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revision 1.1347 by mlosch, Mon Dec 13 13:54:53 2010 UTC revision 1.1556 by mlosch, Wed Dec 21 12:59:51 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/seaice: add diagnostics for snow precipitation  o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
8       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
9       this factor is absolutely required, because the lw exitance (= out-going
10       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
11       where the reflectivity rho = 1-emissivity for conservation reasons. Once
12       this is established, we can remove the CPP-Flag (if we want to).
13    o pkg/seaice:
14      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
15        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
16      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
17        what the name implies (and not emissivity*BoltzmannConstant), this means
18        the old default value of 5.5e-8 now means
19        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
20        S/R exf_readparms
21      - FV-discretization of the B-grid LSOR solver, turn on with
22        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
23        of the calling routine dynsolver, so that B and C-grid code look a
24        little more alike.
25      - fix index bugs in ostres.F (B-grid code)
26    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
27    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
28      default for SEAICE_emissivity, if useEXF; requires setting a wrong
29      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
30      backward compatiblity
31    o model/src: use sigmaR in calc_ivdc
32    
33    checkpoint63g (2011/12/16)
34    o pkg/seaice/seaice_growth.F:
35      fix heat conservation of the coupled ocean-seaice system.
36      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
37      solid vs liquid water treatment is resolved via QNET.
38    o pkg/seaice/seaice_growth.F:
39      add missing term for sublimation in saltFlux, which was breaking conservation.
40    o pkg/seaice/seaice_model.F:
41      Remove this patholigical case treatment in evolution branch,
42      where it is un-necessary and breaks conservation.
43      Update global_ocean.cs32x15/results accordingly for
44      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
45    o model/src:
46      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
47      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
48    o pkg/obcs:
49      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
50      tendency for temperature and salinity that is then applied to update
51      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
52      horizontal advection and diffusion contributions on the boundary (in
53      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
54      removing the mask in S/R timestep_tracer. The advantage of this approach is
55      that the updated tracer values include contributions from the surface
56      forcing and vertical diffusion.
57      This modification changes exp4.stevens because of vertical diffusion.
58    o model/src:
59      change non-curvilinear grid setting to also work with exch2 + blank tiles:
60      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
61        face dimensions.
62      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
63        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
64        and INI_SPHERICAL_POLAR_GRID.
65      change test-experiment global_ocean.90x40x15:
66      - split the domain in many more tiles (9x4 tiles of 10x10 each);
67      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
68      - update results of both test (std & dwnslp).
69    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
70       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
71    o model/src:
72      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
73        and fix initialisation when using sigma-coords.
74    o model/src:
75     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
76       to their current value at the beginning of forward_step.F": add a new run-time
77       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
78     - set doResetHFactors=T in the following test exp:
79        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
80        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
81        and tutorial_global_oce_in_p (nonLinFS in p)
82    o pkg/ecco
83      - added IES cost term
84    o verification/advect_xz
85      - scale down the depth by 1/100 (from 200 km to just 2.km)
86      - add secondary test using divergent flow, r-star and implicit vertical advection.
87      - add note (check_conserve_TS.txt) and matlab script to check global
88        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
89    o pkg/rbcs:
90      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
91    o pkg/obcs (Stevens BCs):
92      - fix various problems in the phase speed computations of the Stevens
93        boundary conditions:
94        - sign error for western and southern boundaries,
95        - time tendencies were underestimated by factor of dTracerLev and some just
96          zero (for multidim advection schemes) -> now estimate time tendencies
97          from difference between previous (n) time level and the one before (n-1);
98          this requires storing a field per tracer per boundary, also in the pickup
99          files.
100        - replace deltaTmom in cflMer/Zon computation with dTracerLev
101        - set default phase velocity to cflMer/Zon
102      - update verification experiment exp4.stevens
103    o pkg/generic_advdiff (implicit_r):
104      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
105        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
106      - fix implicit vertical diffusion or advection with NonLin FreeSurf
107        (was using current recip_hFacC instead of future recip_hFacC): set future
108        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
109        solver S/R ;
110      - fill diagnostics of vertical advective fluxes (computed from tendency)
111        when using implicit vert. advection;
112      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
113         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
114         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
115         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
116    o pkg/diagnostics:
117      - add diags for T & S tendency which goes through Adams-Bashforth.
118    
119    checkpoint63f (2011/11/30)
120    o pkg/obcs/obcs_calc_stevens.F:
121      - join some loops to reduce number of if-statements
122      - fix a bug in code for northern and southern boundaries.
123    o pkg/seaice/seaice_init_varia.F
124      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
125        caused zero ice-velocities for the B-grid code
126    o pkg/seaice/seaice_init_fixed.F
127      - fix a bug in the initialisation of the second metric terms
128        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
129      - this affects all seaice configurations with useCurviLinearGrid = .true.
130        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
131        = .true. (default)
132      - the only verification experiment affected is global_ocean.cs32x15:
133        icedyn, seaice, and seaice_dynmix (AD)
134    o pkg/thsice/thsice_diagnostics_state.F
135      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
136        not contain garbage that can lead to surprises in diagstats_calc.F
137    o model/src:
138      - move bi,bj loops inside INTEGR_CONTINUITY ;
139      - call INTEGR_CONTINUITY directly from forward_step.F
140        (previously called from momentum_correction_step.F)
141      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
142        forward_step.F and pkg/ecco/the_main_loop.F
143    o model/src/do_oceanic_phys.F:
144      - reset addMass to zero only if useICEFRONT ;
145      - separated k-loop for rhoInSitu calculation ;
146      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
147        and at constant T,S (= WdRHOdP);
148      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
149        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
150        transport of locally-referenced potential density);
151        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
152    o gluemnc:
153      - replace ncrcat with ncks when adding variables to *.glob.nc
154      - change the way variables without record dimensions are handled so that
155        files that have variables with and without record variables can be glued:
156        add a record dimension with a new unique name to be able to differentiate
157        between variable with and without a-prior record dimensions. Remove
158        this record dimension before adding the variable to the *.glob.nc file.
159        This procedure automatically works also for grid.*.nc files that do not
160        have any record dimension.
161    o verification/cpl_aim+ocn:
162      - generate new reference output on baudelaire (gfortran, mpich2) (previously
163        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
164    o pkg/obcs/obcs_calc_stevens.F:
165      - add code for northern and southern boundaries.
166      - reorder some loops to save some operations and so that drFBar can be scalar
167    o model/src:
168      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
169        truncation) and add diagnostics for Adams-Bashforth tendency increment.
170      - update test-exp. AD output:
171        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
172      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
173        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
174        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
175        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
176        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
177        tutorial_plume_on_slope.
178    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
179      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
180      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
181      does not even come with an F77 compiler anymore, this should not be
182      a limitation
183    
184    checkpoint63e (2011/11/06)
185    o pkg/seaice adjoint of LSR:
186      - substantially rework STORE dirs.
187      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
188        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
189        and only perform SOLV_MAX_FIXED adjoint iters.
190        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
191        always goes to same record, meaning that the last forward field will be
192        the one used in the adjoint - an approximation.
193      - now produces non-zero LSR-related gradients, and acceptable gradients for
194        An's zonal (x-z) test case (to be checked in)
195      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
196        (but these are screwed up by the thermodynamics in the first place);
197        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
198        output_adm.txt also reflects changes to seaice_lsr
199      - global_ocean.cs32x15:
200        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
201          (output_adm.seaice.txt was updated)
202        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
203          (output_adm.seaice_dynmix.txt)
204    o test-exp. exp4+stevens:
205      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
206    o pkg/seaice (lsr solver):
207      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
208        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
209      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
210      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
211        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
212      - compute (with new S/R) and print initial (+ free-driff sol. if available)
213        and final residual of linearised system.
214    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
215      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
216    o pkg/obcs: Stevens BCs (still only for east and west)
217      - fix Stevens BCs by using intermediate velocities of previous
218        time step as "baroclinic" contribution rather velocity of one grid cell
219        inside the boundaries; more consistent but makes the entire treatment
220        more complicated, requires new pickup files and two new S/Rs:
221        obcs_copy_uv_n and obcs_save_uv_n
222        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
223        (undefined by default)
224      - silently move computation of some grid factors into separate loops to
225        save some recomputations
226      - add a hack for non-linear free surface
227      - add a verification experiment to exp4 that tests this code
228    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
229    
230    checkpoint63d (2011/10/25)
231    o pkg/obcs + seaice-dynamics:
232      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
233        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
234        values (consistent with an implicit method).
235      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
236        return to older implementation (same results as before); note that none of
237        the "experimental" OBCS_SEAICE options are implemented in the new version.
238      - switch test exp. seaice_obcs to use new version (update output).
239    o pkg/seaice:
240      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
241      - add parenthesis in Water-Ice drag calculations (evp & lsr);
242      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
243        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
244      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
245        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
246    o pkg/layers:
247      - Include potential density as new coordinate (Thanks to David Munday)
248    o pkg/dic:
249      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
250        carbonate computation/output to CALC_PCO2_APPROX
251    o pkg/generic_advdiff
252      - make TAF generate code that vectorizes:
253        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
254    o model/src:
255      - improve vectorization also for adjoint code of
256        solve_tridiagonal and solve_pentadiagonal. As this requires up to
257        5 new 3D-fields, this code is only turned on for the combination of
258        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
259        for singular matrix check (only for TARGET_NEC_SX).
260      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
261        ALLOW_AUTODIFF. This flag now needs to be set outside of
262        solve_tri/pentadiagonal.F
263    o pkg/exf:
264      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
265        optional namelist EXF_NML_OBCS).
266      - add many debug-print (to trace down where pkg/cal error msg comes from)
267    o pkg/mom_vecinv/mom_vi_hdissip.F
268      - rearrange loops so that vectorization is improved and in particular
269        the adjoint routine vectorizes. The code is a little longer now, but I
270        think easier to read.
271        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
272    o pkg/seaice:
273      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
274    o pkg/exch2:
275      - alternative code (without tile x tile matrix) for cumulated (global) sum;
276        used as default; keep using matrix version in adjustment.cs-32x32x1.
277    o tools/build_options:
278      - after merging some MPI and/or multi-threads specific optfiles so that
279        the modified default optfile support both built (using genmake2 -mpi
280        for the MPI built, using genmake2 -omp for OpenMP built),
281        move now obsolete optfiles to tools/build_options/unsupported/
282       (add copy of email sent to support list in doc/optfiles_changes.txt)
283    
284    checkpoint63c (2011/09/28)
285    o pkg/ebm:
286      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
287        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
288    o pkg/seaice (SItracer pickup)
289    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
290      To be done:
291      - thorough testing of missing fields in S/R seaice_read_pickup
292      - thorough matching between generic tracers and specific fields used
293        (e.g. volume-weighted age, area-weighted age, salinity, ...)
294    o pkg/grdchk:
295      - all procs calculate and print finite-difference gradient (for testreport)
296      - change description output used by testreport;
297      - AD testing: also compare and report Finite-difference gradient;
298        => update all output_adm*.txt
299    o test exp. global_ocean_ebm:
300      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
301        and turn on exactConserve; update (fwd) output.
302    o pkg/seaice (LSR):
303      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
304      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
305        * identical results with non-CS topology (but save up to half of EXCH calls)
306        * no much changes in cs-32 verification tests since no ice at face edges
307         (differences due to convergence criteria, since nb of iterations changed)
308        * expect some differences on lat-lon-cap grid.
309        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
310    o pkg/exch2:
311      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
312        many tiles); until alternative coding is added, just add a stop.
313    o pkg/kpp:
314      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
315        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
316    o optfiles:
317      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
318        into corresponding standard one, which now support different build:
319        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
320      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
321    o pkg/obcs (seaice):
322      - add missing EXCH for uIce,vIce after applying OBCS;
323      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
324        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
325        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
326      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
327      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
328        and eedata.mth for MPI and mutlti-threaded testing.
329    o pkg/flt:
330      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
331      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
332      - fix pickup and trajectories + profiles output with multi-threads;
333      - add parameter to select group of fields to write along trajectory and
334        profile (default unchanged);
335      - only call PORT_RAND* function when flt_noise <> 0;
336      - add multi-threaded test for verification exp. flt_example.
337    o eesupp/src:
338      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
339      - USE_OMP_THREADING: check that number of threads (from eedata) matches
340        actual number (from env.var. setting).
341    o pkg/ebm:
342      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
343      - add multi-threaded test for verification exp. global_ocean_ebm
344    
345    checkpoint63b (2011/08/29)
346    o pkg/ebm:
347      - fix sign of runoff;
348      - update directly forcing fields (Qnet,EmPmR) to use standard
349        external_forcing_surf.F (remove ebm_forcing_surf.F);
350      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
351      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
352        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
353      - update global_ocean_ebm parameters file data and update output (fwd+ad).
354    o verification/matrix_example:
355      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
356        MPI and mutlti-threaded testing.
357    o pkg/matrix:
358      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
359      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
360      - fix for multi-threaded (remove DATA statement);
361      - use standard DIFFERENT_MULTIPLE function;
362      - add MATRIX_OPTIONS.h
363    o verification/matrix_example:
364       To allow to split the domain in several tiles, change the domain size
365        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
366        Western side) of land points.
367    o (*_)write_pickup:
368      - fix few bugs in mypackage_read/write_pickup.F
369      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
370        array of length 1 (was caught by compiler syntax-check).
371    o pkg/diagnostics (velocity potential solver):
372      - fix initialisation of main diagonal matrix (for overlap values)
373    o tools/build_options:
374      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
375        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
376      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
377        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
378        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
379        and use "-devel" testreport option for standard testing on baudelaire.
380    o pkg/grdchk:
381      - Assume that all gradient-check position are within the same tile
382        corresponding to global indices (iGloTile,jGloTile) and that
383        positions (i,j indices or nbeg) are local to this tile;
384      - set tile local-indices and proc. number according to tile global-indices;
385      - remove grdchkwhichproc from namelist (retired param);
386      - send adjoint gradient to all procs so that all procs print it to STDOUT;
387      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
388    o adding package bbl (Bottom Boundary Layer)
389      description in MITgcm/pkg/bbl/bbl_description.tex
390      example/test experiment in MITgcm_contrib/bbl
391    o adjoint verifications
392      - changed 5 experiments to multi-tiles
393        * global_ocean.90x40x15
394        * obcs_ctrl
395        * offline_exf_seaice
396        * tutorial_dic_adjoffline
397        * tutorial_tracer_adjsens
398        changed reference output for those that crossed tile boundaries
399        (changed choices of gradient check positions)
400      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
401      - temporary bug fix in grdchk_loc.F for obcs
402    o genmake2 & testreport
403      - add target "obj" (just for OBJFILES files) to Makefile;
404      - add option to specify FEXTRAFLAGS on command line.
405    o pkg/mypackage:
406      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
407    
408    checkpoint63a (2011/08/02)
409    o pkg/diagnostics (velocity potential):
410      - fix velocity-potential calculation when using OBCS: balance net inflow
411        at each level (new S/R OBCS_DIAG_BALANCE).
412      - fix some of the problems with OBCS in stream-function calculation.
413    o pkg/exf/exf_readparms.F
414      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
415        EXF_NML_OBCS) more consistent, so that you need not have these lists
416        in data.exf when they are not used.
417    o optim/optim_readdata.F:
418      - add some output about obcs variables that might help debugging
419      - add a check about nvarlength
420    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
421    o pkg/diagnostics (velocity potential):
422      - fix mask for OBCS (still problems in stream-function with OBCS);
423      - add specific parameter (default = main code CG2D params) for solver;
424      - in case of poor convergence, use solution corresponding to lowest residual.
425    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
426      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
427      and should be avoided where possible.
428    o model/src (rStar):
429      - include r* effect on reference-state (PhiRef) in totPhiHyd
430        (so that it's really the potential anomaly at the cell center);
431        affect solution only if z* with full pressure in EOS.
432      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
433        update output (because of z* in totPhiHyd and viscA4 changes);
434      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
435        @ constant r) until interpolation at constant r is implemented.
436    o pkg/diagnostics
437      - fix RCENTER diagnostics in case cell center is not at interface middle
438    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
439      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
440      that THETA and SALT are "conservative temperature" and "absolute
441      salinity"
442    o pkg/ctrl
443      - fix computation of endrec in s/r ctrl_init_rec
444      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
445    o pkg/seaice/seaice_growth.F
446      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
447        remove then obsolete STORE directives
448      - fix STORE directives for tice and tices, so that only the
449        appropriate part of the fields are stored (and not the entire
450        field); update global_ocean.cs32x15.seaice AD output.
451      - cosmetic changes: adjust CPP flags and indentation for better
452        legibilty
453    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
454      Chris Wilson)
455    o pkg/gmredi:
456       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
457       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
458    
459    checkpoint63  (2011/07/11)
460    o pkg/exch2:
461     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
462     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
463       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
464       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
465    o pkg/diagnostics:
466     - deal with pairs of post-processed diags which are computed together; in
467       particular, re-order list of diags within 1 file to save 2nd computation.
468     - add S/R to compute velocity stream-function (called after velocity-potential
469       calculation) from divergence free transport -> new diagnostics "PsiVEL".
470     - add parameter to select grid-point location where PsiVEL == 0.
471    o eesupp/src:
472       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
473       (specific S/R needed with exch2 topology - for now, just print an error msg)
474    o pkg/shelfice
475     - Implement friction velocity-dependent transfer coefficients following
476       Holland and Jenkins, JPO, 1999
477       Original code by M. Losch with small modifs.
478       Enable with CPP option SHI_ALLOW_GAMMAFRICT
479       and runtime flag SHELFICEuseGammaFrict
480    o verification lab_sea & global_ocean.cs32x15:
481     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
482       does not miss some dependencies (but is slower) and also works with many files
483       (default makedepend limitation for AD built).
484     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
485    o pkg/diagnostics:
486     - add run-time parameter "useMissingValue" (def=False) to fill land-point
487        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
488       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
489     - Extend the use of "missing_value" setting from data.diagnostics for the case
490       of counter-diagnostics (where fraction-weight is zero). This applies both to
491       MNC and MDS output files.
492    o pkg/seaice/seaice_growth.F:
493      - add 'a priori' cap of latent heat flux based on actual mass considerations
494        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
495        non-legacy seaice_solve4temp.
496      - add diagnostic of the residual sublimation freshwater flux (the freshwater
497        flux taken from the ocean if the total actual latent heat fluxes exceed
498        the maximum)
499      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
500       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
501      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
502       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
503      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
504      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
505    o verification 1D_ocean_ice_column:
506       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
507       update results
508    o pkg/diagnostics:
509     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
510       which are not filled-up but computed from other diags ; In this case, the mate
511       diag points to the primary (filled-up) diag to used for post processing.
512     - Update Velocity-potential computation using post-processed diag framework.
513     ==> Change the ordering of fields and time-periods in MDS output file
514       when using periodic averaging: now writes one time record with the full set
515       of fields for this time period, then the next time reccord (it used to be
516       one field with the full set of time records then the next field).
517         Note: this is now similar to NetCDF (MNC) output file. <==
518    
519    checkpoint62z (2011/06/21)
520    o adjoint monitor:
521     - Add adjoint monitor output for packages exf, seaice
522       and update relevant testreport output
523    o pkg/seaice:
524     - re-order diags inits so that they appear in order in available_diagnostics.log
525     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
526       area/heff/hsnow preceeding thermodynamic growth/melt.
527     - modified diag: SIdA; output actual effect, as the description states.
528     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
529     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
530       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
531        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
532     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
533     - added diagnostics for seaice generic tracers (SItr*).
534     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
535     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
536     I. Fenty: 18-Jun-2011:
537     Minor changes to seaice package:
538     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
539        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
540       - Differentiated "regularization variables" from "floor variables"
541        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
542        * hiceMin became SEAICE_hice_reg (old hiceMin)
543          (with _reg meaning regularization variable)
544       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
545        so as to ensure energy conservation when going between phases
546      - A22 was not used anywhere
547     2) Changed regularization procedure for heffActual and hsnowActual to ensure
548        well-boundedness and smooth adjoint in seaice_growth.F
549     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
550        because the old regularization always set heffActual >= 0.05 cm
551     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
552        on AREA when HEFF > 0.
553      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
554        requiring that DISABLE_AREA_FLOOR *not* be defined
555     Affected verifications:
556      - 1D_ocean_ice_column (output.txt output_adm.txt)
557      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
558    o pkg/diagnostics:
559      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
560      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
561        (was _RL, now integer) with option = 0 to retrieve all levels.
562      - add pieces of code to compute velocity potential at each level (new diagnostics
563        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
564        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
565      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
566        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
567        and in diagnostics_fract_fill.F (do not need a valid pointer for the
568        diagnostics counter-mate); check that definition of counter-diagnostic
569        includes a valid counter-mate (in diagnostics_set_levels.F).
570    o model/src (rStar):
571      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
572        affect solution only if z* with full pressure in EOS;
573        update output of test-exp global_ocean.90x40x15.
574    o pkg/seaice:
575      - introduce siEps=1e-5 parameter
576      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
577      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
578      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
579        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
580        as well as ice cover age and ridging index (attached to AREA).
581        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
582        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
583        Up to SItrMaxNum=3 tracers can be used simultaneously.
584    o pkg/salt_plume:
585      -introduce SPsalFRAC run time parameter that sets the fraction of the
586       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
587       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
588    o model debug options:
589      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
590        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
591      - Refine debug-msg printing selection (3 new levels):
592        debugMode  : controls printing of debug messages (sequence of S/R calls).
593        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
594         debLevZero =  0 ; /* level of disabled aux. msg printing */
595         debLevA =  1 ; /* level of minimum  aux. msg printing */
596         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
597         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
598         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
599         debLevE =  5 ; /* level of extensive debug printing */
600        New debugLevel default: with default debugMode value (=F),
601          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
602          and if debugMode=T, default debugLevel = 4 (debLevD).
603        Relation with previous settings:
604         debLevB (=2) corresponds to former debLevA (=1)
605         debLevD (=4) corresponds to former debLevB (=2)
606        Note:
607         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
608         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
609            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
610      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
611        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
612    o pkg/obcs:
613      - change OBCSfixTopo default from True to False (should not change the results);
614        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
615    o pkg/thsice:
616      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
617        2nd layer seaice sublimation (unlikely to happen)
618      - use Interior mask for OBCS in thsice_advection.F (similar to what is
619        done in gad_advection & seaice_advection).
620    o adjoint:
621      bug fix spotted by Gael Forget:
622      seaice_advection and thsice_advection still had
623      legacy CPP options to avoid CS corner updates for adjoint
624    o pkg/seaice:
625      => Change some of the defaults (2011/05/29):
626         - change SEAICEuseFluxForm default (from False to True)
627         - change DIFF1 default (from 0.004 m/s to 0. m/s)
628         And print warnings if DIFF1 is not set in data.seaice and centered
629          avection scheme is used without any diffusion.
630      also:
631      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
632      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
633      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
634        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
635        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
636      update results of test exp.:
637         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
638             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
639             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
640         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
641         seaice_obcs: output (SEAICEuseFluxForm=T)
642      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
643          for standard fwd & AD lab_sea tests (to keep the same output).
644    o pkg/seaice/seaice_growth.F:
645      - use Ian Fenty's capping formulas for actual ice
646      thickness thoughout EVOLUTION branch.
647      - put treatment pathological case #2) in CPP brackets
648      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
649      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
650    o pkg/seaice:
651      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
652      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
653      also pass fac as a param, which can be 1. (to update the tendency
654      field) or the time step (to update the field itself).
655      - seaice_advdiff.F: for multidim, call seaice_diffusion with
656      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
657      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
658      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
659      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
660    o pkg/seaice:
661      diffusion with centered advection scheme (diffus.F & advect.F):
662      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
663        to just compute the laplacian of input-field.
664      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
665      - fix flux-form version in diffus.F to conserve tracer.
666      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
667       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
668    
669    checkpoint62y (2011/05/26)
670    o pkg/seaice:
671     - seaice_growth.F : in EVOLUTION branch, always include
672       a_QSWbyATM_cover in qnet (as it should be).
673     - verification/global_ocean.cs32x15 : update results accordingly
674       (output.seaice.txt output_adm.seaice.txt).
675    o pkg/seaice + obcs:
676     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
677       equivalent of assuming no tracer gradient outside the OB region.
678       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
679     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
680       after changes above);
681     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
682       only at OB location (instead of over a band of OLx width).
683    o pkg/seaice:
684     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
685       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
686    o pkg/obcs:
687      - split header file "OBCS.h" into 4 separated files:
688        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
689       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
690         (contain no conditional statement which depends on OBCS options).
691      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
692        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
693    o ctrl, cost, grdchk & autodiff pkgs:
694      - make options file more standard (like other {PKG}_OPTIONS.h file but
695        with AD_CONFIG.h); clean-up some of the included header files.
696    o pkg/obcs:
697      - do not mask tracer when applying OB (tracer == 0 could generate problems)
698      - apply tracer OB values to tracer field only at OB location (instead of
699        over a band of OLx width)
700      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
701      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
702        obcs_apply_tloc.F & obcs_apply_sloc.F
703    o obcs in model/src:
704      - call OBCS_APPLY_W only if NonHydrostatic.
705      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
706      - reset dEtaHdt and wVel to zero outside OB interior region ;
707      - leave tracer unchanged outside OB interior region: This has no effect
708        on the solution but just to prevent unrealistic tracer value outside OB.
709      - zero out velocity outside OB interior region: This has no effect on
710        the solution but just to prevent unrealistic velocity outside OB.
711    o obcs and non-lin free-surf:
712       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
713       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
714       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
715       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
716       update results of test-exp. exp4(nlfs).
717    o exp4 (nlfs) test-exp:
718       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
719       with NonLin-FreeSurf); update output.nlfs.txt
720    o obcs and 2d/3d solver norm:
721       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
722       and outside OB interior region (will allow to place OB further inside the
723       domain). Depending on the domain, can affects cg2d-Norm (previous
724       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
725       and cg3d-Norm (previous Norm was computed before canceling OB terms),
726       e.g. in tutorial_plume_on_slope.
727      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
728    o pkg rbcs:
729      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
730      - add capability to apply relaxation to horizontal velocity uVel & vVel.
731    o pkg/grdchk: add gradient check for control variable xx_shifwflx
732    o pkg/shelfice/shelfice_init_fixed.F
733      fix CPP-flag combinations
734    o pkg/seaice: Merge iceage code of Pierre Rampal
735      * update/change/correct ice age calculations
736      * add age updates for pathological cases
737      Probably needs more testing...
738    
739    checkpoint62x (2011/05/13)
740    o pkg/mom_vecinv:
741       high-order vorticity scheme: use interior masks (maskInW & S)
742       to zero-out (outside OB) gradient of vorticity.
743    o verification exp.:
744       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
745       hs94.128x64x5 and seaice_obcs ; update results.
746    o pkg/obcs:
747      fix bug in OBeta for YZ sections in obcs_exf_load.F
748    o pkg/ctrl, pkg/shelfice, and optim:
749      - add new control variable xx_shifwflx (fresh water flux underneath ice
750        shelves). This is almost as tedious as obcs-ctrl, because the
751        variables needs its own mask.
752      - add a cost function term that penalizes the deviation of xx_shifwflx
753        from the first guess (zero) in analogy to other control variables
754    o pkg/shelfice:
755      - start basic adjoint
756    o pkg/ctrl:
757      - remove extra 2D field "for good measure" when initializing in
758        ctrl_set_globfld_[xy/xz/yz].F
759      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
760      - improve error messages in ctrl_set_unpack_*
761    o OBC implementation in momentum:
762       use interior masks (maskInC,W & S) in momentum S/R:
763       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
764       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
765       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
766       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
767       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
768        (and also with Leith/Smagorinsky harmonic-viscosity).
769       Update output of experiment dome and exp4 (+nlfs).
770    o exp4 test-exp:
771      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
772        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
773        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
774        time-varying OB at Western-side for wVel (NonHyd); update output.
775      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
776        and biharmonic-viscosity ; also use prescribed time varying OB.
777    o pkg/obcs:
778      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
779    o model/src:
780      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
781      - initialise startTime & nIter0 with unlikely values: allows to set one
782        from the other without ambiguity.
783    o seaice_obcs test-exp.:
784      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
785    o pkg/obcs:
786      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
787        no longer needed with maskInC,W,S in pkg/generic_advdiff.
788    o pkg/seaice:
789      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
790        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
791      - fixed bug in the initialization of sea ice salinity variable HSALT
792        in seaice_init_varia.F  (removed dependence on ICE2WATR)
793    o fizhi-cs test exp.:
794       switch reference output convention for these 2 non-standard test-exp,
795        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
796          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
797       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
798    o model/inc:
799      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
800        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
801    o pkg/seaice:
802      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
803    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
804      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
805        and initial HSALT
806    
807    checkpoint62w (2011/04/26)
808    o pkg/mom_fluxform:
809      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
810      - use parameter "sideDragFactor" in no-slip BC side-drag part.
811      - update output of exp. global_ocean.90x40x15
812    o pkg/mom_vecinv:
813      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
814    o update seaice exp.:
815      use more consistent parameter values (remove "backward compatability only":
816       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
817      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
818       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
819    o update test-exp global_ocean.90x40x15:
820      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
821      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
822      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
823      o turn on zStar & viscA4 in standard set-up (dir input/)
824        and update output files: output.txt & output.dwnslp.txt
825    o new AD-test experiment: obcs_ctrl
826      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
827    o pkg/dic:
828      fix two bugs in handling water vapour pressure in carbonate chemistry
829      and air-sea fluxes. Found by Val Bennington and Galen McKinley
830      (add DIC Option = WATERVAP_BUG to recover old results)
831      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
832    o adding allowInteriorFreezing option to check for water below freezing point
833      at depth and bring the negative heat anomaly to the surface level
834    o pkgs _fields_load:
835      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
836      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
837        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
838        rbcs to get interpolation weights and time reccord number.
839      - fix multi-threading in aim_fields_load.F
840      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
841    o external_fields_load:
842      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
843       interpolation weights) to use in a periodic time-series ; do not divide by
844       time-step to convert to integer:
845       - this fixes case where externForcingPeriod is not multiple of time-step
846          (Thanks to Christopher L. Wolfe)
847       - this fixes case where externForcingPeriod is an odd multiple of time-step
848         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
849      store index of time-record which is currently loaded:
850       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
851       - needed for the adjoint but not yet used because of extensive recomputations;
852         (to be fixed soon)
853    
854    checkpoint62v (2011/04/02)
855    o verification/1D_ocean_ice_column added to test Ian Fenty's
856      pkg/seaice_growth.F modifications for improving sea ice code differentiability
857    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
858      (new velocity statistics after changing maskInW & maskInS definition)
859    o pkg/generic_advdiff with OBCS:
860      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
861      equivalent to assumption of no tracer gradient outside the OB region.
862      This will affect the results if using obcs+biharmonic diffusion.
863      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
864    o pkg/obcs:
865      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
866      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
867      in Interior region. No impact on solution but affects Velocity monitor stats.
868    o pkg/ptracers (adjoint)
869      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
870      tape file for each tracer
871    o model/inc/src and pkg/autodiff: add parameters that allow to turn
872      of parts of the adjoint code at run time. For now, there are only
873      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
874      parameters are set in data.pkg.
875      This is the lazy coward's version of doing this, but still useful for
876      debugging. In order to do it right, everything needs to be moved to
877      pkg/autodiff.
878    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
879      the end; this fixes the adjoint balancing code for open boundaries.
880    o pkg/ctrl:
881      - change behavior of xx_${varname}period to be analogous to exf-conventions:
882        xx_${varname}period =   0.,  means time-independent control part
883        xx_${varname}period = -12., means one-year-periodic monthly control part
884      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
885        clean up ctrl_init a little, remove unused variables
886      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
887      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
888    
889    checkpoint62u (2011/03/15)
890    o model/src:
891      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
892        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
893      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
894        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
895    o pkg/ctrl/obcs/ecco:
896      - remove obsolete, unused, and partially broken code:
897        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
898        ALLOW_CTRL_OBCS_BALANCE
899      - put a stop statement into ecco/cost_obcsvol.F, but also add
900        cost_obcsvol to ecco_ad_diff.list
901    o pkg/ecco: fix counting cost function contributions for obcs (code
902      by Matt M.) and diffkr for diagnostics
903    o pkg/ecco, pkg/ctrl, pkg/grdchk:
904      add cost penalty terms for initial uvel, vvel, eta controls
905      and I/O for prior error files
906    o pkg/mdsio:
907       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
908       (new argument) to check for tiled file in mdsioLocalDir : this fix the
909       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
910    o pkg/ctrl:
911     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
912       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
913       unused and superfluous variables
914     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
915    o pkg/ecco
916     - enable adjoint of Stevens OB
917    o pkg/ctrl/ecco/grdchk:
918      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
919        Fortunately, we do not have any tests for the numerous cpp-flagged
920        option of "obcs as control parameters" so we will never know
921        if this is an improvement (but at least now things compile).
922      - remove an obsolete initialization from ecco_cost_init_barfiles.F
923      - fix some problems within never used ifdefs to make the code compile
924    o pkg/obcs:
925     - Refine Interior mask definition to work with more complex OB (e.g.
926       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
927       read in Interior mask from file. Check if Interior mask is consistent
928       with OB list of indices.
929    o pkg/seaice
930     - beginning code for a seaice tracer package,
931       but currently only used for seaice age: SEAICE_AGE
932       SEAICE_num = 4
933       iTracer = 1: area-weighted ice age
934               = 2: volume-weighted ice age
935               = 3, 4: template for one-year vs. multi-year ice
936       data.seaice has new namelist SEAICE_PARM03 for arrays related to
937       SEAICE_num
938    
939    checkpoint62t (2011/03/05)
940    o pkg/obcs:
941     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
942       then normal component. This ensures that the normal component is set
943       correctly even when it conficts with tangential setting from an other OB.
944       Affects results of test-experiment seaice_obcs: update the output.txt
945    o pkg/obcs:
946     - add code to monitor statistics of dynamical fields at OB.
947     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
948       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
949       - change default: balance the Net inflow through all OB (instead of balancing
950         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
951     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
952       to match Nortern OB inflow (OBCS_balanceFacN=0).
953    o pkg/seaice:
954     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
955    o pkg/seaice (seaice_growth v 1.113):
956     - reverting seaice_growth to v 1.111 in order to have code with exact bit
957       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
958       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
959       runtime flag SEAICEareaFormula is kept but is inactive
960    o model/src:
961     - add new param to scale curvilinear grid distance and area when using
962       a different sphere radius from the grid-files.
963     - test/check multi-threads EXCH applied to local variable (cg2d_x)
964    o adjoint:
965     - enable adjoint of Stevens OB
966     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
967       (a bit delicate because of potentially modified adj. common block structure;
968       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
969    
970    checkpoint62s (2011/02/15)
971    o pkg/seaice (seaice_growth v 1.112):
972     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
973       computing the ice cover tendency from effective thickness tendencies. Include
974       Ian Fenty's formula.
975     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
976       SEAICEareaFormula.
977     - simplify notations for the various d_HEFF/d_AREA terms.
978    o pkg/gmredi:
979     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
980       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
981       add a verification test-run (front_relax.bvp) to test GM_useBVP.
982    o pkg/seaice (seaice_growth v 1.111):
983     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
984     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
985       also melt ice.
986    o pkg/seaice:
987     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
988     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
989    o pkg/cheapaml:
990     - from Nico Wienders: New version of this package.
991    o pkg/flt:
992     - add CPP options to prevent floats to re-enter the opposite side of
993       a periodic domain (default: keep periodicity)
994    o pkg/gmredi:
995     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
996       (needed for multi-dim advection).
997     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
998    o model/src:
999     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
1000    o tutorial_tracer_adjsens
1001     - extend to NLFS and replace maskC by hFacC
1002       (change reference output accordingly)
1003    
1004    checkpoint62r (2011/01/24)
1005    o testreport:
1006     - add option -deloutp (-do) to remove output file after successful run
1007     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
1008       extract exact list of procs from this file ; adjust COMMAND by
1009       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
1010    o pkg/ecco: replace old ineffective way of penalizing deviations from
1011      first guess (of obcs) with code by Matt Mazloff
1012    o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
1013      exf/cal
1014      - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
1015        and handle case of obcs?period == 0
1016        Not affected by these changes: There is still an inconsistency in
1017        the computation of start/endrec for the obcs variables for ALLOW_CAL
1018        defined (see comment by Menemenlis, 7-Mar-2003)
1019      - make S/R ctrl_get_gen_rec return something meaningful even if
1020        ALLOW_CAL is not defined
1021      - ctrl_getobcs?: simplify code so that it does not need to use
1022                       S/R exf_swapfields
1023    o testreport:
1024       allow to test MPI with different number of processors for each experiment:
1025       create file "SIZE.h.mpi" in each build dir.
1026       Note: update of "-command" argument not yet implemented.
1027    o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
1028      alleviate the need for additional 3D tapes when using
1029      the non-inear free surface in the adjoint. This is done
1030      by adding an 'update' of hfacc etc. to their current
1031      value at the beginning of forward_step.F.
1032    o pkg/seaice
1033      seaice_lsr: move stress-divergence computations out of outer pseudo-
1034      timestepping loop
1035    o pkg/obcs/obcs_prescribe_read.F: move 'CALL OBCS_EXTERNAL_FIELDS_LOAD'
1036      up, so that the calls of the ctrl_* subroutines are really at the end
1037      of the routine.
1038    o pkg/gmredi:
1039      allow to specify a 2-D horizontal map and a 1-D vertical profil
1040      as scaling factor for Isopycnal diffusivity (Redi) and GM diffusivity.
1041    o pkg/seaice:
1042      move lsr iterations from seaice_dynsolver to seaice_lsr.
1043    o pkg/seaice:
1044      reduce memory footprint of seaice mutldim advection tapes,
1045      by using a 2D tape independent of the generic_advdiff ones,
1046      and setting GAD_AREA=1 etc. rather than GAD_AREA=101 etc.
1047    
1048    checkpoint62q (2010/12/29)
1049    o model/src:
1050      - check horizontal grid-spacing for unset or zero/negative values.
1051      - change AD test hs94.1x64x5 to be truly a 2-D set-up.
1052    o pkg/flt:
1053      - use (recent) mdsio S/R MDS_READVEC_LOC instead of local FLT_MDSREADVECTOR
1054      - precision of input and output files set according to readBinaryPrec
1055        and writeBinaryPrec (previously always 64.b), pickup remains at 64 bits.
1056      - initial float position from tiled file was not converted to index space
1057        (looks like a bug): fixed to make it similar to initial pos. global file.
1058    o global_ocean.cs32x15:
1059       change SIZE.h of AD set-up to get same tiling as with MPI.
1060       Update output_adm, output_adm.thsice (pass@14) & output_adm.seaice (fail@11)
1061    o model/src:
1062       add flag to control printing of domain fields (bathymetry, hFac ...) in
1063       ini_mask_etc (call to plot_fieds_xy*).
1064    o pkg/thsice:
1065       if useEXF, some forcing fields are not valid in overlap: fixed by computing
1066       over the interior only + apply EXCH at the end (like with SEAICE advection).
1067    o pkg/mdsio:
1068      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
1069        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
1070      - change barrier call for safe multi-threads access to 3-D shared buffer.
1071      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
1072      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
1073        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
1074    o pkg/flt:
1075      - add fourth-order Runge-Kutta integration
1076      - add basic exch2 support (only 1 facet supported so far!)
1077    o pkg/mdsio+rw:
1078      new S/R to read local (or tile independent) vector (read counterpart of
1079       mds_writevec_loc, and front-end write_glvec_rl/rs).
1080    o global_ocean.cs32x15: additional input_ad.seaice experiment
1081        that uses pkg/seaice rather than pkg/thsice.
1082        (using multidim advection for seaice)
1083    o towards more F95 syntax for array specification in namelist:
1084      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
1085        of all verification experiments.
1086           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
1087          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
1088      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
1089    o global_ocean.cs32x15: additional input.seaice experiment
1090        that uses pkg/seaice rather than pkg/thsice.
1091    
1092    checkpoint62p (2010/12/17)
1093    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
1094        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
1095    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
1096        allow for use of multim. advection in seaice adjoint.
1097    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
1098      - first attempt to close budgets by taking into account the freshwater
1099        flux implied by the sublimation of snow and ice. So far only the
1100        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
1101        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
1102    o eesupp/src:
1103      new S/R with new option (NML_EXTENDED_F77) to change array specification
1104      from F95 standard to commonly accepted extended F77 form.
1105      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
1106      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
1107      for less tolerant f77 compiler (e.g., pgf77, g77).
1108  o globalFiles:  o globalFiles:
1109    commented out in parameter file "data" since it's not safe with MPI    commented out in parameter file "data" since it's not safe with MPI
1110    (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much    (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
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