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revision 1.1370 by jmc, Thu Jan 27 20:52:10 2011 UTC revision 1.1562 by jmc, Sun Dec 25 22:29:37 2011 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/exf (vertor interpolation):
8      - rotate vector component toward local grid-axis orientation using grid-angles
9        (stored in GRID.h) instead of locally computed rotation angle; keep old code
10        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
11    o pkg/seaice:
12      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
13        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
14    o pkg/PKG_OPTIONS.h files:
15      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
16        outside of the #ifdef ALLOW_THISPKG / #endif block.
17      - update verification/*/code/PKG_OPTIONS.h files.
18    o add a verification experiment (offline_exf_seaice/input.seaice) that test
19      the B-grid LSOR solver
20    o pkg/seaice: sort out emissivity and long wave radiation step 2:
21      - add emissivity for snow and ice as new run-time parameters
22        (unfortunately) that default to the corresponding exf values; this
23        changes results in most verification experiments so that for backward
24        compatibility these parameter have to be set explicitly to inconsistent
25        values (ugly);
26      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
27        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
28        until we agree how to handle this bug properly
29    o pkg/exf (interpolation):
30      - add a set of run-time param ({inputfield}_interpMethod), one for
31        each interpolated input field, to select the interpolation method
32        with a value of zero switching off the interpolation;
33      - print interpolation parameters to standard output;
34      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
35        (to use instead runoff_interpMethod=0 in data.exf).
36      - simplify default setting of interpolation parameters (for all fields,
37        set position to match model grid cell-center position, leading to trivial
38        interpolation in case of regular Lat-Lon grid) and fix for the case of
39        non-uniform delY.
40    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
41       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
42       this factor is absolutely required, because the lw exitance (= out-going
43       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
44       where the reflectivity rho = 1-emissivity for conservation reasons. Once
45       this is established, we can remove the CPP-Flag (if we want to).
46    o pkg/seaice:
47      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
48        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
49      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
50        what the name implies (and not emissivity*BoltzmannConstant), this means
51        the old default value of 5.5e-8 now means
52        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
53        S/R exf_readparms
54      - FV-discretization of the B-grid LSOR solver, turn on with
55        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
56        of the calling routine dynsolver, so that B and C-grid code look a
57        little more alike.
58      - fix index bugs in ostres.F (B-grid code)
59    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
60    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
61      default for SEAICE_emissivity, if useEXF; requires setting a wrong
62      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
63      backward compatiblity
64    o model/src: use sigmaR in calc_ivdc
65    
66    checkpoint63g (2011/12/16)
67    o pkg/seaice/seaice_growth.F:
68      fix heat conservation of the coupled ocean-seaice system.
69      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
70      solid vs liquid water treatment is resolved via QNET.
71    o pkg/seaice/seaice_growth.F:
72      add missing term for sublimation in saltFlux, which was breaking conservation.
73    o pkg/seaice/seaice_model.F:
74      Remove this patholigical case treatment in evolution branch,
75      where it is un-necessary and breaks conservation.
76      Update global_ocean.cs32x15/results accordingly for
77      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
78    o model/src:
79      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
80      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
81    o pkg/obcs:
82      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
83      tendency for temperature and salinity that is then applied to update
84      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
85      horizontal advection and diffusion contributions on the boundary (in
86      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
87      removing the mask in S/R timestep_tracer. The advantage of this approach is
88      that the updated tracer values include contributions from the surface
89      forcing and vertical diffusion.
90      This modification changes exp4.stevens because of vertical diffusion.
91    o model/src:
92      change non-curvilinear grid setting to also work with exch2 + blank tiles:
93      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
94        face dimensions.
95      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
96        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
97        and INI_SPHERICAL_POLAR_GRID.
98      change test-experiment global_ocean.90x40x15:
99      - split the domain in many more tiles (9x4 tiles of 10x10 each);
100      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
101      - update results of both test (std & dwnslp).
102    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
103       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
104    o model/src:
105      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
106        and fix initialisation when using sigma-coords.
107    o model/src:
108     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
109       to their current value at the beginning of forward_step.F": add a new run-time
110       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
111     - set doResetHFactors=T in the following test exp:
112        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
113        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
114        and tutorial_global_oce_in_p (nonLinFS in p)
115    o pkg/ecco
116      - added IES cost term
117    o verification/advect_xz
118      - scale down the depth by 1/100 (from 200 km to just 2.km)
119      - add secondary test using divergent flow, r-star and implicit vertical advection.
120      - add note (check_conserve_TS.txt) and matlab script to check global
121        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
122    o pkg/rbcs:
123      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
124    o pkg/obcs (Stevens BCs):
125      - fix various problems in the phase speed computations of the Stevens
126        boundary conditions:
127        - sign error for western and southern boundaries,
128        - time tendencies were underestimated by factor of dTracerLev and some just
129          zero (for multidim advection schemes) -> now estimate time tendencies
130          from difference between previous (n) time level and the one before (n-1);
131          this requires storing a field per tracer per boundary, also in the pickup
132          files.
133        - replace deltaTmom in cflMer/Zon computation with dTracerLev
134        - set default phase velocity to cflMer/Zon
135      - update verification experiment exp4.stevens
136    o pkg/generic_advdiff (implicit_r):
137      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
138        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
139      - fix implicit vertical diffusion or advection with NonLin FreeSurf
140        (was using current recip_hFacC instead of future recip_hFacC): set future
141        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
142        solver S/R ;
143      - fill diagnostics of vertical advective fluxes (computed from tendency)
144        when using implicit vert. advection;
145      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
146         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
147         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
148         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
149    o pkg/diagnostics:
150      - add diags for T & S tendency which goes through Adams-Bashforth.
151    
152    checkpoint63f (2011/11/30)
153    o pkg/obcs/obcs_calc_stevens.F:
154      - join some loops to reduce number of if-statements
155      - fix a bug in code for northern and southern boundaries.
156    o pkg/seaice/seaice_init_varia.F
157      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
158        caused zero ice-velocities for the B-grid code
159    o pkg/seaice/seaice_init_fixed.F
160      - fix a bug in the initialisation of the second metric terms
161        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
162      - this affects all seaice configurations with useCurviLinearGrid = .true.
163        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
164        = .true. (default)
165      - the only verification experiment affected is global_ocean.cs32x15:
166        icedyn, seaice, and seaice_dynmix (AD)
167    o pkg/thsice/thsice_diagnostics_state.F
168      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
169        not contain garbage that can lead to surprises in diagstats_calc.F
170    o model/src:
171      - move bi,bj loops inside INTEGR_CONTINUITY ;
172      - call INTEGR_CONTINUITY directly from forward_step.F
173        (previously called from momentum_correction_step.F)
174      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
175        forward_step.F and pkg/ecco/the_main_loop.F
176    o model/src/do_oceanic_phys.F:
177      - reset addMass to zero only if useICEFRONT ;
178      - separated k-loop for rhoInSitu calculation ;
179      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
180        and at constant T,S (= WdRHOdP);
181      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
182        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
183        transport of locally-referenced potential density);
184        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
185    o gluemnc:
186      - replace ncrcat with ncks when adding variables to *.glob.nc
187      - change the way variables without record dimensions are handled so that
188        files that have variables with and without record variables can be glued:
189        add a record dimension with a new unique name to be able to differentiate
190        between variable with and without a-prior record dimensions. Remove
191        this record dimension before adding the variable to the *.glob.nc file.
192        This procedure automatically works also for grid.*.nc files that do not
193        have any record dimension.
194    o verification/cpl_aim+ocn:
195      - generate new reference output on baudelaire (gfortran, mpich2) (previously
196        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
197    o pkg/obcs/obcs_calc_stevens.F:
198      - add code for northern and southern boundaries.
199      - reorder some loops to save some operations and so that drFBar can be scalar
200    o model/src:
201      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
202        truncation) and add diagnostics for Adams-Bashforth tendency increment.
203      - update test-exp. AD output:
204        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
205      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
206        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
207        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
208        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
209        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
210        tutorial_plume_on_slope.
211    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
212      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
213      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
214      does not even come with an F77 compiler anymore, this should not be
215      a limitation
216    
217    checkpoint63e (2011/11/06)
218    o pkg/seaice adjoint of LSR:
219      - substantially rework STORE dirs.
220      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
221        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
222        and only perform SOLV_MAX_FIXED adjoint iters.
223        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
224        always goes to same record, meaning that the last forward field will be
225        the one used in the adjoint - an approximation.
226      - now produces non-zero LSR-related gradients, and acceptable gradients for
227        An's zonal (x-z) test case (to be checked in)
228      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
229        (but these are screwed up by the thermodynamics in the first place);
230        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
231        output_adm.txt also reflects changes to seaice_lsr
232      - global_ocean.cs32x15:
233        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
234          (output_adm.seaice.txt was updated)
235        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
236          (output_adm.seaice_dynmix.txt)
237    o test-exp. exp4+stevens:
238      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
239    o pkg/seaice (lsr solver):
240      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
241        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
242      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
243      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
244        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
245      - compute (with new S/R) and print initial (+ free-driff sol. if available)
246        and final residual of linearised system.
247    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
248      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
249    o pkg/obcs: Stevens BCs (still only for east and west)
250      - fix Stevens BCs by using intermediate velocities of previous
251        time step as "baroclinic" contribution rather velocity of one grid cell
252        inside the boundaries; more consistent but makes the entire treatment
253        more complicated, requires new pickup files and two new S/Rs:
254        obcs_copy_uv_n and obcs_save_uv_n
255        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
256        (undefined by default)
257      - silently move computation of some grid factors into separate loops to
258        save some recomputations
259      - add a hack for non-linear free surface
260      - add a verification experiment to exp4 that tests this code
261    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
262    
263    checkpoint63d (2011/10/25)
264    o pkg/obcs + seaice-dynamics:
265      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
266        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
267        values (consistent with an implicit method).
268      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
269        return to older implementation (same results as before); note that none of
270        the "experimental" OBCS_SEAICE options are implemented in the new version.
271      - switch test exp. seaice_obcs to use new version (update output).
272    o pkg/seaice:
273      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
274      - add parenthesis in Water-Ice drag calculations (evp & lsr);
275      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
276        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
277      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
278        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
279    o pkg/layers:
280      - Include potential density as new coordinate (Thanks to David Munday)
281    o pkg/dic:
282      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
283        carbonate computation/output to CALC_PCO2_APPROX
284    o pkg/generic_advdiff
285      - make TAF generate code that vectorizes:
286        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
287    o model/src:
288      - improve vectorization also for adjoint code of
289        solve_tridiagonal and solve_pentadiagonal. As this requires up to
290        5 new 3D-fields, this code is only turned on for the combination of
291        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
292        for singular matrix check (only for TARGET_NEC_SX).
293      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
294        ALLOW_AUTODIFF. This flag now needs to be set outside of
295        solve_tri/pentadiagonal.F
296    o pkg/exf:
297      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
298        optional namelist EXF_NML_OBCS).
299      - add many debug-print (to trace down where pkg/cal error msg comes from)
300    o pkg/mom_vecinv/mom_vi_hdissip.F
301      - rearrange loops so that vectorization is improved and in particular
302        the adjoint routine vectorizes. The code is a little longer now, but I
303        think easier to read.
304        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
305    o pkg/seaice:
306      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
307    o pkg/exch2:
308      - alternative code (without tile x tile matrix) for cumulated (global) sum;
309        used as default; keep using matrix version in adjustment.cs-32x32x1.
310    o tools/build_options:
311      - after merging some MPI and/or multi-threads specific optfiles so that
312        the modified default optfile support both built (using genmake2 -mpi
313        for the MPI built, using genmake2 -omp for OpenMP built),
314        move now obsolete optfiles to tools/build_options/unsupported/
315       (add copy of email sent to support list in doc/optfiles_changes.txt)
316    
317    checkpoint63c (2011/09/28)
318    o pkg/ebm:
319      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
320        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
321    o pkg/seaice (SItracer pickup)
322    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
323      To be done:
324      - thorough testing of missing fields in S/R seaice_read_pickup
325      - thorough matching between generic tracers and specific fields used
326        (e.g. volume-weighted age, area-weighted age, salinity, ...)
327    o pkg/grdchk:
328      - all procs calculate and print finite-difference gradient (for testreport)
329      - change description output used by testreport;
330      - AD testing: also compare and report Finite-difference gradient;
331        => update all output_adm*.txt
332    o test exp. global_ocean_ebm:
333      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
334        and turn on exactConserve; update (fwd) output.
335    o pkg/seaice (LSR):
336      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
337      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
338        * identical results with non-CS topology (but save up to half of EXCH calls)
339        * no much changes in cs-32 verification tests since no ice at face edges
340         (differences due to convergence criteria, since nb of iterations changed)
341        * expect some differences on lat-lon-cap grid.
342        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
343    o pkg/exch2:
344      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
345        many tiles); until alternative coding is added, just add a stop.
346    o pkg/kpp:
347      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
348        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
349    o optfiles:
350      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
351        into corresponding standard one, which now support different build:
352        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
353      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
354    o pkg/obcs (seaice):
355      - add missing EXCH for uIce,vIce after applying OBCS;
356      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
357        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
358        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
359      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
360      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
361        and eedata.mth for MPI and mutlti-threaded testing.
362    o pkg/flt:
363      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
364      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
365      - fix pickup and trajectories + profiles output with multi-threads;
366      - add parameter to select group of fields to write along trajectory and
367        profile (default unchanged);
368      - only call PORT_RAND* function when flt_noise <> 0;
369      - add multi-threaded test for verification exp. flt_example.
370    o eesupp/src:
371      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
372      - USE_OMP_THREADING: check that number of threads (from eedata) matches
373        actual number (from env.var. setting).
374    o pkg/ebm:
375      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
376      - add multi-threaded test for verification exp. global_ocean_ebm
377    
378    checkpoint63b (2011/08/29)
379    o pkg/ebm:
380      - fix sign of runoff;
381      - update directly forcing fields (Qnet,EmPmR) to use standard
382        external_forcing_surf.F (remove ebm_forcing_surf.F);
383      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
384      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
385        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
386      - update global_ocean_ebm parameters file data and update output (fwd+ad).
387    o verification/matrix_example:
388      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
389        MPI and mutlti-threaded testing.
390    o pkg/matrix:
391      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
392      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
393      - fix for multi-threaded (remove DATA statement);
394      - use standard DIFFERENT_MULTIPLE function;
395      - add MATRIX_OPTIONS.h
396    o verification/matrix_example:
397       To allow to split the domain in several tiles, change the domain size
398        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
399        Western side) of land points.
400    o (*_)write_pickup:
401      - fix few bugs in mypackage_read/write_pickup.F
402      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
403        array of length 1 (was caught by compiler syntax-check).
404    o pkg/diagnostics (velocity potential solver):
405      - fix initialisation of main diagonal matrix (for overlap values)
406    o tools/build_options:
407      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
408        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
409      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
410        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
411        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
412        and use "-devel" testreport option for standard testing on baudelaire.
413    o pkg/grdchk:
414      - Assume that all gradient-check position are within the same tile
415        corresponding to global indices (iGloTile,jGloTile) and that
416        positions (i,j indices or nbeg) are local to this tile;
417      - set tile local-indices and proc. number according to tile global-indices;
418      - remove grdchkwhichproc from namelist (retired param);
419      - send adjoint gradient to all procs so that all procs print it to STDOUT;
420      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
421    o adding package bbl (Bottom Boundary Layer)
422      description in MITgcm/pkg/bbl/bbl_description.tex
423      example/test experiment in MITgcm_contrib/bbl
424    o adjoint verifications
425      - changed 5 experiments to multi-tiles
426        * global_ocean.90x40x15
427        * obcs_ctrl
428        * offline_exf_seaice
429        * tutorial_dic_adjoffline
430        * tutorial_tracer_adjsens
431        changed reference output for those that crossed tile boundaries
432        (changed choices of gradient check positions)
433      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
434      - temporary bug fix in grdchk_loc.F for obcs
435    o genmake2 & testreport
436      - add target "obj" (just for OBJFILES files) to Makefile;
437      - add option to specify FEXTRAFLAGS on command line.
438    o pkg/mypackage:
439      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
440    
441    checkpoint63a (2011/08/02)
442    o pkg/diagnostics (velocity potential):
443      - fix velocity-potential calculation when using OBCS: balance net inflow
444        at each level (new S/R OBCS_DIAG_BALANCE).
445      - fix some of the problems with OBCS in stream-function calculation.
446    o pkg/exf/exf_readparms.F
447      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
448        EXF_NML_OBCS) more consistent, so that you need not have these lists
449        in data.exf when they are not used.
450    o optim/optim_readdata.F:
451      - add some output about obcs variables that might help debugging
452      - add a check about nvarlength
453    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
454    o pkg/diagnostics (velocity potential):
455      - fix mask for OBCS (still problems in stream-function with OBCS);
456      - add specific parameter (default = main code CG2D params) for solver;
457      - in case of poor convergence, use solution corresponding to lowest residual.
458    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
459      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
460      and should be avoided where possible.
461    o model/src (rStar):
462      - include r* effect on reference-state (PhiRef) in totPhiHyd
463        (so that it's really the potential anomaly at the cell center);
464        affect solution only if z* with full pressure in EOS.
465      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
466        update output (because of z* in totPhiHyd and viscA4 changes);
467      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
468        @ constant r) until interpolation at constant r is implemented.
469    o pkg/diagnostics
470      - fix RCENTER diagnostics in case cell center is not at interface middle
471    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
472      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
473      that THETA and SALT are "conservative temperature" and "absolute
474      salinity"
475    o pkg/ctrl
476      - fix computation of endrec in s/r ctrl_init_rec
477      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
478    o pkg/seaice/seaice_growth.F
479      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
480        remove then obsolete STORE directives
481      - fix STORE directives for tice and tices, so that only the
482        appropriate part of the fields are stored (and not the entire
483        field); update global_ocean.cs32x15.seaice AD output.
484      - cosmetic changes: adjust CPP flags and indentation for better
485        legibilty
486    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
487      Chris Wilson)
488    o pkg/gmredi:
489       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
490       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
491    
492    checkpoint63  (2011/07/11)
493    o pkg/exch2:
494     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
495     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
496       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
497       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
498    o pkg/diagnostics:
499     - deal with pairs of post-processed diags which are computed together; in
500       particular, re-order list of diags within 1 file to save 2nd computation.
501     - add S/R to compute velocity stream-function (called after velocity-potential
502       calculation) from divergence free transport -> new diagnostics "PsiVEL".
503     - add parameter to select grid-point location where PsiVEL == 0.
504    o eesupp/src:
505       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
506       (specific S/R needed with exch2 topology - for now, just print an error msg)
507    o pkg/shelfice
508     - Implement friction velocity-dependent transfer coefficients following
509       Holland and Jenkins, JPO, 1999
510       Original code by M. Losch with small modifs.
511       Enable with CPP option SHI_ALLOW_GAMMAFRICT
512       and runtime flag SHELFICEuseGammaFrict
513    o verification lab_sea & global_ocean.cs32x15:
514     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
515       does not miss some dependencies (but is slower) and also works with many files
516       (default makedepend limitation for AD built).
517     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
518    o pkg/diagnostics:
519     - add run-time parameter "useMissingValue" (def=False) to fill land-point
520        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
521       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
522     - Extend the use of "missing_value" setting from data.diagnostics for the case
523       of counter-diagnostics (where fraction-weight is zero). This applies both to
524       MNC and MDS output files.
525    o pkg/seaice/seaice_growth.F:
526      - add 'a priori' cap of latent heat flux based on actual mass considerations
527        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
528        non-legacy seaice_solve4temp.
529      - add diagnostic of the residual sublimation freshwater flux (the freshwater
530        flux taken from the ocean if the total actual latent heat fluxes exceed
531        the maximum)
532      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
533       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
534      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
535       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
536      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
537      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
538    o verification 1D_ocean_ice_column:
539       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
540       update results
541    o pkg/diagnostics:
542     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
543       which are not filled-up but computed from other diags ; In this case, the mate
544       diag points to the primary (filled-up) diag to used for post processing.
545     - Update Velocity-potential computation using post-processed diag framework.
546     ==> Change the ordering of fields and time-periods in MDS output file
547       when using periodic averaging: now writes one time record with the full set
548       of fields for this time period, then the next time reccord (it used to be
549       one field with the full set of time records then the next field).
550         Note: this is now similar to NetCDF (MNC) output file. <==
551    
552    checkpoint62z (2011/06/21)
553    o adjoint monitor:
554     - Add adjoint monitor output for packages exf, seaice
555       and update relevant testreport output
556    o pkg/seaice:
557     - re-order diags inits so that they appear in order in available_diagnostics.log
558     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
559       area/heff/hsnow preceeding thermodynamic growth/melt.
560     - modified diag: SIdA; output actual effect, as the description states.
561     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
562     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
563       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
564        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
565     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
566     - added diagnostics for seaice generic tracers (SItr*).
567     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
568     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
569     I. Fenty: 18-Jun-2011:
570     Minor changes to seaice package:
571     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
572        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
573       - Differentiated "regularization variables" from "floor variables"
574        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
575        * hiceMin became SEAICE_hice_reg (old hiceMin)
576          (with _reg meaning regularization variable)
577       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
578        so as to ensure energy conservation when going between phases
579      - A22 was not used anywhere
580     2) Changed regularization procedure for heffActual and hsnowActual to ensure
581        well-boundedness and smooth adjoint in seaice_growth.F
582     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
583        because the old regularization always set heffActual >= 0.05 cm
584     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
585        on AREA when HEFF > 0.
586      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
587        requiring that DISABLE_AREA_FLOOR *not* be defined
588     Affected verifications:
589      - 1D_ocean_ice_column (output.txt output_adm.txt)
590      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
591    o pkg/diagnostics:
592      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
593      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
594        (was _RL, now integer) with option = 0 to retrieve all levels.
595      - add pieces of code to compute velocity potential at each level (new diagnostics
596        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
597        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
598      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
599        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
600        and in diagnostics_fract_fill.F (do not need a valid pointer for the
601        diagnostics counter-mate); check that definition of counter-diagnostic
602        includes a valid counter-mate (in diagnostics_set_levels.F).
603    o model/src (rStar):
604      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
605        affect solution only if z* with full pressure in EOS;
606        update output of test-exp global_ocean.90x40x15.
607    o pkg/seaice:
608      - introduce siEps=1e-5 parameter
609      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
610      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
611      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
612        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
613        as well as ice cover age and ridging index (attached to AREA).
614        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
615        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
616        Up to SItrMaxNum=3 tracers can be used simultaneously.
617    o pkg/salt_plume:
618      -introduce SPsalFRAC run time parameter that sets the fraction of the
619       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
620       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
621    o model debug options:
622      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
623        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
624      - Refine debug-msg printing selection (3 new levels):
625        debugMode  : controls printing of debug messages (sequence of S/R calls).
626        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
627         debLevZero =  0 ; /* level of disabled aux. msg printing */
628         debLevA =  1 ; /* level of minimum  aux. msg printing */
629         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
630         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
631         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
632         debLevE =  5 ; /* level of extensive debug printing */
633        New debugLevel default: with default debugMode value (=F),
634          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
635          and if debugMode=T, default debugLevel = 4 (debLevD).
636        Relation with previous settings:
637         debLevB (=2) corresponds to former debLevA (=1)
638         debLevD (=4) corresponds to former debLevB (=2)
639        Note:
640         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
641         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
642            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
643      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
644        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
645    o pkg/obcs:
646      - change OBCSfixTopo default from True to False (should not change the results);
647        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
648    o pkg/thsice:
649      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
650        2nd layer seaice sublimation (unlikely to happen)
651      - use Interior mask for OBCS in thsice_advection.F (similar to what is
652        done in gad_advection & seaice_advection).
653    o adjoint:
654      bug fix spotted by Gael Forget:
655      seaice_advection and thsice_advection still had
656      legacy CPP options to avoid CS corner updates for adjoint
657    o pkg/seaice:
658      => Change some of the defaults (2011/05/29):
659         - change SEAICEuseFluxForm default (from False to True)
660         - change DIFF1 default (from 0.004 m/s to 0. m/s)
661         And print warnings if DIFF1 is not set in data.seaice and centered
662          avection scheme is used without any diffusion.
663      also:
664      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
665      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
666      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
667        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
668        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
669      update results of test exp.:
670         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
671             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
672             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
673         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
674         seaice_obcs: output (SEAICEuseFluxForm=T)
675      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
676          for standard fwd & AD lab_sea tests (to keep the same output).
677    o pkg/seaice/seaice_growth.F:
678      - use Ian Fenty's capping formulas for actual ice
679      thickness thoughout EVOLUTION branch.
680      - put treatment pathological case #2) in CPP brackets
681      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
682      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
683    o pkg/seaice:
684      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
685      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
686      also pass fac as a param, which can be 1. (to update the tendency
687      field) or the time step (to update the field itself).
688      - seaice_advdiff.F: for multidim, call seaice_diffusion with
689      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
690      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
691      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
692      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
693    o pkg/seaice:
694      diffusion with centered advection scheme (diffus.F & advect.F):
695      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
696        to just compute the laplacian of input-field.
697      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
698      - fix flux-form version in diffus.F to conserve tracer.
699      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
700       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
701    
702    checkpoint62y (2011/05/26)
703    o pkg/seaice:
704     - seaice_growth.F : in EVOLUTION branch, always include
705       a_QSWbyATM_cover in qnet (as it should be).
706     - verification/global_ocean.cs32x15 : update results accordingly
707       (output.seaice.txt output_adm.seaice.txt).
708    o pkg/seaice + obcs:
709     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
710       equivalent of assuming no tracer gradient outside the OB region.
711       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
712     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
713       after changes above);
714     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
715       only at OB location (instead of over a band of OLx width).
716    o pkg/seaice:
717     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
718       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
719    o pkg/obcs:
720      - split header file "OBCS.h" into 4 separated files:
721        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
722       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
723         (contain no conditional statement which depends on OBCS options).
724      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
725        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
726    o ctrl, cost, grdchk & autodiff pkgs:
727      - make options file more standard (like other {PKG}_OPTIONS.h file but
728        with AD_CONFIG.h); clean-up some of the included header files.
729    o pkg/obcs:
730      - do not mask tracer when applying OB (tracer == 0 could generate problems)
731      - apply tracer OB values to tracer field only at OB location (instead of
732        over a band of OLx width)
733      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
734      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
735        obcs_apply_tloc.F & obcs_apply_sloc.F
736    o obcs in model/src:
737      - call OBCS_APPLY_W only if NonHydrostatic.
738      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
739      - reset dEtaHdt and wVel to zero outside OB interior region ;
740      - leave tracer unchanged outside OB interior region: This has no effect
741        on the solution but just to prevent unrealistic tracer value outside OB.
742      - zero out velocity outside OB interior region: This has no effect on
743        the solution but just to prevent unrealistic velocity outside OB.
744    o obcs and non-lin free-surf:
745       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
746       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
747       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
748       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
749       update results of test-exp. exp4(nlfs).
750    o exp4 (nlfs) test-exp:
751       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
752       with NonLin-FreeSurf); update output.nlfs.txt
753    o obcs and 2d/3d solver norm:
754       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
755       and outside OB interior region (will allow to place OB further inside the
756       domain). Depending on the domain, can affects cg2d-Norm (previous
757       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
758       and cg3d-Norm (previous Norm was computed before canceling OB terms),
759       e.g. in tutorial_plume_on_slope.
760      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
761    o pkg rbcs:
762      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
763      - add capability to apply relaxation to horizontal velocity uVel & vVel.
764    o pkg/grdchk: add gradient check for control variable xx_shifwflx
765    o pkg/shelfice/shelfice_init_fixed.F
766      fix CPP-flag combinations
767    o pkg/seaice: Merge iceage code of Pierre Rampal
768      * update/change/correct ice age calculations
769      * add age updates for pathological cases
770      Probably needs more testing...
771    
772    checkpoint62x (2011/05/13)
773    o pkg/mom_vecinv:
774       high-order vorticity scheme: use interior masks (maskInW & S)
775       to zero-out (outside OB) gradient of vorticity.
776    o verification exp.:
777       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
778       hs94.128x64x5 and seaice_obcs ; update results.
779    o pkg/obcs:
780      fix bug in OBeta for YZ sections in obcs_exf_load.F
781    o pkg/ctrl, pkg/shelfice, and optim:
782      - add new control variable xx_shifwflx (fresh water flux underneath ice
783        shelves). This is almost as tedious as obcs-ctrl, because the
784        variables needs its own mask.
785      - add a cost function term that penalizes the deviation of xx_shifwflx
786        from the first guess (zero) in analogy to other control variables
787    o pkg/shelfice:
788      - start basic adjoint
789    o pkg/ctrl:
790      - remove extra 2D field "for good measure" when initializing in
791        ctrl_set_globfld_[xy/xz/yz].F
792      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
793      - improve error messages in ctrl_set_unpack_*
794    o OBC implementation in momentum:
795       use interior masks (maskInC,W & S) in momentum S/R:
796       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
797       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
798       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
799       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
800       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
801        (and also with Leith/Smagorinsky harmonic-viscosity).
802       Update output of experiment dome and exp4 (+nlfs).
803    o exp4 test-exp:
804      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
805        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
806        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
807        time-varying OB at Western-side for wVel (NonHyd); update output.
808      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
809        and biharmonic-viscosity ; also use prescribed time varying OB.
810    o pkg/obcs:
811      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
812    o model/src:
813      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
814      - initialise startTime & nIter0 with unlikely values: allows to set one
815        from the other without ambiguity.
816    o seaice_obcs test-exp.:
817      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
818    o pkg/obcs:
819      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
820        no longer needed with maskInC,W,S in pkg/generic_advdiff.
821    o pkg/seaice:
822      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
823        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
824      - fixed bug in the initialization of sea ice salinity variable HSALT
825        in seaice_init_varia.F  (removed dependence on ICE2WATR)
826    o fizhi-cs test exp.:
827       switch reference output convention for these 2 non-standard test-exp,
828        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
829          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
830       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
831    o model/inc:
832      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
833        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
834    o pkg/seaice:
835      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
836    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
837      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
838        and initial HSALT
839    
840    checkpoint62w (2011/04/26)
841    o pkg/mom_fluxform:
842      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
843      - use parameter "sideDragFactor" in no-slip BC side-drag part.
844      - update output of exp. global_ocean.90x40x15
845    o pkg/mom_vecinv:
846      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
847    o update seaice exp.:
848      use more consistent parameter values (remove "backward compatability only":
849       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
850      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
851       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
852    o update test-exp global_ocean.90x40x15:
853      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
854      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
855      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
856      o turn on zStar & viscA4 in standard set-up (dir input/)
857        and update output files: output.txt & output.dwnslp.txt
858    o new AD-test experiment: obcs_ctrl
859      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
860    o pkg/dic:
861      fix two bugs in handling water vapour pressure in carbonate chemistry
862      and air-sea fluxes. Found by Val Bennington and Galen McKinley
863      (add DIC Option = WATERVAP_BUG to recover old results)
864      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
865    o adding allowInteriorFreezing option to check for water below freezing point
866      at depth and bring the negative heat anomaly to the surface level
867    o pkgs _fields_load:
868      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
869      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
870        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
871        rbcs to get interpolation weights and time reccord number.
872      - fix multi-threading in aim_fields_load.F
873      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
874    o external_fields_load:
875      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
876       interpolation weights) to use in a periodic time-series ; do not divide by
877       time-step to convert to integer:
878       - this fixes case where externForcingPeriod is not multiple of time-step
879          (Thanks to Christopher L. Wolfe)
880       - this fixes case where externForcingPeriod is an odd multiple of time-step
881         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
882      store index of time-record which is currently loaded:
883       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
884       - needed for the adjoint but not yet used because of extensive recomputations;
885         (to be fixed soon)
886    
887    checkpoint62v (2011/04/02)
888    o verification/1D_ocean_ice_column added to test Ian Fenty's
889      pkg/seaice_growth.F modifications for improving sea ice code differentiability
890    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
891      (new velocity statistics after changing maskInW & maskInS definition)
892    o pkg/generic_advdiff with OBCS:
893      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
894      equivalent to assumption of no tracer gradient outside the OB region.
895      This will affect the results if using obcs+biharmonic diffusion.
896      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
897    o pkg/obcs:
898      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
899      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
900      in Interior region. No impact on solution but affects Velocity monitor stats.
901    o pkg/ptracers (adjoint)
902      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
903      tape file for each tracer
904    o model/inc/src and pkg/autodiff: add parameters that allow to turn
905      of parts of the adjoint code at run time. For now, there are only
906      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
907      parameters are set in data.pkg.
908      This is the lazy coward's version of doing this, but still useful for
909      debugging. In order to do it right, everything needs to be moved to
910      pkg/autodiff.
911    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
912      the end; this fixes the adjoint balancing code for open boundaries.
913    o pkg/ctrl:
914      - change behavior of xx_${varname}period to be analogous to exf-conventions:
915        xx_${varname}period =   0.,  means time-independent control part
916        xx_${varname}period = -12., means one-year-periodic monthly control part
917      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
918        clean up ctrl_init a little, remove unused variables
919      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
920      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
921    
922    checkpoint62u (2011/03/15)
923    o model/src:
924      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
925        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
926      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
927        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
928    o pkg/ctrl/obcs/ecco:
929      - remove obsolete, unused, and partially broken code:
930        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
931        ALLOW_CTRL_OBCS_BALANCE
932      - put a stop statement into ecco/cost_obcsvol.F, but also add
933        cost_obcsvol to ecco_ad_diff.list
934    o pkg/ecco: fix counting cost function contributions for obcs (code
935      by Matt M.) and diffkr for diagnostics
936    o pkg/ecco, pkg/ctrl, pkg/grdchk:
937      add cost penalty terms for initial uvel, vvel, eta controls
938      and I/O for prior error files
939    o pkg/mdsio:
940       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
941       (new argument) to check for tiled file in mdsioLocalDir : this fix the
942       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
943    o pkg/ctrl:
944     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
945       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
946       unused and superfluous variables
947     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
948    o pkg/ecco
949     - enable adjoint of Stevens OB
950    o pkg/ctrl/ecco/grdchk:
951      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
952        Fortunately, we do not have any tests for the numerous cpp-flagged
953        option of "obcs as control parameters" so we will never know
954        if this is an improvement (but at least now things compile).
955      - remove an obsolete initialization from ecco_cost_init_barfiles.F
956      - fix some problems within never used ifdefs to make the code compile
957    o pkg/obcs:
958     - Refine Interior mask definition to work with more complex OB (e.g.
959       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
960       read in Interior mask from file. Check if Interior mask is consistent
961       with OB list of indices.
962    o pkg/seaice
963     - beginning code for a seaice tracer package,
964       but currently only used for seaice age: SEAICE_AGE
965       SEAICE_num = 4
966       iTracer = 1: area-weighted ice age
967               = 2: volume-weighted ice age
968               = 3, 4: template for one-year vs. multi-year ice
969       data.seaice has new namelist SEAICE_PARM03 for arrays related to
970       SEAICE_num
971    
972    checkpoint62t (2011/03/05)
973    o pkg/obcs:
974     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
975       then normal component. This ensures that the normal component is set
976       correctly even when it conficts with tangential setting from an other OB.
977       Affects results of test-experiment seaice_obcs: update the output.txt
978    o pkg/obcs:
979     - add code to monitor statistics of dynamical fields at OB.
980     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
981       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
982       - change default: balance the Net inflow through all OB (instead of balancing
983         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
984     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
985       to match Nortern OB inflow (OBCS_balanceFacN=0).
986    o pkg/seaice:
987     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
988    o pkg/seaice (seaice_growth v 1.113):
989     - reverting seaice_growth to v 1.111 in order to have code with exact bit
990       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
991       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
992       runtime flag SEAICEareaFormula is kept but is inactive
993    o model/src:
994     - add new param to scale curvilinear grid distance and area when using
995       a different sphere radius from the grid-files.
996     - test/check multi-threads EXCH applied to local variable (cg2d_x)
997    o adjoint:
998     - enable adjoint of Stevens OB
999     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
1000       (a bit delicate because of potentially modified adj. common block structure;
1001       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
1002    
1003    checkpoint62s (2011/02/15)
1004    o pkg/seaice (seaice_growth v 1.112):
1005     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
1006       computing the ice cover tendency from effective thickness tendencies. Include
1007       Ian Fenty's formula.
1008     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
1009       SEAICEareaFormula.
1010     - simplify notations for the various d_HEFF/d_AREA terms.
1011    o pkg/gmredi:
1012     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
1013       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
1014       add a verification test-run (front_relax.bvp) to test GM_useBVP.
1015    o pkg/seaice (seaice_growth v 1.111):
1016     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
1017     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
1018       also melt ice.
1019    o pkg/seaice:
1020     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
1021     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
1022    o pkg/cheapaml:
1023     - from Nico Wienders: New version of this package.
1024    o pkg/flt:
1025     - add CPP options to prevent floats to re-enter the opposite side of
1026       a periodic domain (default: keep periodicity)
1027  o pkg/gmredi:  o pkg/gmredi:
1028   - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners   - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
1029     (needed for multi-dim advection).     (needed for multi-dim advection).
1030     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
1031  o model/src:  o model/src:
1032   - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.   - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
1033    o tutorial_tracer_adjsens
1034     - extend to NLFS and replace maskC by hFacC
1035       (change reference output accordingly)
1036    
1037  checkpoint62r (2011/01/24)  checkpoint62r (2011/01/24)
1038  o testreport:  o testreport:
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