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revision 1.1367 by mlosch, Wed Jan 19 13:52:14 2011 UTC revision 1.1545 by jmc, Thu Dec 8 03:49:58 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 model/src:
8     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.    
9       to their current value at the beginning of forward_step.F": add a new run-time
10       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
11     - set doResetHFactors=T in the following test exp:
12        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
13        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
14        and tutorial_global_oce_in_p (nonLinFS in p)
15    o pkg/ecco
16      - added IES cost term
17    o verification/advect_xz
18      - scale down the depth by 1/100 (from 200 km to just 2.km)
19      - add secondary test using divergent flow, r-star and implicit vertical advection.
20      - add note (check_conserve_TS.txt) and matlab script to check global
21        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
22    o pkg/rbcs:
23      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
24    o pkg/obcs (Stevens BCs):
25      - fix various problems in the phase speed computations of the Stevens
26        boundary conditions:
27        - sign error for western and southern boundaries,
28        - time tendencies were underestimated by factor of dTracerLev and some just
29          zero (for multidim advection schemes) -> now estimate time tendencies
30          from difference between previous (n) time level and the one before (n-1);
31          this requires storing a field per tracer per boundary, also in the pickup
32          files.
33        - replace deltaTmom in cflMer/Zon computation with dTracerLev
34        - set default phase velocity to cflMer/Zon
35      - update verification experiment exp4.stevens
36    o pkg/generic_advdiff (implicit_r):
37      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
38        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
39      - fix implicit vertical diffusion or advection with NonLin FreeSurf
40        (was using current recip_hFacC instead of future recip_hFacC): set future
41        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
42        solver S/R ;
43      - fill diagnostics of vertical advective fluxes (computed from tendency)
44        when using implicit vert. advection;
45      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
46         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
47         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
48         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
49    o pkg/diagnostics:
50      - add diags for T & S tendency which goes through Adams-Bashforth.
51    
52    checkpoint63f (2011/11/30)
53    o pkg/obcs/obcs_calc_stevens.F:
54      - join some loops to reduce number of if-statements
55      - fix a bug in code for northern and southern boundaries.
56    o pkg/seaice/seaice_init_varia.F
57      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
58        caused zero ice-velocities for the B-grid code
59    o pkg/seaice/seaice_init_fixed.F
60      - fix a bug in the initialisation of the second metric terms
61        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
62      - this affects all seaice configurations with useCurviLinearGrid = .true.
63        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
64        = .true. (default)
65      - the only verification experiment affected is global_ocean.cs32x15:
66        icedyn, seaice, and seaice_dynmix (AD)
67    o pkg/thsice/thsice_diagnostics_state.F
68      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
69        not contain garbage that can lead to surprises in diagstats_calc.F
70    o model/src:
71      - move bi,bj loops inside INTEGR_CONTINUITY ;
72      - call INTEGR_CONTINUITY directly from forward_step.F
73        (previously called from momentum_correction_step.F)
74      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
75        forward_step.F and pkg/ecco/the_main_loop.F
76    o model/src/do_oceanic_phys.F:
77      - reset addMass to zero only if useICEFRONT ;
78      - separated k-loop for rhoInSitu calculation ;
79      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
80        and at constant T,S (= WdRHOdP);
81      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
82        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
83        transport of locally-referenced potential density);
84        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
85    o gluemnc:
86      - replace ncrcat with ncks when adding variables to *.glob.nc
87      - change the way variables without record dimensions are handled so that
88        files that have variables with and without record variables can be glued:
89        add a record dimension with a new unique name to be able to differentiate
90        between variable with and without a-prior record dimensions. Remove
91        this record dimension before adding the variable to the *.glob.nc file.
92        This procedure automatically works also for grid.*.nc files that do not
93        have any record dimension.
94    o verification/cpl_aim+ocn:
95      - generate new reference output on baudelaire (gfortran, mpich2) (previously
96        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
97    o pkg/obcs/obcs_calc_stevens.F:
98      - add code for northern and southern boundaries.
99      - reorder some loops to save some operations and so that drFBar can be scalar
100    o model/src:
101      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
102        truncation) and add diagnostics for Adams-Bashforth tendency increment.
103      - update test-exp. AD output:
104        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
105      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
106        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
107        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
108        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
109        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
110        tutorial_plume_on_slope.
111    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
112      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
113      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
114      does not even come with an F77 compiler anymore, this should not be
115      a limitation
116    
117    checkpoint63e (2011/11/06)
118    o pkg/seaice adjoint of LSR:
119      - substantially rework STORE dirs.
120      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
121        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
122        and only perform SOLV_MAX_FIXED adjoint iters.
123        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
124        always goes to same record, meaning that the last forward field will be
125        the one used in the adjoint - an approximation.
126      - now produces non-zero LSR-related gradients, and acceptable gradients for
127        An's zonal (x-z) test case (to be checked in)
128      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
129        (but these are screwed up by the thermodynamics in the first place);
130        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
131        output_adm.txt also reflects changes to seaice_lsr
132      - global_ocean.cs32x15:
133        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
134          (output_adm.seaice.txt was updated)
135        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
136          (output_adm.seaice_dynmix.txt)
137    o test-exp. exp4+stevens:
138      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
139    o pkg/seaice (lsr solver):
140      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
141        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
142      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
143      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
144        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
145      - compute (with new S/R) and print initial (+ free-driff sol. if available)
146        and final residual of linearised system.
147    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
148      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
149    o pkg/obcs: Stevens BCs (still only for east and west)
150      - fix Stevens BCs by using intermediate velocities of previous
151        time step as "baroclinic" contribution rather velocity of one grid cell
152        inside the boundaries; more consistent but makes the entire treatment
153        more complicated, requires new pickup files and two new S/Rs:
154        obcs_copy_uv_n and obcs_save_uv_n
155        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
156        (undefined by default)
157      - silently move computation of some grid factors into separate loops to
158        save some recomputations
159      - add a hack for non-linear free surface
160      - add a verification experiment to exp4 that tests this code
161    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
162    
163    checkpoint63d (2011/10/25)
164    o pkg/obcs + seaice-dynamics:
165      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
166        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
167        values (consistent with an implicit method).
168      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
169        return to older implementation (same results as before); note that none of
170        the "experimental" OBCS_SEAICE options are implemented in the new version.
171      - switch test exp. seaice_obcs to use new version (update output).
172    o pkg/seaice:
173      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
174      - add parenthesis in Water-Ice drag calculations (evp & lsr);
175      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
176        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
177      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
178        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
179    o pkg/layers:
180      - Include potential density as new coordinate (Thanks to David Munday)
181    o pkg/dic:
182      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
183        carbonate computation/output to CALC_PCO2_APPROX
184    o pkg/generic_advdiff
185      - make TAF generate code that vectorizes:
186        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
187    o model/src:
188      - improve vectorization also for adjoint code of
189        solve_tridiagonal and solve_pentadiagonal. As this requires up to
190        5 new 3D-fields, this code is only turned on for the combination of
191        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
192        for singular matrix check (only for TARGET_NEC_SX).
193      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
194        ALLOW_AUTODIFF. This flag now needs to be set outside of
195        solve_tri/pentadiagonal.F
196    o pkg/exf:
197      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
198        optional namelist EXF_NML_OBCS).
199      - add many debug-print (to trace down where pkg/cal error msg comes from)
200    o pkg/mom_vecinv/mom_vi_hdissip.F
201      - rearrange loops so that vectorization is improved and in particular
202        the adjoint routine vectorizes. The code is a little longer now, but I
203        think easier to read.
204        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
205    o pkg/seaice:
206      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
207    o pkg/exch2:
208      - alternative code (without tile x tile matrix) for cumulated (global) sum;
209        used as default; keep using matrix version in adjustment.cs-32x32x1.
210    o tools/build_options:
211      - after merging some MPI and/or multi-threads specific optfiles so that
212        the modified default optfile support both built (using genmake2 -mpi
213        for the MPI built, using genmake2 -omp for OpenMP built),
214        move now obsolete optfiles to tools/build_options/unsupported/
215       (add copy of email sent to support list in doc/optfiles_changes.txt)
216    
217    checkpoint63c (2011/09/28)
218    o pkg/ebm:
219      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
220        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
221    o pkg/seaice (SItracer pickup)
222    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
223      To be done:
224      - thorough testing of missing fields in S/R seaice_read_pickup
225      - thorough matching between generic tracers and specific fields used
226        (e.g. volume-weighted age, area-weighted age, salinity, ...)
227    o pkg/grdchk:
228      - all procs calculate and print finite-difference gradient (for testreport)
229      - change description output used by testreport;
230      - AD testing: also compare and report Finite-difference gradient;
231        => update all output_adm*.txt
232    o test exp. global_ocean_ebm:
233      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
234        and turn on exactConserve; update (fwd) output.
235    o pkg/seaice (LSR):
236      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
237      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
238        * identical results with non-CS topology (but save up to half of EXCH calls)
239        * no much changes in cs-32 verification tests since no ice at face edges
240         (differences due to convergence criteria, since nb of iterations changed)
241        * expect some differences on lat-lon-cap grid.
242        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
243    o pkg/exch2:
244      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
245        many tiles); until alternative coding is added, just add a stop.
246    o pkg/kpp:
247      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
248        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
249    o optfiles:
250      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
251        into corresponding standard one, which now support different build:
252        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
253      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
254    o pkg/obcs (seaice):
255      - add missing EXCH for uIce,vIce after applying OBCS;
256      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
257        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
258        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
259      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
260      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
261        and eedata.mth for MPI and mutlti-threaded testing.
262    o pkg/flt:
263      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
264      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
265      - fix pickup and trajectories + profiles output with multi-threads;
266      - add parameter to select group of fields to write along trajectory and
267        profile (default unchanged);
268      - only call PORT_RAND* function when flt_noise <> 0;
269      - add multi-threaded test for verification exp. flt_example.
270    o eesupp/src:
271      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
272      - USE_OMP_THREADING: check that number of threads (from eedata) matches
273        actual number (from env.var. setting).
274    o pkg/ebm:
275      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
276      - add multi-threaded test for verification exp. global_ocean_ebm
277    
278    checkpoint63b (2011/08/29)
279    o pkg/ebm:
280      - fix sign of runoff;
281      - update directly forcing fields (Qnet,EmPmR) to use standard
282        external_forcing_surf.F (remove ebm_forcing_surf.F);
283      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
284      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
285        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
286      - update global_ocean_ebm parameters file data and update output (fwd+ad).
287    o verification/matrix_example:
288      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
289        MPI and mutlti-threaded testing.
290    o pkg/matrix:
291      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
292      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
293      - fix for multi-threaded (remove DATA statement);
294      - use standard DIFFERENT_MULTIPLE function;
295      - add MATRIX_OPTIONS.h
296    o verification/matrix_example:
297       To allow to split the domain in several tiles, change the domain size
298        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
299        Western side) of land points.
300    o (*_)write_pickup:
301      - fix few bugs in mypackage_read/write_pickup.F
302      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
303        array of length 1 (was caught by compiler syntax-check).
304    o pkg/diagnostics (velocity potential solver):
305      - fix initialisation of main diagonal matrix (for overlap values)
306    o tools/build_options:
307      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
308        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
309      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
310        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
311        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
312        and use "-devel" testreport option for standard testing on baudelaire.
313    o pkg/grdchk:
314      - Assume that all gradient-check position are within the same tile
315        corresponding to global indices (iGloTile,jGloTile) and that
316        positions (i,j indices or nbeg) are local to this tile;
317      - set tile local-indices and proc. number according to tile global-indices;
318      - remove grdchkwhichproc from namelist (retired param);
319      - send adjoint gradient to all procs so that all procs print it to STDOUT;
320      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
321    o adding package bbl (Bottom Boundary Layer)
322      description in MITgcm/pkg/bbl/bbl_description.tex
323      example/test experiment in MITgcm_contrib/bbl
324    o adjoint verifications
325      - changed 5 experiments to multi-tiles
326        * global_ocean.90x40x15
327        * obcs_ctrl
328        * offline_exf_seaice
329        * tutorial_dic_adjoffline
330        * tutorial_tracer_adjsens
331        changed reference output for those that crossed tile boundaries
332        (changed choices of gradient check positions)
333      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
334      - temporary bug fix in grdchk_loc.F for obcs
335    o genmake2 & testreport
336      - add target "obj" (just for OBJFILES files) to Makefile;
337      - add option to specify FEXTRAFLAGS on command line.
338    o pkg/mypackage:
339      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
340    
341    checkpoint63a (2011/08/02)
342    o pkg/diagnostics (velocity potential):
343      - fix velocity-potential calculation when using OBCS: balance net inflow
344        at each level (new S/R OBCS_DIAG_BALANCE).
345      - fix some of the problems with OBCS in stream-function calculation.
346    o pkg/exf/exf_readparms.F
347      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
348        EXF_NML_OBCS) more consistent, so that you need not have these lists
349        in data.exf when they are not used.
350    o optim/optim_readdata.F:
351      - add some output about obcs variables that might help debugging
352      - add a check about nvarlength
353    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
354    o pkg/diagnostics (velocity potential):
355      - fix mask for OBCS (still problems in stream-function with OBCS);
356      - add specific parameter (default = main code CG2D params) for solver;
357      - in case of poor convergence, use solution corresponding to lowest residual.
358    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
359      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
360      and should be avoided where possible.
361    o model/src (rStar):
362      - include r* effect on reference-state (PhiRef) in totPhiHyd
363        (so that it's really the potential anomaly at the cell center);
364        affect solution only if z* with full pressure in EOS.
365      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
366        update output (because of z* in totPhiHyd and viscA4 changes);
367      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
368        @ constant r) until interpolation at constant r is implemented.
369    o pkg/diagnostics
370      - fix RCENTER diagnostics in case cell center is not at interface middle
371    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
372      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
373      that THETA and SALT are "conservative temperature" and "absolute
374      salinity"
375    o pkg/ctrl
376      - fix computation of endrec in s/r ctrl_init_rec
377      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
378    o pkg/seaice/seaice_growth.F
379      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
380        remove then obsolete STORE directives
381      - fix STORE directives for tice and tices, so that only the
382        appropriate part of the fields are stored (and not the entire
383        field); update global_ocean.cs32x15.seaice AD output.
384      - cosmetic changes: adjust CPP flags and indentation for better
385        legibilty
386    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
387      Chris Wilson)
388    o pkg/gmredi:
389       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
390       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
391    
392    checkpoint63  (2011/07/11)
393    o pkg/exch2:
394     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
395     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
396       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
397       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
398    o pkg/diagnostics:
399     - deal with pairs of post-processed diags which are computed together; in
400       particular, re-order list of diags within 1 file to save 2nd computation.
401     - add S/R to compute velocity stream-function (called after velocity-potential
402       calculation) from divergence free transport -> new diagnostics "PsiVEL".
403     - add parameter to select grid-point location where PsiVEL == 0.
404    o eesupp/src:
405       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
406       (specific S/R needed with exch2 topology - for now, just print an error msg)
407    o pkg/shelfice
408     - Implement friction velocity-dependent transfer coefficients following
409       Holland and Jenkins, JPO, 1999
410       Original code by M. Losch with small modifs.
411       Enable with CPP option SHI_ALLOW_GAMMAFRICT
412       and runtime flag SHELFICEuseGammaFrict
413    o verification lab_sea & global_ocean.cs32x15:
414     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
415       does not miss some dependencies (but is slower) and also works with many files
416       (default makedepend limitation for AD built).
417     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
418    o pkg/diagnostics:
419     - add run-time parameter "useMissingValue" (def=False) to fill land-point
420        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
421       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
422     - Extend the use of "missing_value" setting from data.diagnostics for the case
423       of counter-diagnostics (where fraction-weight is zero). This applies both to
424       MNC and MDS output files.
425    o pkg/seaice/seaice_growth.F:
426      - add 'a priori' cap of latent heat flux based on actual mass considerations
427        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
428        non-legacy seaice_solve4temp.
429      - add diagnostic of the residual sublimation freshwater flux (the freshwater
430        flux taken from the ocean if the total actual latent heat fluxes exceed
431        the maximum)
432      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
433       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
434      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
435       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
436      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
437      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
438    o verification 1D_ocean_ice_column:
439       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
440       update results
441    o pkg/diagnostics:
442     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
443       which are not filled-up but computed from other diags ; In this case, the mate
444       diag points to the primary (filled-up) diag to used for post processing.
445     - Update Velocity-potential computation using post-processed diag framework.
446     ==> Change the ordering of fields and time-periods in MDS output file
447       when using periodic averaging: now writes one time record with the full set
448       of fields for this time period, then the next time reccord (it used to be
449       one field with the full set of time records then the next field).
450         Note: this is now similar to NetCDF (MNC) output file. <==
451    
452    checkpoint62z (2011/06/21)
453    o adjoint monitor:
454     - Add adjoint monitor output for packages exf, seaice
455       and update relevant testreport output
456    o pkg/seaice:
457     - re-order diags inits so that they appear in order in available_diagnostics.log
458     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
459       area/heff/hsnow preceeding thermodynamic growth/melt.
460     - modified diag: SIdA; output actual effect, as the description states.
461     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
462     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
463       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
464        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
465     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
466     - added diagnostics for seaice generic tracers (SItr*).
467     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
468     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
469     I. Fenty: 18-Jun-2011:
470     Minor changes to seaice package:
471     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
472        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
473       - Differentiated "regularization variables" from "floor variables"
474        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
475        * hiceMin became SEAICE_hice_reg (old hiceMin)
476          (with _reg meaning regularization variable)
477       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
478        so as to ensure energy conservation when going between phases
479      - A22 was not used anywhere
480     2) Changed regularization procedure for heffActual and hsnowActual to ensure
481        well-boundedness and smooth adjoint in seaice_growth.F
482     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
483        because the old regularization always set heffActual >= 0.05 cm
484     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
485        on AREA when HEFF > 0.
486      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
487        requiring that DISABLE_AREA_FLOOR *not* be defined
488     Affected verifications:
489      - 1D_ocean_ice_column (output.txt output_adm.txt)
490      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
491    o pkg/diagnostics:
492      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
493      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
494        (was _RL, now integer) with option = 0 to retrieve all levels.
495      - add pieces of code to compute velocity potential at each level (new diagnostics
496        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
497        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
498      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
499        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
500        and in diagnostics_fract_fill.F (do not need a valid pointer for the
501        diagnostics counter-mate); check that definition of counter-diagnostic
502        includes a valid counter-mate (in diagnostics_set_levels.F).
503    o model/src (rStar):
504      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
505        affect solution only if z* with full pressure in EOS;
506        update output of test-exp global_ocean.90x40x15.
507    o pkg/seaice:
508      - introduce siEps=1e-5 parameter
509      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
510      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
511      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
512        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
513        as well as ice cover age and ridging index (attached to AREA).
514        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
515        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
516        Up to SItrMaxNum=3 tracers can be used simultaneously.
517    o pkg/salt_plume:
518      -introduce SPsalFRAC run time parameter that sets the fraction of the
519       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
520       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
521    o model debug options:
522      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
523        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
524      - Refine debug-msg printing selection (3 new levels):
525        debugMode  : controls printing of debug messages (sequence of S/R calls).
526        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
527         debLevZero =  0 ; /* level of disabled aux. msg printing */
528         debLevA =  1 ; /* level of minimum  aux. msg printing */
529         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
530         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
531         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
532         debLevE =  5 ; /* level of extensive debug printing */
533        New debugLevel default: with default debugMode value (=F),
534          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
535          and if debugMode=T, default debugLevel = 4 (debLevD).
536        Relation with previous settings:
537         debLevB (=2) corresponds to former debLevA (=1)
538         debLevD (=4) corresponds to former debLevB (=2)
539        Note:
540         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
541         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
542            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
543      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
544        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
545    o pkg/obcs:
546      - change OBCSfixTopo default from True to False (should not change the results);
547        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
548    o pkg/thsice:
549      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
550        2nd layer seaice sublimation (unlikely to happen)
551      - use Interior mask for OBCS in thsice_advection.F (similar to what is
552        done in gad_advection & seaice_advection).
553    o adjoint:
554      bug fix spotted by Gael Forget:
555      seaice_advection and thsice_advection still had
556      legacy CPP options to avoid CS corner updates for adjoint
557    o pkg/seaice:
558      => Change some of the defaults (2011/05/29):
559         - change SEAICEuseFluxForm default (from False to True)
560         - change DIFF1 default (from 0.004 m/s to 0. m/s)
561         And print warnings if DIFF1 is not set in data.seaice and centered
562          avection scheme is used without any diffusion.
563      also:
564      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
565      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
566      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
567        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
568        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
569      update results of test exp.:
570         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
571             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
572             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
573         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
574         seaice_obcs: output (SEAICEuseFluxForm=T)
575      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
576          for standard fwd & AD lab_sea tests (to keep the same output).
577    o pkg/seaice/seaice_growth.F:
578      - use Ian Fenty's capping formulas for actual ice
579      thickness thoughout EVOLUTION branch.
580      - put treatment pathological case #2) in CPP brackets
581      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
582      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
583    o pkg/seaice:
584      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
585      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
586      also pass fac as a param, which can be 1. (to update the tendency
587      field) or the time step (to update the field itself).
588      - seaice_advdiff.F: for multidim, call seaice_diffusion with
589      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
590      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
591      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
592      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
593    o pkg/seaice:
594      diffusion with centered advection scheme (diffus.F & advect.F):
595      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
596        to just compute the laplacian of input-field.
597      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
598      - fix flux-form version in diffus.F to conserve tracer.
599      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
600       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
601    
602    checkpoint62y (2011/05/26)
603    o pkg/seaice:
604     - seaice_growth.F : in EVOLUTION branch, always include
605       a_QSWbyATM_cover in qnet (as it should be).
606     - verification/global_ocean.cs32x15 : update results accordingly
607       (output.seaice.txt output_adm.seaice.txt).
608    o pkg/seaice + obcs:
609     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
610       equivalent of assuming no tracer gradient outside the OB region.
611       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
612     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
613       after changes above);
614     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
615       only at OB location (instead of over a band of OLx width).
616    o pkg/seaice:
617     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
618       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
619    o pkg/obcs:
620      - split header file "OBCS.h" into 4 separated files:
621        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
622       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
623         (contain no conditional statement which depends on OBCS options).
624      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
625        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
626    o ctrl, cost, grdchk & autodiff pkgs:
627      - make options file more standard (like other {PKG}_OPTIONS.h file but
628        with AD_CONFIG.h); clean-up some of the included header files.
629    o pkg/obcs:
630      - do not mask tracer when applying OB (tracer == 0 could generate problems)
631      - apply tracer OB values to tracer field only at OB location (instead of
632        over a band of OLx width)
633      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
634      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
635        obcs_apply_tloc.F & obcs_apply_sloc.F
636    o obcs in model/src:
637      - call OBCS_APPLY_W only if NonHydrostatic.
638      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
639      - reset dEtaHdt and wVel to zero outside OB interior region ;
640      - leave tracer unchanged outside OB interior region: This has no effect
641        on the solution but just to prevent unrealistic tracer value outside OB.
642      - zero out velocity outside OB interior region: This has no effect on
643        the solution but just to prevent unrealistic velocity outside OB.
644    o obcs and non-lin free-surf:
645       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
646       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
647       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
648       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
649       update results of test-exp. exp4(nlfs).
650    o exp4 (nlfs) test-exp:
651       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
652       with NonLin-FreeSurf); update output.nlfs.txt
653    o obcs and 2d/3d solver norm:
654       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
655       and outside OB interior region (will allow to place OB further inside the
656       domain). Depending on the domain, can affects cg2d-Norm (previous
657       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
658       and cg3d-Norm (previous Norm was computed before canceling OB terms),
659       e.g. in tutorial_plume_on_slope.
660      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
661    o pkg rbcs:
662      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
663      - add capability to apply relaxation to horizontal velocity uVel & vVel.
664    o pkg/grdchk: add gradient check for control variable xx_shifwflx
665    o pkg/shelfice/shelfice_init_fixed.F
666      fix CPP-flag combinations
667    o pkg/seaice: Merge iceage code of Pierre Rampal
668      * update/change/correct ice age calculations
669      * add age updates for pathological cases
670      Probably needs more testing...
671    
672    checkpoint62x (2011/05/13)
673    o pkg/mom_vecinv:
674       high-order vorticity scheme: use interior masks (maskInW & S)
675       to zero-out (outside OB) gradient of vorticity.
676    o verification exp.:
677       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
678       hs94.128x64x5 and seaice_obcs ; update results.
679    o pkg/obcs:
680      fix bug in OBeta for YZ sections in obcs_exf_load.F
681    o pkg/ctrl, pkg/shelfice, and optim:
682      - add new control variable xx_shifwflx (fresh water flux underneath ice
683        shelves). This is almost as tedious as obcs-ctrl, because the
684        variables needs its own mask.
685      - add a cost function term that penalizes the deviation of xx_shifwflx
686        from the first guess (zero) in analogy to other control variables
687    o pkg/shelfice:
688      - start basic adjoint
689    o pkg/ctrl:
690      - remove extra 2D field "for good measure" when initializing in
691        ctrl_set_globfld_[xy/xz/yz].F
692      - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
693      - improve error messages in ctrl_set_unpack_*
694    o OBC implementation in momentum:
695       use interior masks (maskInC,W & S) in momentum S/R:
696       - multiply divergence, tension and some del^i.u or del^j.v by maskInC
697       - multiply del2u,del2v by maskInW/S (biharmonic viscosity)
698       - multiply horiz. grad of vorticity by maskInW/S (in Leith scheme)
699       - multiply gradient of wVel by maskInW/S in del2w calculation (NonHyd)
700       Motivation: fix/clean implementation of OBC with biharmonic-viscosity
701        (and also with Leith/Smagorinsky harmonic-viscosity).
702       Update output of experiment dome and exp4 (+nlfs).
703    o exp4 test-exp:
704      - turn on: nonHydrostatic, exactConserv, viscA4 (with momDissip_In_AB=F)
705        and prescribe time-varying OB (without pkg/exf) for zonal-velocity
706        at Western & Eastern Boundaries (+/- 1 per-cent); Also prescribe
707        time-varying OB at Western-side for wVel (NonHyd); update output.
708      - add secondary set-up (.nlfs) using NonLin FreeSurf (z*) + mom_vecinv
709        and biharmonic-viscosity ; also use prescribed time varying OB.
710    o pkg/obcs:
711      fix bug in OBWeta,OBWeta indices in obcs_apply_r_star.F
712    o model/src:
713      - fix startTime setting when baseTime<>0 & nIter0=0 are specified ;
714      - initialise startTime & nIter0 with unlikely values: allows to set one
715        from the other without ambiguity.
716    o seaice_obcs test-exp.:
717      add small diffK4T,S to test biharmonic diffusivity with OBCS ; update output.
718    o pkg/obcs:
719      - remove calls to OBCS_COPY_TRACER after EXCH for T,S & pTracer:
720        no longer needed with maskInC,W,S in pkg/generic_advdiff.
721    o pkg/seaice:
722      - retired SEAICE_SALINITY and SEAICE_salinity in favor of
723        SEAICE_VARIABLE_SALINITY and SIsalFRAC, respectively.
724      - fixed bug in the initialization of sea ice salinity variable HSALT
725        in seaice_init_varia.F  (removed dependence on ICE2WATR)
726    o fizhi-cs test exp.:
727       switch reference output convention for these 2 non-standard test-exp,
728        from: pgi  6.1-5 on faulks (FC.6, -of linux_ia32_pgf77+authors_fc5)
729          to: ifort 11.1 on baudelaire (FC.13, -of linux_amd64_ifort11)
730       reason: faulks might get retired soon and pkg/fizhi has still Pb with gfortran
731    o model/inc:
732      - change type of PmEpR array (from _RS to _RL) to fix restart (with "-use_r4")
733        of exp. global_ocean.90x40x15 (Suncronous time-stepping + Real-FW + NonLin-FS)
734    o pkg/seaice:
735      - fix calculation of saltFlux and saltPlumeFlux when using SEAICE_SALINITY
736    o verification/lab_sea, 1D_ocean_ice_column, seaice_obcs, global_ocean.cs32x15
737      - updated output*.txt files due to bug fixes in salt, saltPlumeFlux,
738        and initial HSALT
739    
740    checkpoint62w (2011/04/26)
741    o pkg/mom_fluxform:
742      - fix calculation of del2u & del2v (no-slip BC) when using Non-Lin Free-Surf.
743      - use parameter "sideDragFactor" in no-slip BC side-drag part.
744      - update output of exp. global_ocean.90x40x15
745    o pkg/mom_vecinv:
746      mask del2u & del2v (no effect on results, but cleaner & closer to mom_fluxform)
747    o update seaice exp.:
748      use more consistent parameter values (remove "backward compatability only":
749       ICE2WATR, SEAICE_lhSublim, SEAICE_cpAir, SEAICE_rhoAir + set rhoConstFresh)
750      related to thermodynamics seaice. Update output (fwd+AD) of exp.:
751       1D_ocean_ice_column (x2), lab_sea (x8), ioffline_exf_seaice (x2) & seaice_obcs
752    o update test-exp global_ocean.90x40x15:
753      o use default CD_CODE_OPTIONS file (Adams-Bashforth on CD Mom & Coriolis).
754      o increase Overlap size from 2 to 3 (to allow to test bi-harmonic Visc.)
755      o new pickup-files from a 100.yr run with pkg/down_slope (input.dwnslp params)
756      o turn on zStar & viscA4 in standard set-up (dir input/)
757        and update output files: output.txt & output.dwnslp.txt
758    o new AD-test experiment: obcs_ctrl
759      (From Matt MITgcm_Contrib/SOSE/BoxAdj) to test OBCS as control vector.
760    o pkg/dic:
761      fix two bugs in handling water vapour pressure in carbonate chemistry
762      and air-sea fluxes. Found by Val Bennington and Galen McKinley
763      (add DIC Option = WATERVAP_BUG to recover old results)
764      update output of tutorial_global_oce_biogeo (fwd+AD) & tutorial_dic_adjoffline
765    o adding allowInteriorFreezing option to check for water below freezing point
766      at depth and bring the negative heat anomaly to the surface level
767    o pkgs _fields_load:
768      - extend GET_PERIODIC_INTERVAL to deal with non-periodic case (from pkg/rbcs)
769      - use new S/R GET_PERIODIC_INTERVAL in pkgs:
770        bulk_force, cheapaml, cfc, dic, obcs (+ ctrl/ctrl_get_gen_rec), offline and
771        rbcs to get interpolation weights and time reccord number.
772      - fix multi-threading in aim_fields_load.F
773      - apply EXCH to temp arrays [0,1] after reading in dic_fields_load.F
774    o external_fields_load:
775      new S/R GET_PERIODIC_INTERVAL to calculate which time-record (and linear
776       interpolation weights) to use in a periodic time-series ; do not divide by
777       time-step to convert to integer:
778       - this fixes case where externForcingPeriod is not multiple of time-step
779          (Thanks to Christopher L. Wolfe)
780       - this fixes case where externForcingPeriod is an odd multiple of time-step
781         (was wrong by half of time-step); update results of tutorial_global_oce_in_p.
782      store index of time-record which is currently loaded:
783       - works without any assumption on sequence of calls to EXTERNAL_FIELDS_LOAD ;
784       - needed for the adjoint but not yet used because of extensive recomputations;
785         (to be fixed soon)
786    
787    checkpoint62v (2011/04/02)
788    o verification/1D_ocean_ice_column added to test Ian Fenty's
789      pkg/seaice_growth.F modifications for improving sea ice code differentiability
790    o update output of exp4, internal_wave, seaice_obcs, tutorial_plume_on_slope
791      (new velocity statistics after changing maskInW & maskInS definition)
792    o pkg/generic_advdiff with OBCS:
793      use maksInW & maskInS in advective flux and in biharmonic diffusion calculation:
794      equivalent to assumption of no tracer gradient outside the OB region.
795      This will affect the results if using obcs+biharmonic diffusion.
796      update output_adm.txt of experiment bottom_ctrl_5x5 (not expected since no obc)
797    o pkg/obcs:
798      change definition of maskInW & maskInS: leave OB edges inside (maskIn=1)
799      (e.g., maskInW(OB_Ie)=1 ) so that velocity normal-component at OB is still
800      in Interior region. No impact on solution but affects Velocity monitor stats.
801    o pkg/ptracers (adjoint)
802      New option AUTODIFF_PTRACERS_SPLIT_FILES for writing separate
803      tape file for each tracer
804    o model/inc/src and pkg/autodiff: add parameters that allow to turn
805      of parts of the adjoint code at run time. For now, there are only
806      useKPPinAdMode, useGMrediInAdMode, and useSEAICEinAdMode. These
807      parameters are set in data.pkg.
808      This is the lazy coward's version of doing this, but still useful for
809      debugging. In order to do it right, everything needs to be moved to
810      pkg/autodiff.
811    o pkg/autodiff: fix global_sum_tile_ad.F by resetting adsumPhi at
812      the end; this fixes the adjoint balancing code for open boundaries.
813    o pkg/ctrl:
814      - change behavior of xx_${varname}period to be analogous to exf-conventions:
815        xx_${varname}period =   0.,  means time-independent control part
816        xx_${varname}period = -12., means one-year-periodic monthly control part
817      - introduce helper routine ctrl_init_rec (part of ctrl_init.F) to
818        clean up ctrl_init a little, remove unused variables
819      - ctrl_init: fixed the handling of the start/endrec for obcs-variables
820      - move "call cal_GetMonthsRec" from s/r ctrl_get_gen to s/r ctrl_get_gen_rec
821    
822    checkpoint62u (2011/03/15)
823    o model/src:
824      - for the adjoint, change NonLin-FreeSurf initialisation sequence: fill-in
825        h0Fac from INITIALISE_FIXED and reset hFac to h0Fac in INITIALISE_VARIA ;
826      - in initialise_varia.F (except for ALLOW_DEPTH_CONTROL) remove 2nd call to
827        INI_DEPTHS, INI_MASKS_ETC & INI_LINEAR_PHISURF.
828    o pkg/ctrl/obcs/ecco:
829      - remove obsolete, unused, and partially broken code:
830        ctrl_obcsvol/ctrl_obcsbal/ctrl_volflux and code within
831        ALLOW_CTRL_OBCS_BALANCE
832      - put a stop statement into ecco/cost_obcsvol.F, but also add
833        cost_obcsvol to ecco_ad_diff.list
834    o pkg/ecco: fix counting cost function contributions for obcs (code
835      by Matt M.) and diffkr for diagnostics
836    o pkg/ecco, pkg/ctrl, pkg/grdchk:
837      add cost penalty terms for initial uvel, vvel, eta controls
838      and I/O for prior error files
839    o pkg/mdsio:
840       move mds_check4file.F from eesupp/src to mdsio_check4file.F ; add option
841       (new argument) to check for tiled file in mdsioLocalDir : this fix the
842       restart from pickup_som , pickup_dic (& dic_co2atm) with mdsioLocalDir.
843    o pkg/ctrl:
844     - ctrl_obcsbal.F, ctrl_obcsvol.F: replace last calls of ctrl_getrec by
845       ctrl_get_gen_rec, put a stop statement into ctrl_getrec. Remove
846       unused and superfluous variables
847     - ctrl_get_gen_rec.F: catch the case of xx_genperiod=0.
848    o pkg/ecco
849     - enable adjoint of Stevens OB
850    o pkg/ctrl/ecco/grdchk:
851      - remove global declaration of tmpfldx/yz and tmpfldx/yz2.
852        Fortunately, we do not have any tests for the numerous cpp-flagged
853        option of "obcs as control parameters" so we will never know
854        if this is an improvement (but at least now things compile).
855      - remove an obsolete initialization from ecco_cost_init_barfiles.F
856      - fix some problems within never used ifdefs to make the code compile
857    o pkg/obcs:
858     - Refine Interior mask definition to work with more complex OB (e.g.
859       if OB_Ie < OB_Iw); In case default setting is not sufficient, allows to
860       read in Interior mask from file. Check if Interior mask is consistent
861       with OB list of indices.
862    o pkg/seaice
863     - beginning code for a seaice tracer package,
864       but currently only used for seaice age: SEAICE_AGE
865       SEAICE_num = 4
866       iTracer = 1: area-weighted ice age
867               = 2: volume-weighted ice age
868               = 3, 4: template for one-year vs. multi-year ice
869       data.seaice has new namelist SEAICE_PARM03 for arrays related to
870       SEAICE_num
871    
872    checkpoint62t (2011/03/05)
873    o pkg/obcs:
874     - obcs_apply_uv.F: change to a 2 steps method, first tangential component;
875       then normal component. This ensures that the normal component is set
876       correctly even when it conficts with tangential setting from an other OB.
877       Affects results of test-experiment seaice_obcs: update the output.txt
878    o pkg/obcs:
879     - add code to monitor statistics of dynamical fields at OB.
880     - take OBCS_BALANCE code out of obcs_calc.F into new S/R OBCS_BALANCE_FLOW :
881       - fix to OBCS_BALANCE code (right hFac ; deal with simple OB intersection).
882       - change default: balance the Net inflow through all OB (instead of balancing
883         each OB separately); keep the old method if setting OBC_balanceFacX < 0.
884     - switch on useOBCSbalance in dome experiment: only correct Western OB outflow
885       to match Nortern OB inflow (OBCS_balanceFacN=0).
886    o pkg/seaice:
887     - redefined actual sea ice age to be ICEAGE/HEFF ifdef SEAICE_AGE_VOL
888    o pkg/seaice (seaice_growth v 1.113):
889     - reverting seaice_growth to v 1.111 in order to have code with exact bit
890       compatibility with MITgcm_contrib/ifenty/Fenty_seaice_thermo_code_merge
891       CPP option SEAICE_OCN_MELT_ACT_ON_AREA removed in v 1.112 is reintroduced
892       runtime flag SEAICEareaFormula is kept but is inactive
893    o model/src:
894     - add new param to scale curvilinear grid distance and area when using
895       a different sphere radius from the grid-files.
896     - test/check multi-threads EXCH applied to local variable (cg2d_x)
897    o adjoint:
898     - enable adjoint of Stevens OB
899     - add dummy_in_dynamics to enable extraction of ADJrhoinsitu
900       (a bit delicate because of potentially modified adj. common block structure;
901       current switch is ALLOW_AUTODIFF_MONITOR_DIAG, could be changed later)
902    
903    checkpoint62s (2011/02/15)
904    o pkg/seaice (seaice_growth v 1.112):
905     - introduce SEAICEareaFormula run time parameter, which selects the recipe for
906       computing the ice cover tendency from effective thickness tendencies. Include
907       Ian Fenty's formula.
908     - remove 'undef SEAICE_OCN_MELT_ACT_ON_AREA' which may now be achieved using
909       SEAICEareaFormula.
910     - simplify notations for the various d_HEFF/d_AREA terms.
911    o pkg/gmredi:
912     - add Boundary-Value-Problem bolus transport (Ferrari etal, OM 2010) code
913       from Christopher Wolfe (UCSD); add partial cell factor in vertical derivative;
914       add a verification test-run (front_relax.bvp) to test GM_useBVP.
915    o pkg/seaice (seaice_growth v 1.111):
916     - for SEAICE_DO_OPEN_WATER_GROWTH, replace Gael's implementation with Ian's.
917     - the new SEAICE_DO_OPEN_WATER_MELT allows open-water air-sea heat fluxes to
918       also melt ice.
919    o pkg/seaice:
920     - McPhee formula for Ice-Ocean fluxes (provided by Ian Fenty).
921     - can be used by #define MCPHEE_OCEAN_ICE_HEAT_FLUX in SEAICE_OPTIONS.h
922    o pkg/cheapaml:
923     - from Nico Wienders: New version of this package.
924    o pkg/flt:
925     - add CPP options to prevent floats to re-enter the opposite side of
926       a periodic domain (default: keep periodicity)
927    o pkg/gmredi:
928     - apply exchange to GM_PsiX,GM_PsiY to get valid values near CS-corners
929       (needed for multi-dim advection).
930     - switch on GM Advective form in global_ocean.cs32x15 and update output.txt
931    o model/src:
932     - fix wrong re-setting of addMass array (ALLOW_ADDFLUID) for atmospheric run.
933    o tutorial_tracer_adjsens
934     - extend to NLFS and replace maskC by hFacC
935       (change reference output accordingly)
936    
937    checkpoint62r (2011/01/24)
938    o testreport:
939     - add option -deloutp (-do) to remove output file after successful run
940     - add option -mfile (-mf) for MPI machile-file and for each test-exp,
941       extract exact list of procs from this file ; adjust COMMAND by
942       replacing TR_MFILE & TR_NPROC with local machile-file & Nb of MPI procs.
943  o pkg/ecco: replace old ineffective way of penalizing deviations from  o pkg/ecco: replace old ineffective way of penalizing deviations from
944    first guess (of obcs) with code by Matt Mazloff    first guess (of obcs) with code by Matt Mazloff
945  o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without  o pkg/ctrl: add code that allows the use of ALLOW_OBCS?_CONTROL without
946    exf/cal    exf/cal
947    - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl    - ctrl_init: fix initialisation (computation of diffrec) for obcs-ctrl
948      and handle case of obcs?period == 0      and handle case of obcs?period == 0
949      Not affected by these changes: There is still an inconsistency in      Not affected by these changes: There is still an inconsistency in
950      the computation of start/endrec for the obcs variables for ALLOW_CAL      the computation of start/endrec for the obcs variables for ALLOW_CAL
951      defined (see comment by Menemenlis, 7-Mar-2003)      defined (see comment by Menemenlis, 7-Mar-2003)
952    - make S/R ctrl_get_gen_rec return something meaningful even if    - make S/R ctrl_get_gen_rec return something meaningful even if
953      ALLOW_CAL is not defined      ALLOW_CAL is not defined
954    - ctrl_getobcs?: simplify code so that it does not need to use    - ctrl_getobcs?: simplify code so that it does not need to use
955                     S/R exf_swapfields                     S/R exf_swapfields
956  o testreport:  o testreport:
957     allow to test MPI with different number of processors for each experiment:     allow to test MPI with different number of processors for each experiment:
# Line 24  o testreport: Line 960  o testreport:
960  o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:  o model/src, pkg/autodiff, pkg/ecco, pkg/seaice:
961    alleviate the need for additional 3D tapes when using    alleviate the need for additional 3D tapes when using
962    the non-inear free surface in the adjoint. This is done    the non-inear free surface in the adjoint. This is done
963    by adding an 'update' of hfacc etc. to their current    by adding an 'update' of hfacc etc. to their current
964    value at the beginning of forward_step.F.    value at the beginning of forward_step.F.
965  o pkg/seaice  o pkg/seaice
966    seaice_lsr: move stress-divergence computations out of outer pseudo-    seaice_lsr: move stress-divergence computations out of outer pseudo-
967    timestepping loop    timestepping loop
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