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revision 1.1746 by mlosch, Fri Oct 5 15:19:00 2012 UTC revision 1.1881 by m_bates, Tue Jun 18 21:30:33 2013 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    
8    checkpoint64i (2013/06/18)
9    o pkg/cheapaml:
10      - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
11        that enable the use of seaice (pkg/thsice thermo & pkg/seaice dynamics)
12        with pkg/cheapaml.
13    o utils/python: add subpackage for cubed sphere function, first example is
14        simple cs.pcol to plot 2D fields on a map
15    o pkg/streamice:
16      - This is a new package in MITgcm, which solves dynamic equations for ice
17         sheets and ice streams
18      - At the moment it is independent of atmosphere/ocean dynamics, or any
19        other physical packages in MITgcm, even ShelfIce (although it is anticipat-
20        ed that this will change)
21      - There is a new verification exercise that tests it, halfpipe_streamice,
22        evolves a 40x80 km ice stream/ice shelf (at coarse resolution) in a
23        rectangular embayment
24      - halfpipe_streamice is forward-only for now, will have TAF test soon
25      - for questions, email dgoldber@mit.edu
26    o pkg/thsice:
27      - fix filling of snow-precip diagnostic (SIsnwPrc) (left from the removing
28        of snowPrc from common bloc, on May 2nd, thsice_step_fwd.F revision 1.40);
29      - remove diagnostics 'SI_FrcFx' ( now identical to 'SI_Fract' with new
30         call sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect );
31      - allow precip from pkg/cheapaml to make snow over seaice.
32    o pkg/cfc:
33      - move in separated header file (CFC_ATMOS.h) time-serie arrays of Atmos CFC
34      - remove atmos CFC 2-D arrays from common bloc (now local variables)
35      - change some hard-coded constant to run time parameter for reading and
36        and interpolating atmospheric CFC ; keep same default as previously.
37      - more flexible reading of Atmos CFC (number of records no longer hard-coded)
38      - put arguments in standard order: myTime, myIter, myThid
39      - use standard S/R GET_PERIODIC_INTERVAL for time interpolation of
40        atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
41      - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
42      - new routine to print summary of CFC params and check for consistency.
43    o pkg/cfc:
44      - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
45        update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
46      - fix interpolation of atmphspheric CFC between Sorthern and Northern
47        hemisphere value.
48    o pkg/seaice:
49      - allow to use seaice dynamics without pkg/exf (e.g., using pkg/cheapaml)
50    o pkg/seaice: add Adams-Bashforth2 time discretization for ice dynamics;
51                  so far only for JFNK-solver, turn on with SEAICEuseAB2 = .TRUE.
52      - requires an additional time level that is stored in the pickup
53      - you can start with AB2 from a pickup without this time level with
54        pickupStrictlyMatch = .false.
55    
56    checkpoint64h (2013/05/26)
57    o pkg/cheapaml:
58      - replace one ()**.5 with SQRT + use temp var "cdu = tau/Du" (coare3_flux);
59        affect machine truncation (but exp cheapAML_box still pass with 13 digits).
60      - consistent treatment of uWind,vWind location: assume everywhere in
61        pkg/cheapaml that they are on C-grid (@ uVel,vVel location)
62        (Note: was already the case for Tair,Qair advection);
63        add option (INCONSISTENT_WIND_LOCATION) to recover old results.
64      - compute diabatic forcing only in the interior (excluding overlap regions)
65      - fill in array "Qsw" (for short-wave heating);
66      - add diagnostic for precip ; fill-in diagnostics for cheapAML state vars
67        before any update (consistent with MITgcm state var diagnostics);
68      - cheapaml_fields_load.F & cheapaml_init_varia.F : only fill outer edges if
69        non periodic ; + adjusted for uWind,vWind (C-grid).
70    o pkg/seaice:
71      - remove dependence of pkg/seaice versus pkg/exf (file: pkg/pkg_depend) and
72        add explicitly pkg/exf in experiments that currently use pkg/seaice.
73      - allows to compile pkg/seaice without pkg/exf.
74    o tools/OAD_support:
75      - use a local copy (ourRWCPinBd) to ensure index ourRWCP stays within bounds
76        of array "ourStepOf" in function rvNextAction (revolve.F90).
77    o pkg/aim_compon_interf renamed to pkg/atm_compon_interf
78      - change pkg name (to be used with other atmospheric physics pkg)
79        but by-pass CVS when making the new pkg so that we keep the CVS history.
80    o pkg/offline:
81      - call OFFLINE_FIELDS_LOAD from pkg/offline/offline_init_varia.F
82        (previously called from pkg/dic_surfforcing_init.F)
83    o model/src:
84      - re-order sequence of calls within packages_init_variables.F, using
85        standard order, except for:
86         DIAGNOSTICS_INIT_VARIA and OFFLINE_INIT_VARIA (called @ the top),
87         CTRL_MAP_INI and OBCS_INIT_VARIABLES (called @ the bottom)
88    o new pkg: atm_phys
89      - add entry point and source code (previously in contrib
90          verification_other/atm_gray/code_gray/) for new pkg "atm_phys"
91        (atmospheric physics pkg from P. O'Gorman and T. Schneider, JCl, 2008).
92      - re-order sequence of calls within packages_readparms.F,
93         packages_init_fixed.F and packages_write_pickup.F
94        (but skip packages_init_variables.F because of TAF issues).
95      - update contrib/*/atm_gray/ experiment.
96    o pkg/seaice (ITD code):
97      - simplify and fix the writing of pickup-files for ITD case
98    o pkg/seaice (ITD code):
99      - introduce floe size dependent lateral melt for ITD case;
100      - cleaning (avoid division by zero, change to f77 syntax, remove tabs)
101      - update seaice_itd experiment main output.
102    o pkg/thsice:
103      - remove snowPrc from common block THSICE_FLUX, in THSICE_VARS.h and
104        declared it locally (without bi,bj) in thsice_main.F & aim_do_physics.F;
105        changed accordingly pkg/atm2d.
106    
107    checkpoint64g (2013/05/01)
108    o pkg/exf ALLOW_RUNOFTEMP
109      - if defined,  river and glacier runoff temperature can be read-in from
110        runoftempfile; runoftempfile needs to have same format as runofffile
111    o pkg/thsice (& pkg/bulk_force):
112      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
113        for energy content of Precip + RunOff & Evap (like with pkg/exf).
114      - change computation domain to always be the interior (without overlap).
115      - fix bug (wrong overlap) when using EXF and stressReduction > 0.
116    o verification/tutorial_global_oce_biogeo:
117      - add preliminary OpenAD setup (still has problems)
118    o pkg/seaice:
119      - turn some parameters for choosing the convergence criterion of
120        the inexact Newton method (JFNK) into runtime parameters for convenience
121      - clean up seaice_calc_viscosities.F: remove/retire two options for
122        SEAICetaZmethod (1,2), introduce area weighting for method 3; this changes
123        the results of lab_sea/input because a division has been replaced by
124        a multiplication with the reciprocal (sumNorm)
125      - modify offline_exf_seaice/input.dyn_jfnk/data.seaice to improve
126        convergence of solver (changes results, of course), and to test some
127        new features
128    o model/src:
129      - remove unused (since Aug 2006) S/R SET_WRITE_GLOBAL_PICKUP and its call.
130      - remove unused forcing field "dQdT" and associated parameter "dQdTFile".
131      - move forcing adjustment (balancing surface forcing) in specific S/R
132        where might also be applied exchanges (if needed) to forcing arrays.
133    o pkg/shelfice:
134      - allow to specify the Ice-Shelf mass per unit area (instead of
135        shelficeLoadAnomaly) and do the conversion from one to the other
136      - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
137        to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
138        (b) will be loaded in time (before calling INI_PRESSURE) in case it is
139        needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
140      - update isomip experiment forward output (get machine truncation error
141        from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
142    o verification/offline_exf_seaice:
143      revise data.seaice in input.thermo and input_ad and update results accordingly
144        HO = 0.2, SEAICE_areaLossFormula = 2,
145        SEAICE_growMeltByConv = .TRUE.,
146        SEAICE_doOpenWaterMelt = .TRUE.,
147      Improve consistency with input.thsice and fix the spurious 500m ice corners
148    o verification/global_ocean.cs32x15:
149      - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
150        in icedyn (thsice+seaice-dyn) test and update output.
151    o verification/offline_exf_seaice:
152      - adjust list of tested variables (with testreport) and update
153        standard test output with better slection of monitored fields.
154    o pkg/cd_code:
155      - swtich off Adams-Bashforth on the 1rst iteration. Update output of
156        experiment lab_sea.hb87
157    o tools/genmake2:
158      - change default makedepend from the system default to tools/xmakedepend:
159        When no makedepend is specified, select tools/xmakedepend it the test pass,
160        otherwise select the system default (if exist and pass the test) or
161        try to build cyrus-makedepend ; stop if none of the 3 works.
162    o pkg/exf & pkg/thsice:
163      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
164        for energy content of Precip + RunOff & Evap. Assumes:
165       1) Rain has same temp as Air.
166       2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
167       3) Run-Off comes at the temp of surface water (with same Cp)
168       4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
169        put directly into Latent Heat flux & should use water-vapor heat capacity.
170       5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
171        with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
172    o pkg/seaice: simplify the use of CPP flags in JFNK-related files
173        (compile when SEAICE_ALLOW_JFNK is defined)
174    o pkg/thsice:
175      - fix oceanic flux diagnostics & timeave (left from new sequence of calls
176        implementation): move THSICE_AVE call after the advection (called directly
177        from thsice_do_advect.F).
178    o verification/global_ocean.90x40x15 and OpenAD:
179      New experiment for OpenAD is identical to the one in input_ad except that
180        multiDimAdvection=.FALSE.,
181      There is still an issue with this.
182    o pkg/thsice:
183      - account for ice velocity (ocean relative velocity) in turbulent heat flux
184        at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
185        and offline_exf_seaice (main test).
186    
187    checkpoint64f (2013/03/31)
188    o verification/OpenAD:
189      - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
190    o verification/isomip, pkg/shelfice and OpenAD:
191      - add OpenAD setup to this exp and make shelfice package work with OpenAD
192    o verification/tutorial_global_oce_biogeo:
193      - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
194    o verification/offline_exf_seaice:
195      - replace adjoint experiment (now similar to fwd input.thermo/ setup).
196    o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
197      - add OpenAD setup to this exp and make ptracers package work with OpenAD
198    o pkg/seaice/seaice_evp.F:
199       mask the asymmetric contribution of the ice-ocean stress (when
200       the turningAngle is non-zero) over open water to avoid stripes
201       in the EVP-solutions after many EVP-substeps. This does not change
202       the verification experiment (because turningAngle=0 in that experiment),
203       but will affect other EVP solutions with turningAngle.ne.0
204    o verification, AD & TLM output:
205      - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
206        additions and multiplications which affect results at machine truncation
207        level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
208        lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
209        (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
210        digits of matching.
211    o pkg/seaice:
212       modify lsr-algorithm so that it vectorizes AND converges by using a
213       "zebra" method: split vector loop into two with step size 2; this
214       solves a general convergence problem for the JFNK solver on a vector
215       computer. It has the potential to even improve convergence for
216       non-vector machines, but it does change the results so it is turned
217       off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
218       SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
219    
220    checkpoint64e (2013/03/05)
221    o pkg/ecco and several verification experiments:
222       Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
223       from ecco package, and revert to unified routine in model/src/
224       Adjust verification experiments accordingly, especially gloal_oce_llc90
225       Should conclude long-standing work by Gael to reconsile the_main_loop with
226       ECCO and will enable OpenAD's revolve loop in ECCO setup.
227    o pkg/generic_advdiff:
228      - implement compressible flow method for multi-dim advection (similar to
229        gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
230        TAF generates many recomputations) to use it; no yet coded with implicit
231        vertical advection.
232      - change experiment advect_cs (new output) and advect_xy (same output)
233        to test compressible flow multi-dim advection.
234    o pkg/generic_advdiff:
235      - fix SOM advection for unusual cases (linear Free-Surf in r*, other
236        cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
237    o pkg/seaice:
238      - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
239        bug affects two verification experiments (lab_sea and lab_sea.hb87),
240        recover old (wrong) results by setting noSlipFac = 2. in
241        seaice_calc_strainrates.F;
242      - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
243      - add runtime parameter SEAICE_JFNKepsilon for that finite difference
244        gradient in the Jacobian times vector operation (s/r seaice_jacvec)
245      - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
246    o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
247      - new subroutines seaice_lsr_tridiagu/v
248      - introduce loop bounds i/jmin/max to be able to use a restricted
249        additive Schwarz method, but not used for now.
250      - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
251      - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
252    o OpenAD support
253       Reorganize S/R call for overall time-stepping loop to facilitate
254       OpenAD revolve loop replacement
255       (new S/R main_do_loop.F)
256    o model/src:
257      - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
258      - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
259        ADAMS_BASHFORTH2.
260    o pkg/cheapaml:
261      - add new parameter (default=F, same as before) to disable full domain
262        (including land) periodicity in X & Y dir.
263      - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
264        prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
265        into single S/R CHEAPAML_TIMESTEP.
266    
267    checkpoint64d (2013/02/17)
268    o pkg/monitor (angular momentum):
269      - do not add Eta contribution to the total AM if using rigid-lid;
270      - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
271      - horizontal discretisation: compute Zonal wind contribution separately for
272        each component (instead of from cell centered averaged) and use the 4
273        grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
274      - Check that AM is conserved with linear dynamics (momAdvection=F and linear
275        FreeSurf) if using vectorInvariant momentum.
276    o model/src (horizontal grid):
277      - move initialisation of all horizontal grid arrays to null value
278        from specific horizontal grid S/R to main S/R INI_GRID;
279      - add 2 new arrays to project model C-grid velocity on to zonal direction
280        (similar to AngleCosC & -AngleSinC but at U and V point location) and
281        compute them in S/R CALC_GRID_ANGLES.
282    o pkg/seaice: replace a hard coded parameter by a runtime parameter
283        SEAICE_JFNK_tolIter
284    o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
285        preconditioner for JFNK (run LSR into the overlaps as far as possible,
286        i.e OLx/y-2, but overwrite the solution in the overlaps)
287      - extend loop range in seaice_calc_viscosity
288      - add new parameters SEAICE_OLx/y (default = OLx/y-2)
289      - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
290      - slightly modify loops in tridiagonal solver lsr-preconditioner
291      - by default remove the extra exchange in seaice_preconditioner with a
292        replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
293      - modify offline_exf_seaice so that old results without RAS are reproduced
294        for output.dyn_jfnk.txt
295      in seaice_fgmres.F (unrelated to RAS)
296      - add a cpp-flag option for a re-ordered mapping (potentially more
297        efficient), but because this changes the results, turn it off by
298        default
299      - replace the save statement by local common blocks
300    o utils/matlab:
301      - fix tile-offset in rdmnc.m when output was produced using EXCH2.
302      - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
303        instead of local script "load_cs.m".
304    o pkg/seaice:
305      - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
306        to the scalarProductMetric and the unrolling. By chance this does not
307        change the verification experiment, because of the particular domain
308        decomposition
309    o pkg/diagnostics:
310      - change default missing_value from UNSET_RL to -999.
311    o pkg/layers: improve vectorization of layers_fluxcalc.F
312      - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
313        time spent in this routine by more than a factor of 3 on an NEC-SX8
314      - step 2: replace search algorithm by a bisection algorithm found in
315        Press et al. Numerical Recipes in Fortran. This algorithm can be
316        vectorized and finds the correct bin in approx. log2(Nlayers) steps.
317        For now, use this algorithm only for TARGET_NEC_SX defined.
318      - moved the search algorithm into a separate subroutine, that is kept
319        within the same file for automatic inlining.
320      - modified catching potential errors
321    o pkg/ecco:
322      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
323    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
324      - modifications for ALLOW_GENTIM2D_CONTROL
325      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
326      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
327      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
328      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
329    o model/src:
330      - account for moist thermodynamics in (dry) potential temperature equation;
331        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
332        and cpl_aim+ocn.
333      - also switch to standard compiler (gfortran, was using ifort previously)
334        for fizhi-cs experiments reference output.
335    o pkg/ctrl:
336      - 1st step toward generic time-varying control variable (2D) via CPP option
337        ALLOW_GENTIM2D_CONTROL
338      - note new namelist ctrl_nml_genarr in data.ctrl
339    o verification/global_ocean.cs32x15:
340      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
341        thsice calling sequence and update "output.icedyn.txt" output file.
342    o pkg/ptracers:
343      - from Ryan A.: code to allow to restart a tracer at regular time interval
344        specifying a reset frequency and a reset-phase (for each tracers).
345    o pkg/thsice:
346      - implement new sequence of calls for thsice+seaice:
347          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
348          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
349      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
350        in CPP_OPTIONS.h) to recover old sequence;
351      - update diagnostics for Intermediate State thsice diagnostics: now filled
352        just before advection (instead of just after advection in old sequence);
353      - update output of experiment offline_exf_seaice (standard test);
354      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
355        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
356    o pkg/aim_v23:
357      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
358      - use standard pkg/mdsio routines to read & write CO2 pickup file;
359      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
360      - Implement new sequence of calls for seaice advection (with thsice and
361        seaice diffusion): do ice advection after ice-Thermodynamic (previously
362        was done before); change aim_do_physics.F (split the bi,bj loops block);
363      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
364    o pkg/thsice:
365      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
366        where just seaice diffusion is used without seaice-dynamics.
367    
368    checkpoint64c (2013/01/18)
369    o pkg/seaice:
370      - add a parameter JFNKres_tFac that can replace JFNKres_t
371        (= JFNKres_tFac*JFNKresidual before JFNK solver)
372      - add a line search option to the JFNK solver
373      - move update of u/vIce and computation of initial residual into a separate
374        routine (same file); makes the code a little easier to read (?)
375      - the line search requires computation of the residual and for some reason
376        I cannot do the update of u/vIce at the beginning of the Newton loop
377        without changing the results, so we move computation of the new residual
378        also to the end of the Newton loop, even without the line search
379    o pkg/mdsio:
380      - write missing value (corresponding to undefined array value) to meta files;
381        skip this if missing value is one (UNSET_RL would be a better value for the
382        case of undefined missing value but it's current the default missing-value);
383        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
384    o pkg/exf & thsice:
385      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
386        diagnostics) even when SHORTWAVE_HEATING is #undef;
387    o verification/cfc_example:
388      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
389        illustrate how to use it).
390    o verification/offline_exf_seaice:
391      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
392        files to only one time-record.
393      in input.thermo: narrow the 2 bands of low initial ice-concentration near
394        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
395        snapshot output; same mcPheePiston value as in thsice with
396        surf-current=0.2m/s.
397      in input.thsice: similar set-up as in input.thermo (channel with same seaice
398        initial conditions).
399    o verification/cfc_example:
400      - update file "data" with more standard choice (default rotationPeriod,
401        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
402        set deltaTFreeSurf to deltaTtracer) and update the output.
403    o pkg/layers:
404      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
405      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
406    o verification/offline_exf_seaice:
407      - set all {field}period to zero for constant-in-time forcing (not tested
408        anywhere else).
409    o verification/offline_exf_seaice:
410      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
411      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
412    o model/src:
413      - implement Finite-Volume method for (hydrostatic) presure gradient
414        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
415    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
416      - In order to be compatible with the default EVP code, this requires changing
417        the EVP code around a little; and because any small change immediately
418        breaks the lab_sea.hb87 verification experiment, the reference output is
419        updated two times (each time the remaining aggrement was only 2 digits):
420        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
421        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
422        The adjoint test lab_sea.evp also needed to be updated.
423      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
424        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
425        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
426        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
427        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
428        kept obscure, because I need to test it a little more.
429    o pkg/cheapaml:
430      - fix few incorrect type (_RL/_RS) in subroutine calls.
431    o pkg/seaice:
432      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
433        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
434    o model/src:
435      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
436        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
437        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
438    o pkg/cheapaml:
439      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
440        update output of experiment cheapAML_box.
441      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
442        and set them only in one place (cheapaml_readparms.F).
443      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
444      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
445        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
446    o model/src/the_main_loop.F:
447      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
448    o pkg/seaice:
449      - remove legacy branch code.
450      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
451    o verification/*/code*/SEAICE_OPTIONS.h:
452      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
453        SEAICE_CAP_HEFF).
454    o pkg/cheapaml:
455      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
456        to load new forcing fields.
457      - add missing "_d 0" where it's needed; + some editing (improve indentation).
458      - remove switch to "-r8" compiler option (no longer needed) in verification
459        cheapAML_box, keep same output (small trucation error differences).
460    o verification/offline_exf_seaice:
461      - add thermodynamics only test.
462    o verification/cheapAML_box:
463      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
464        keep same output (same 14 digits for cg2d).
465      - switch on "-r8" compiler option (some numerical values are missing
466        the "_d 0") and update output (only 6 digits for cg2d were preserved).
467    
468    checkpoint64b (2012/12/24)
469    o pkg/cheapaml:
470      - remove un-used variables (Qnet,EmPmR) from pickup files.
471      - store tendency of advected variables into cheapaml pickup file
472        and fix the AB-2 restart.
473    o verification/offline_exf_seaice and lab_sea adjoint:
474      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
475      - switch to 4 time steps in offline, consistent with lab_sea.
476      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
477      - update results after change of experiment seaice.
478    o pkg/seaice:
479      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
480        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
481        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
482        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
483    o model/src:
484      - add run-time parameter to select CG2D solver minimum-residual solution
485        (in case of a poor convergence).
486    o pkg/seaice/seaice_lsr.F
487      - move calculation of matrix coefficients into new
488        S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
489        file; the main purpose of this change is to be able to reuse the code
490        in S/R SEAICE_PRECONDITIONER
491      - modify the computation of the residual so that the mass of sea-ice
492        is not used twice; this simplifies the calculations, but since
493        the residual is never used except when LSR_mixIniGuess.ge.4---and this is
494        not tested in testreport---this does not affect the testreport results.
495    o verification/seaice_obcs:
496      - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
497        verification/lab_sea/input.salt_plume; changes results/output.txt*
498    o model/src:
499      - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
500    o pkg/seaice:
501      - improve description of parameters in seaice_fgmres.F and start
502        cleaning up the code
503      - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
504        second argument
505      - add a metric based on grid cell area to SEAICE_SCALPROD; update
506        results of offline_exf_seaice.dyn_jfnk
507      - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
508    o pkg/aim_v23:
509      - fix an other bug in dissipation heating (grid-cell area was missing).
510    o model/src + pkg/seaice:
511      - add global (multi-tile) linear solver for pair of tri-diagonal system
512        along X and Y lines, respectively for U and V component.
513        Note: 1) MPI and cube-exchange not yet coded.
514            2) probably not accurate for poorly conditioned / large size problem.
515      - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
516        default: not compiled and not used.
517    o pkg/seaice:
518      - first attempt at a multi-threaded fgmres solver for the JFNK solver:
519        introduce bi/bj loops and use global_sum_tile_rl instead of
520        mpi_allreduce in seaice_fgmres.F
521      - improve diagnostics output for fgmres solver (seaice_fgmres.F)
522      - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
523      - add a verification experiment for JFNK in offline_exf_seaice
524    o verification:
525      - change (for now, only fwd test) offline_exf_seaice experiment:
526        use a re-entrant channel with idealized coastline (trapezoidal shape)
527        at southern boundary to explore seaice dynamics and thermodynamics
528        with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
529        secondary test (input.thsice) use thermodynamics only with SST relaxation.
530      - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
531    o pkg/exf:
532      - disable "sstExtrapol" when Nr=1
533    o verification:
534      - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
535        to test pkg/cheapaml.
536    o pkg/aim_v23 & pkg/shap_filt:
537      - fix dissipation heating (erroneous gravity multiplication factor).
538    o pkg/seaice:
539      - remove unused field pressPre from jfnk solver
540      - rename two subroutines in seaice_preconditioner.F
541    o eesupp/src:
542       - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
543    o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
544       - remove wrong parts of the rhs and the lhs (were in there
545         because I did not understand the concept of this preconditioner)
546       - add an exchange between u- and v-sweep. This increases communication
547         by a factor of two but improves the convergence of jfnk. Ideally,
548         one would like the u- and v-sweep to be independent. So far within
549         undocumented ifdefs
550       - reorganize the extra computations for printing the residuals
551    o tools/genmake2:
552      - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
553        since it's not necessary (and was preventing to use MNC in some cases).
554    
555    checkpoint64a (2012/11/16)
556    o pkg/autodiff:
557      - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
558        autodiff_readparms.F no longer depends on calling order (within
559        packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
560        rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
561        and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
562    o pkg/obcs:
563      - adding tidal velocity forcing capability to obcs
564        for usage example, see verification/seaice_obcs/input.tides
565    o pkg/seaice:
566      - turn the LSR-relaxation parameters WFAU/V into runtime parameters
567        SEAICE_LSRrelaxU/V
568      - introduce runtime parameter SEAICEetaZmethod (=0 by default)
569    o pkg/aim_v23:
570      - implement heating from friction (bottom friction and stratospheric drag).
571    o pkg/shap_filt:
572      - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
573        dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
574    o model/src:
575      - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
576        time-constant addMass field from file (addMassFile);
577      - support for heating due to friction (and Kinetic Energy dissipation):
578        add option, run-time switch and 3-D field array + support code ; each pkg
579        or S/R can add heating contribution (if there is a sink of KE); the sum is
580        accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
581    o pkg/seaice:
582      - complete merge of ITD code into seaice_growth.F
583        from MITgcm_contrib/torge/itd/code/
584        no verification so far, but Torge Martin tested
585        "1-D test case and Beaufort set up;
586        deliver okay results after 1 model year."
587      - complete merge of SEAICE_SIZE.h into all relevant routines
588      - move computation of eta at Z-points into calc_viscosities
589        + introduce global field etaZ
590        + add different methods for computing etaZ, for now the old
591          method (simple averages of eta to Z-points) is hardwired
592        + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
593          seaice_preconditioner
594      - simplify computations for SEAICE_ZETA_SMOOTHREG
595      - seaice_preconditioner:
596        + replace one remaining press by pressLoc (mistake)
597        + adjust printing of residuals
598      - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
599        + add (SEAICE.h) and rename some counters (initiliased in
600          seaice_init_fixed.F)
601        + add _BEGIN/END_MASTER (myThid)  around print statements
602        + print total number of iterations and failures over SEAICE_monFreq
603          interval to STDOUT
604      - move control over output-messages by fgmres to seaice_jfnk to save
605        some operations
606      - move resetting initial guess for fgmres outside of seaice_fgmres_driver
607        in order to make restarts with sol .ne. zero (fgmres with restarts)
608        (seaice_jfnk.F, seaice_fgmres.F)
609      - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
610        a serious convergence problem when open boundaries are involved
611    o pkg/ggl90: fix computation of control volumes for the case of
612      ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
613      up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
614    o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
615    o pkg/autodiff
616      - Add inAdMode switch for SEAICEuseDYNAMICS:
617        SEAICEuseDYNAMICSinAdMode
618        (extend logic in ADAUTODIFF_INADMODE_SET)
619    o pkg/seaice
620      - Step 1 of merging ice-thickness distribution (ITD) code from
621        MITgcm_contrib/torge/itd/ (author: Torge Martin)
622        The code implements concept laid out in Thorndike et al. (1975);
623        code is enabled via CPP flag SEAICE_ITD
624        nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
625        code is not complete yet!!
626      - SEAICE_SIZE.h now included in almost all seaice routines
627    o verification (using seaice):
628      - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
629        global_ocean.cs32x15.seaice ; update results.
630      - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
631      - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
632        offline_exf_seaice (previously compiling B-grid).
633    o pkg/exf:
634      - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
635        to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
636        forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
637    o pkg/layers (adjust changes from Sept 19):
638      - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
639        this allows to remove "layers_maxNum" dimension from all layers arrays.
640    o pkg/layers (adjust changes from Sept 19):
641      - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
642      - snap-shot extended to all type of layers (not just the 1rst type);
643      - remove layers variables when corresponding CPP option is undef.
644    o pkg/layers:
645      - rename pkg/layers variable and add new output (layer exist & un-weighted
646        velocity in layer)
647    o pkg/seaice:
648      - simplify (?) ocean-drag coefficent computations by using
649        the same routine in all three solvers (saves some code lines)
650      - remove global fields DRAGA and DRAGS from C-grid code and
651        declare them locally in lsr.F (the only place where they are
652        still used)
653      - update AD output of lab_sea.evp (very sensitive anyway).
654    o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
655      (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
656      and SEAICEuseJFNK=.true. A few things to note:
657      - involves a FGMRES, that is parallel but very inefficient,
658        because of many scalar products (global sums) in the Gram-Schmidt
659        orthogonalization method. Needs to be replaced. Original code
660        from J.-F. Lemieux
661      - preconditioner for FGMRES is a stripped down version of LSOR
662      - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
663        preconditioner. For the preconditioner, the default is set to 10.
664      - Jacobian times vector is computed with finite differences
665      - marginally related to JFNK-solver: add a smooth regularization for
666        zeta with tanh that will improve convergence (Lemieux and Tremblay,
667        2009) for any implicit solver (not implemented for EVP because EVP
668        does not need this regularization in the first place). Define
669        SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
670    o eesupp/src:
671      - check in genmake2 that intrinsic S/R flush is available.
672      - add S/R to flush IO unit (if intrinsic S/R flush is available)
673      - flush standard & error msg unit before MPI termination
674      - if debugMode, flush IO unit after printing msg
675    o pkg/ctrl:
676      - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
677        to ctrl_set_unpack_xyz.
678    
679    checkpoint64 (2012/10/09)
680  o pkg/shelfice  o pkg/shelfice
681    in mom_fluxform.F, mom_vecinv.F:    - in mom_fluxform.F, mom_vecinv.F:
682    CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)      CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
683    Bug fix KappaRU -> KappaRV      Bug fix KappaRU -> KappaRV
684    does not change verification/isomip but may change other setups      does not change verification/isomip but may change other setups
685    (presumably constant KappaRU=KappaRV)      (presumably constant KappaRU=KappaRV)
686    - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)    - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
687  o pkg/obcs:  o pkg/obcs:
688    - fixed some indexing bugs in obcs_seaice_sponge.F    - fixed some indexing bugs in obcs_seaice_sponge.F

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