):
565      - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
566        this allows to remove "layers_maxNum" dimension from all layers arrays.
567    o pkg/layers (adjust changes from Sept 19):
568      - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
569      - snap-shot extended to all type of layers (not just the 1rst type);
570      - remove layers variables when corresponding CPP option is undef.
571    o pkg/layers:
572      - rename pkg/layers variable and add new output (layer exist & un-weighted
573        velocity in layer)
574    o pkg/seaice:
575      - simplify (?) ocean-drag coefficent computations by using
576        the same routine in all three solvers (saves some code lines)
577      - remove global fields DRAGA and DRAGS from C-grid code and
578        declare them locally in lsr.F (the only place where they are
579        still used)
580      - update AD output of lab_sea.evp (very sensitive anyway).
581    o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
582      (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
583      and SEAICEuseJFNK=.true. A few things to note:
584      - involves a FGMRES, that is parallel but very inefficient,
585        because of many scalar products (global sums) in the Gram-Schmidt
586        orthogonalization method. Needs to be replaced. Original code
587        from J.-F. Lemieux
588      - preconditioner for FGMRES is a stripped down version of LSOR
589      - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
590        preconditioner. For the preconditioner, the default is set to 10.
591      - Jacobian times vector is computed with finite differences
592      - marginally related to JFNK-solver: add a smooth regularization for
593        zeta with tanh that will improve convergence (Lemieux and Tremblay,
594        2009) for any implicit solver (not implemented for EVP because EVP
595        does not need this regularization in the first place). Define
596        SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
597    o eesupp/src:
598      - check in genmake2 that intrinsic S/R flush is available.
599      - add S/R to flush IO unit (if intrinsic S/R flush is available)
600      - flush standard & error msg unit before MPI termination
601      - if debugMode, flush IO unit after printing msg
602    o pkg/ctrl:
603      - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
604        to ctrl_set_unpack_xyz.
605    
606    checkpoint64 (2012/10/09)
607    o pkg/shelfice
608      - in mom_fluxform.F, mom_vecinv.F:
609        CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
610        Bug fix KappaRU -> KappaRV
611        does not change verification/isomip but may change other setups
612        (presumably constant KappaRU=KappaRV)
613      - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
614    o pkg/obcs:
615      - fixed some indexing bugs in obcs_seaice_sponge.F
616      - added obcs relaxation subroutines for HSALT and HSNOW
617      - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
618    o pkg/seaice:
619      - add "multicategory" parameterization for snow in analogy to ice,
620        default is off for now.
621    o pkg/obcs:
622      - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
623        see verification/seaice_obcs/input.seaiceSponge for example application.
624      - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
625        index setting by master-thread. This fix multi-threads Pb in previous modifs.
626    o pkg/layers :
627      - add diagnostics to pkg/layers
628      - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
629        (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
630    o pkg/generic_advdiff/gad_implicit_r.F :
631      - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
632    o pkg/seaice/seaice_growth.F:
633      - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
634    o pkg/obcs:
635      - change default setting of OBCS_UVICE_OLD from defined to undef;
636      - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
637        in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
638      - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
639      - change OB null index value (OB_indexNone) to -99 ; this fix the problem
640        with Southern & Western OB at a tile edge (at least in a simple set-up).
641    o pkg/obcs:
642      - change settings of OB index in case OB coincides with tile edge (shared by
643        2 tiles), so that common OB location is registered by both tiles (instead of
644        only 1). However, for Southern and Western OB, index value = 0 is not
645        recognized as valid OB index (=default null value) and needs to be fixed.
646      - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
647      - new parameter "OB_indexNone" for null index value (for now, still zero)
648        to replace hard-coded null index value of zero.
649    o pkg/exch2:
650      - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
651        always check buffer-size (but outside the loop); move checking for valid
652        index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
653        print each tile and point connection only if |W2_printMsg|>= 2 and 3.
654    o pkg/ctrl (pack & unpack):
655      - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
656        (locally defined) for different variables (+ remove the variable-specific
657        file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
658        (to be extended to other local file names in ctrl.h).
659    o pkg/flt:
660      - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
661    o pkg/mdsio:
662      - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
663    o tools/genmake2:
664      - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
665        (added by Alistair in version 1.51 for building without make depend);
666      - remove Header files list (H_SRC_FILES) from the dependence of targets
667         ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
668        place in version 1.23): this save going through staf when unrelated header
669        file has been modified.
670       Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
671        "make depend" step, still need to do "make links" before "make adtaf".
672    o eesupp/src (+ few pkg src files) & genmake2:
673      - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
674      - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
675      - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
676         upper/lower case ; account for space between "#" and undef/define)
677    o pkg/flt (with exch2):
678      - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
679      - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
680    
681    checkpoint63s (2012/09/05)
682    o pkg/ecco:
683      - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
684      - add more relevant #ifdef ALLOW_SMOOTH ones.
685      - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
686    o pkg/ctrl:
687      - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
688        ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
689      - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
690        doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
691        ctrlSmoothCorrel3D (new).
692        The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
693      - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
694      - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
695        controls when useAtmWind, and vice versa.
696      - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
697      - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
698          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
699      - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
700          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
701      - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
702        replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
703    o pkg/smooth:
704      - remove un-necessary includes.
705      - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
706        Those CPP options were never defined, and not necessary.
707    o model/src:
708      - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
709      - standard treatment of useSMOOTH.
710    o pkg/autodiff:
711      - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
712        useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
713    o pkg/exch2:
714      - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
715        + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
716      - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
717        and tiles to process mapping.
718      - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
719        moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
720        rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
721        from w2_eeboot.F to w2_readparms.F.
722    o eesupp/src:
723      - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
724        ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
725        also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
726      - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
727        is defined (remove condition on usingMPI) to match cases where MPI_INIT
728        has been called.
729      - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
730      - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
731        (so that on 1 proc, get same myPid independently of usingMPI)
732      - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
733        useCubedSphereExchange with EXCH-1 (safer).
734      - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
735    o pkg/ggl90:
736      - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
737        used in ALLOW_GGL90_SMOOTH code.
738    o pkg/flt:
739      - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
740        floats at the Southern end of the domain).
741    o eesupp/inc:
742      - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
743        but not used (and not to be used) anywhere, just for documentation.
744    o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
745      - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
746        a) can damage previously written records in any other multi-record files.
747        b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
748  o tools/genmake2:  o tools/genmake2:
749    - define variable MAKE within Makefile and use it in place of 'make';    - define variable MAKE within Makefile and use it in place of 'make';
750    - 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 752  o tools/genmake2:
752      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;
753    - always print usual warning comment 'this file is automatically generated'    - always print usual warning comment 'this file is automatically generated'
754      from script convert_cpp_cmd2defines (+ remove this warning from genmake2).      from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
755    o pkg/cheapaml:
756      - updated to correspond to the code used in accepted paper (Nico Wienders).
757  o pkg/exf:  o pkg/exf:
758      added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.      added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
759      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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