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revision 1.1424 by mlosch, Thu May 5 09:24:44 2011 UTC revision 1.1555 by mlosch, Tue Dec 20 10:06:51 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/ctrl:  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      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
15        what the name implies (and not emissivity*BoltzmannConstant), this means
16        the old default value of 5.5e-8 now means
17        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
18        S/R exf_readparms
19      - FV-discretization of the B-grid LSOR solver, turn on with
20        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
21        of the calling routine dynsolver, so that B and C-grid code look a
22        little more alike.
23    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
24    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
25      default for SEAICE_emissivity, if useEXF; requires setting a wrong
26      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
27      backward compatiblity
28    o model/src: use sigmaR in calc_ivdc
29    
30    checkpoint63g (2011/12/16)
31    o pkg/seaice/seaice_growth.F:
32      fix heat conservation of the coupled ocean-seaice system.
33      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
34      solid vs liquid water treatment is resolved via QNET.
35    o pkg/seaice/seaice_growth.F:
36      add missing term for sublimation in saltFlux, which was breaking conservation.
37    o pkg/seaice/seaice_model.F:
38      Remove this patholigical case treatment in evolution branch,
39      where it is un-necessary and breaks conservation.
40      Update global_ocean.cs32x15/results accordingly for
41      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
42    o model/src:
43      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
44      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
45    o pkg/obcs:
46      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
47      tendency for temperature and salinity that is then applied to update
48      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
49      horizontal advection and diffusion contributions on the boundary (in
50      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
51      removing the mask in S/R timestep_tracer. The advantage of this approach is
52      that the updated tracer values include contributions from the surface
53      forcing and vertical diffusion.
54      This modification changes exp4.stevens because of vertical diffusion.
55    o model/src:
56      change non-curvilinear grid setting to also work with exch2 + blank tiles:
57      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
58        face dimensions.
59      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
60        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
61        and INI_SPHERICAL_POLAR_GRID.
62      change test-experiment global_ocean.90x40x15:
63      - split the domain in many more tiles (9x4 tiles of 10x10 each);
64      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
65      - update results of both test (std & dwnslp).
66    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
67       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
68    o model/src:
69      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
70        and fix initialisation when using sigma-coords.
71    o model/src:
72     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
73       to their current value at the beginning of forward_step.F": add a new run-time
74       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
75     - set doResetHFactors=T in the following test exp:
76        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
77        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
78        and tutorial_global_oce_in_p (nonLinFS in p)
79    o pkg/ecco
80      - added IES cost term
81    o verification/advect_xz
82      - scale down the depth by 1/100 (from 200 km to just 2.km)
83      - add secondary test using divergent flow, r-star and implicit vertical advection.
84      - add note (check_conserve_TS.txt) and matlab script to check global
85        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
86    o pkg/rbcs:
87      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
88    o pkg/obcs (Stevens BCs):
89      - fix various problems in the phase speed computations of the Stevens
90        boundary conditions:
91        - sign error for western and southern boundaries,
92        - time tendencies were underestimated by factor of dTracerLev and some just
93          zero (for multidim advection schemes) -> now estimate time tendencies
94          from difference between previous (n) time level and the one before (n-1);
95          this requires storing a field per tracer per boundary, also in the pickup
96          files.
97        - replace deltaTmom in cflMer/Zon computation with dTracerLev
98        - set default phase velocity to cflMer/Zon
99      - update verification experiment exp4.stevens
100    o pkg/generic_advdiff (implicit_r):
101      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
102        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
103      - fix implicit vertical diffusion or advection with NonLin FreeSurf
104        (was using current recip_hFacC instead of future recip_hFacC): set future
105        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
106        solver S/R ;
107      - fill diagnostics of vertical advective fluxes (computed from tendency)
108        when using implicit vert. advection;
109      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
110         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
111         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
112         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
113    o pkg/diagnostics:
114      - add diags for T & S tendency which goes through Adams-Bashforth.
115    
116    checkpoint63f (2011/11/30)
117    o pkg/obcs/obcs_calc_stevens.F:
118      - join some loops to reduce number of if-statements
119      - fix a bug in code for northern and southern boundaries.
120    o pkg/seaice/seaice_init_varia.F
121      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
122        caused zero ice-velocities for the B-grid code
123    o pkg/seaice/seaice_init_fixed.F
124      - fix a bug in the initialisation of the second metric terms
125        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
126      - this affects all seaice configurations with useCurviLinearGrid = .true.
127        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
128        = .true. (default)
129      - the only verification experiment affected is global_ocean.cs32x15:
130        icedyn, seaice, and seaice_dynmix (AD)
131    o pkg/thsice/thsice_diagnostics_state.F
132      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
133        not contain garbage that can lead to surprises in diagstats_calc.F
134    o model/src:
135      - move bi,bj loops inside INTEGR_CONTINUITY ;
136      - call INTEGR_CONTINUITY directly from forward_step.F
137        (previously called from momentum_correction_step.F)
138      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
139        forward_step.F and pkg/ecco/the_main_loop.F
140    o model/src/do_oceanic_phys.F:
141      - reset addMass to zero only if useICEFRONT ;
142      - separated k-loop for rhoInSitu calculation ;
143      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
144        and at constant T,S (= WdRHOdP);
145      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
146        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
147        transport of locally-referenced potential density);
148        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
149    o gluemnc:
150      - replace ncrcat with ncks when adding variables to *.glob.nc
151      - change the way variables without record dimensions are handled so that
152        files that have variables with and without record variables can be glued:
153        add a record dimension with a new unique name to be able to differentiate
154        between variable with and without a-prior record dimensions. Remove
155        this record dimension before adding the variable to the *.glob.nc file.
156        This procedure automatically works also for grid.*.nc files that do not
157        have any record dimension.
158    o verification/cpl_aim+ocn:
159      - generate new reference output on baudelaire (gfortran, mpich2) (previously
160        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
161    o pkg/obcs/obcs_calc_stevens.F:
162      - add code for northern and southern boundaries.
163      - reorder some loops to save some operations and so that drFBar can be scalar
164    o model/src:
165      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
166        truncation) and add diagnostics for Adams-Bashforth tendency increment.
167      - update test-exp. AD output:
168        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
169      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
170        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
171        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
172        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
173        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
174        tutorial_plume_on_slope.
175    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
176      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
177      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
178      does not even come with an F77 compiler anymore, this should not be
179      a limitation
180    
181    checkpoint63e (2011/11/06)
182    o pkg/seaice adjoint of LSR:
183      - substantially rework STORE dirs.
184      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
185        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
186        and only perform SOLV_MAX_FIXED adjoint iters.
187        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
188        always goes to same record, meaning that the last forward field will be
189        the one used in the adjoint - an approximation.
190      - now produces non-zero LSR-related gradients, and acceptable gradients for
191        An's zonal (x-z) test case (to be checked in)
192      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
193        (but these are screwed up by the thermodynamics in the first place);
194        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
195        output_adm.txt also reflects changes to seaice_lsr
196      - global_ocean.cs32x15:
197        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
198          (output_adm.seaice.txt was updated)
199        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
200          (output_adm.seaice_dynmix.txt)
201    o test-exp. exp4+stevens:
202      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
203    o pkg/seaice (lsr solver):
204      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
205        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
206      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
207      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
208        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
209      - compute (with new S/R) and print initial (+ free-driff sol. if available)
210        and final residual of linearised system.
211    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
212      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
213    o pkg/obcs: Stevens BCs (still only for east and west)
214      - fix Stevens BCs by using intermediate velocities of previous
215        time step as "baroclinic" contribution rather velocity of one grid cell
216        inside the boundaries; more consistent but makes the entire treatment
217        more complicated, requires new pickup files and two new S/Rs:
218        obcs_copy_uv_n and obcs_save_uv_n
219        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
220        (undefined by default)
221      - silently move computation of some grid factors into separate loops to
222        save some recomputations
223      - add a hack for non-linear free surface
224      - add a verification experiment to exp4 that tests this code
225    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
226    
227    checkpoint63d (2011/10/25)
228    o pkg/obcs + seaice-dynamics:
229      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
230        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
231        values (consistent with an implicit method).
232      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
233        return to older implementation (same results as before); note that none of
234        the "experimental" OBCS_SEAICE options are implemented in the new version.
235      - switch test exp. seaice_obcs to use new version (update output).
236    o pkg/seaice:
237      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
238      - add parenthesis in Water-Ice drag calculations (evp & lsr);
239      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
240        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
241      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
242        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
243    o pkg/layers:
244      - Include potential density as new coordinate (Thanks to David Munday)
245    o pkg/dic:
246      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
247        carbonate computation/output to CALC_PCO2_APPROX
248    o pkg/generic_advdiff
249      - make TAF generate code that vectorizes:
250        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
251    o model/src:
252      - improve vectorization also for adjoint code of
253        solve_tridiagonal and solve_pentadiagonal. As this requires up to
254        5 new 3D-fields, this code is only turned on for the combination of
255        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
256        for singular matrix check (only for TARGET_NEC_SX).
257      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
258        ALLOW_AUTODIFF. This flag now needs to be set outside of
259        solve_tri/pentadiagonal.F
260    o pkg/exf:
261      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
262        optional namelist EXF_NML_OBCS).
263      - add many debug-print (to trace down where pkg/cal error msg comes from)
264    o pkg/mom_vecinv/mom_vi_hdissip.F
265      - rearrange loops so that vectorization is improved and in particular
266        the adjoint routine vectorizes. The code is a little longer now, but I
267        think easier to read.
268        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
269    o pkg/seaice:
270      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
271    o pkg/exch2:
272      - alternative code (without tile x tile matrix) for cumulated (global) sum;
273        used as default; keep using matrix version in adjustment.cs-32x32x1.
274    o tools/build_options:
275      - after merging some MPI and/or multi-threads specific optfiles so that
276        the modified default optfile support both built (using genmake2 -mpi
277        for the MPI built, using genmake2 -omp for OpenMP built),
278        move now obsolete optfiles to tools/build_options/unsupported/
279       (add copy of email sent to support list in doc/optfiles_changes.txt)
280    
281    checkpoint63c (2011/09/28)
282    o pkg/ebm:
283      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
284        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
285    o pkg/seaice (SItracer pickup)
286    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
287      To be done:
288      - thorough testing of missing fields in S/R seaice_read_pickup
289      - thorough matching between generic tracers and specific fields used
290        (e.g. volume-weighted age, area-weighted age, salinity, ...)
291    o pkg/grdchk:
292      - all procs calculate and print finite-difference gradient (for testreport)
293      - change description output used by testreport;
294      - AD testing: also compare and report Finite-difference gradient;
295        => update all output_adm*.txt
296    o test exp. global_ocean_ebm:
297      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
298        and turn on exactConserve; update (fwd) output.
299    o pkg/seaice (LSR):
300      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
301      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
302        * identical results with non-CS topology (but save up to half of EXCH calls)
303        * no much changes in cs-32 verification tests since no ice at face edges
304         (differences due to convergence criteria, since nb of iterations changed)
305        * expect some differences on lat-lon-cap grid.
306        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
307    o pkg/exch2:
308      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
309        many tiles); until alternative coding is added, just add a stop.
310    o pkg/kpp:
311      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
312        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
313    o optfiles:
314      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
315        into corresponding standard one, which now support different build:
316        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
317      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
318    o pkg/obcs (seaice):
319      - add missing EXCH for uIce,vIce after applying OBCS;
320      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
321        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
322        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
323      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
324      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
325        and eedata.mth for MPI and mutlti-threaded testing.
326    o pkg/flt:
327      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
328      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
329      - fix pickup and trajectories + profiles output with multi-threads;
330      - add parameter to select group of fields to write along trajectory and
331        profile (default unchanged);
332      - only call PORT_RAND* function when flt_noise <> 0;
333      - add multi-threaded test for verification exp. flt_example.
334    o eesupp/src:
335      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
336      - USE_OMP_THREADING: check that number of threads (from eedata) matches
337        actual number (from env.var. setting).
338    o pkg/ebm:
339      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
340      - add multi-threaded test for verification exp. global_ocean_ebm
341    
342    checkpoint63b (2011/08/29)
343    o pkg/ebm:
344      - fix sign of runoff;
345      - update directly forcing fields (Qnet,EmPmR) to use standard
346        external_forcing_surf.F (remove ebm_forcing_surf.F);
347      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
348      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
349        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
350      - update global_ocean_ebm parameters file data and update output (fwd+ad).
351    o verification/matrix_example:
352      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
353        MPI and mutlti-threaded testing.
354    o pkg/matrix:
355      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
356      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
357      - fix for multi-threaded (remove DATA statement);
358      - use standard DIFFERENT_MULTIPLE function;
359      - add MATRIX_OPTIONS.h
360    o verification/matrix_example:
361       To allow to split the domain in several tiles, change the domain size
362        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
363        Western side) of land points.
364    o (*_)write_pickup:
365      - fix few bugs in mypackage_read/write_pickup.F
366      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
367        array of length 1 (was caught by compiler syntax-check).
368    o pkg/diagnostics (velocity potential solver):
369      - fix initialisation of main diagonal matrix (for overlap values)
370    o tools/build_options:
371      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
372        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
373      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
374        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
375        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
376        and use "-devel" testreport option for standard testing on baudelaire.
377    o pkg/grdchk:
378      - Assume that all gradient-check position are within the same tile
379        corresponding to global indices (iGloTile,jGloTile) and that
380        positions (i,j indices or nbeg) are local to this tile;
381      - set tile local-indices and proc. number according to tile global-indices;
382      - remove grdchkwhichproc from namelist (retired param);
383      - send adjoint gradient to all procs so that all procs print it to STDOUT;
384      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
385    o adding package bbl (Bottom Boundary Layer)
386      description in MITgcm/pkg/bbl/bbl_description.tex
387      example/test experiment in MITgcm_contrib/bbl
388    o adjoint verifications
389      - changed 5 experiments to multi-tiles
390        * global_ocean.90x40x15
391        * obcs_ctrl
392        * offline_exf_seaice
393        * tutorial_dic_adjoffline
394        * tutorial_tracer_adjsens
395        changed reference output for those that crossed tile boundaries
396        (changed choices of gradient check positions)
397      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
398      - temporary bug fix in grdchk_loc.F for obcs
399    o genmake2 & testreport
400      - add target "obj" (just for OBJFILES files) to Makefile;
401      - add option to specify FEXTRAFLAGS on command line.
402    o pkg/mypackage:
403      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
404    
405    checkpoint63a (2011/08/02)
406    o pkg/diagnostics (velocity potential):
407      - fix velocity-potential calculation when using OBCS: balance net inflow
408        at each level (new S/R OBCS_DIAG_BALANCE).
409      - fix some of the problems with OBCS in stream-function calculation.
410    o pkg/exf/exf_readparms.F
411      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
412        EXF_NML_OBCS) more consistent, so that you need not have these lists
413        in data.exf when they are not used.
414    o optim/optim_readdata.F:
415      - add some output about obcs variables that might help debugging
416      - add a check about nvarlength
417    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
418    o pkg/diagnostics (velocity potential):
419      - fix mask for OBCS (still problems in stream-function with OBCS);
420      - add specific parameter (default = main code CG2D params) for solver;
421      - in case of poor convergence, use solution corresponding to lowest residual.
422    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
423      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
424      and should be avoided where possible.
425    o model/src (rStar):
426      - include r* effect on reference-state (PhiRef) in totPhiHyd
427        (so that it's really the potential anomaly at the cell center);
428        affect solution only if z* with full pressure in EOS.
429      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
430        update output (because of z* in totPhiHyd and viscA4 changes);
431      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
432        @ constant r) until interpolation at constant r is implemented.
433    o pkg/diagnostics
434      - fix RCENTER diagnostics in case cell center is not at interface middle
435    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
436      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
437      that THETA and SALT are "conservative temperature" and "absolute
438      salinity"
439    o pkg/ctrl
440      - fix computation of endrec in s/r ctrl_init_rec
441      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
442    o pkg/seaice/seaice_growth.F
443      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
444        remove then obsolete STORE directives
445      - fix STORE directives for tice and tices, so that only the
446        appropriate part of the fields are stored (and not the entire
447        field); update global_ocean.cs32x15.seaice AD output.
448      - cosmetic changes: adjust CPP flags and indentation for better
449        legibilty
450    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
451      Chris Wilson)
452    o pkg/gmredi:
453       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
454       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
455    
456    checkpoint63  (2011/07/11)
457    o pkg/exch2:
458     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
459     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
460       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
461       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
462    o pkg/diagnostics:
463     - deal with pairs of post-processed diags which are computed together; in
464       particular, re-order list of diags within 1 file to save 2nd computation.
465     - add S/R to compute velocity stream-function (called after velocity-potential
466       calculation) from divergence free transport -> new diagnostics "PsiVEL".
467     - add parameter to select grid-point location where PsiVEL == 0.
468    o eesupp/src:
469       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
470       (specific S/R needed with exch2 topology - for now, just print an error msg)
471    o pkg/shelfice
472     - Implement friction velocity-dependent transfer coefficients following
473       Holland and Jenkins, JPO, 1999
474       Original code by M. Losch with small modifs.
475       Enable with CPP option SHI_ALLOW_GAMMAFRICT
476       and runtime flag SHELFICEuseGammaFrict
477    o verification lab_sea & global_ocean.cs32x15:
478     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
479       does not miss some dependencies (but is slower) and also works with many files
480       (default makedepend limitation for AD built).
481     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
482    o pkg/diagnostics:
483     - add run-time parameter "useMissingValue" (def=False) to fill land-point
484        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
485       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
486     - Extend the use of "missing_value" setting from data.diagnostics for the case
487       of counter-diagnostics (where fraction-weight is zero). This applies both to
488       MNC and MDS output files.
489    o pkg/seaice/seaice_growth.F:
490      - add 'a priori' cap of latent heat flux based on actual mass considerations
491        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
492        non-legacy seaice_solve4temp.
493      - add diagnostic of the residual sublimation freshwater flux (the freshwater
494        flux taken from the ocean if the total actual latent heat fluxes exceed
495        the maximum)
496      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
497       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
498      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
499       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
500      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
501      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
502    o verification 1D_ocean_ice_column:
503       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
504       update results
505    o pkg/diagnostics:
506     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
507       which are not filled-up but computed from other diags ; In this case, the mate
508       diag points to the primary (filled-up) diag to used for post processing.
509     - Update Velocity-potential computation using post-processed diag framework.
510     ==> Change the ordering of fields and time-periods in MDS output file
511       when using periodic averaging: now writes one time record with the full set
512       of fields for this time period, then the next time reccord (it used to be
513       one field with the full set of time records then the next field).
514         Note: this is now similar to NetCDF (MNC) output file. <==
515    
516    checkpoint62z (2011/06/21)
517    o adjoint monitor:
518     - Add adjoint monitor output for packages exf, seaice
519       and update relevant testreport output
520    o pkg/seaice:
521     - re-order diags inits so that they appear in order in available_diagnostics.log
522     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
523       area/heff/hsnow preceeding thermodynamic growth/melt.
524     - modified diag: SIdA; output actual effect, as the description states.
525     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
526     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
527       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
528        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
529     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
530     - added diagnostics for seaice generic tracers (SItr*).
531     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
532     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
533     I. Fenty: 18-Jun-2011:
534     Minor changes to seaice package:
535     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
536        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
537       - Differentiated "regularization variables" from "floor variables"
538        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
539        * hiceMin became SEAICE_hice_reg (old hiceMin)
540          (with _reg meaning regularization variable)
541       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
542        so as to ensure energy conservation when going between phases
543      - A22 was not used anywhere
544     2) Changed regularization procedure for heffActual and hsnowActual to ensure
545        well-boundedness and smooth adjoint in seaice_growth.F
546     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
547        because the old regularization always set heffActual >= 0.05 cm
548     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
549        on AREA when HEFF > 0.
550      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
551        requiring that DISABLE_AREA_FLOOR *not* be defined
552     Affected verifications:
553      - 1D_ocean_ice_column (output.txt output_adm.txt)
554      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
555    o pkg/diagnostics:
556      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
557      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
558        (was _RL, now integer) with option = 0 to retrieve all levels.
559      - add pieces of code to compute velocity potential at each level (new diagnostics
560        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
561        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
562      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
563        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
564        and in diagnostics_fract_fill.F (do not need a valid pointer for the
565        diagnostics counter-mate); check that definition of counter-diagnostic
566        includes a valid counter-mate (in diagnostics_set_levels.F).
567    o model/src (rStar):
568      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
569        affect solution only if z* with full pressure in EOS;
570        update output of test-exp global_ocean.90x40x15.
571    o pkg/seaice:
572      - introduce siEps=1e-5 parameter
573      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
574      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
575      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
576        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
577        as well as ice cover age and ridging index (attached to AREA).
578        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
579        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
580        Up to SItrMaxNum=3 tracers can be used simultaneously.
581    o pkg/salt_plume:
582      -introduce SPsalFRAC run time parameter that sets the fraction of the
583       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
584       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
585    o model debug options:
586      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
587        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
588      - Refine debug-msg printing selection (3 new levels):
589        debugMode  : controls printing of debug messages (sequence of S/R calls).
590        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
591         debLevZero =  0 ; /* level of disabled aux. msg printing */
592         debLevA =  1 ; /* level of minimum  aux. msg printing */
593         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
594         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
595         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
596         debLevE =  5 ; /* level of extensive debug printing */
597        New debugLevel default: with default debugMode value (=F),
598          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
599          and if debugMode=T, default debugLevel = 4 (debLevD).
600        Relation with previous settings:
601         debLevB (=2) corresponds to former debLevA (=1)
602         debLevD (=4) corresponds to former debLevB (=2)
603        Note:
604         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
605         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
606            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
607      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
608        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
609    o pkg/obcs:
610      - change OBCSfixTopo default from True to False (should not change the results);
611        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
612    o pkg/thsice:
613      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
614        2nd layer seaice sublimation (unlikely to happen)
615      - use Interior mask for OBCS in thsice_advection.F (similar to what is
616        done in gad_advection & seaice_advection).
617    o adjoint:
618      bug fix spotted by Gael Forget:
619      seaice_advection and thsice_advection still had
620      legacy CPP options to avoid CS corner updates for adjoint
621    o pkg/seaice:
622      => Change some of the defaults (2011/05/29):
623         - change SEAICEuseFluxForm default (from False to True)
624         - change DIFF1 default (from 0.004 m/s to 0. m/s)
625         And print warnings if DIFF1 is not set in data.seaice and centered
626          avection scheme is used without any diffusion.
627      also:
628      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
629      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
630      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
631        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
632        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
633      update results of test exp.:
634         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
635             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
636             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
637         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
638         seaice_obcs: output (SEAICEuseFluxForm=T)
639      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
640          for standard fwd & AD lab_sea tests (to keep the same output).
641    o pkg/seaice/seaice_growth.F:
642      - use Ian Fenty's capping formulas for actual ice
643      thickness thoughout EVOLUTION branch.
644      - put treatment pathological case #2) in CPP brackets
645      (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
646      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
647    o pkg/seaice:
648      - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
649      pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
650      also pass fac as a param, which can be 1. (to update the tendency
651      field) or the time step (to update the field itself).
652      - seaice_advdiff.F: for multidim, call seaice_diffusion with
653      e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
654      seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
655      - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
656      hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
657    o pkg/seaice:
658      diffusion with centered advection scheme (diffus.F & advect.F):
659      - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
660        to just compute the laplacian of input-field.
661      - unroll k loop (harmonic,biharmonic diff) in advect.F to save 1 exch call.
662      - fix flux-form version in diffus.F to conserve tracer.
663      update output of lab_sea.fd & lab_sea.hb87 (1rst set of modif affects
664       machine truncation) and lab_sea.salt_plume (conservative flux-form modif)
665    
666    checkpoint62y (2011/05/26)
667    o pkg/seaice:
668     - seaice_growth.F : in EVOLUTION branch, always include
669       a_QSWbyATM_cover in qnet (as it should be).
670     - verification/global_ocean.cs32x15 : update results accordingly
671       (output.seaice.txt output_adm.seaice.txt).
672    o pkg/seaice + obcs:
673     - use maskInW & maskInS in multi-dim advection and biharmonic diffusion:
674       equivalent of assuming no tracer gradient outside the OB region.
675       update output of seaice_obcs (uses DIFF1 <>0 => biharmonic diffusion)
676     - remove calls to OBCS_COPY_TRACER after EXCH calls (no longer needed
677       after changes above);
678     - obcs+seaice cleaning: apply seaice-tracer OB values to tracer field
679       only at OB location (instead of over a band of OLx width).
680    o pkg/seaice:
681     - fix wrong indices in old (non Flux-Form) diffusion default S/R diffus.F
682       (dxG(I+1, ...) changed to dxG(I, ...), no impact on Lat-Lon grid)
683    o pkg/obcs:
684      - split header file "OBCS.h" into 4 separated files:
685        OBCS_PARAMS.h, OBCS_GRID.h, OBCS_FIELDS.h & OBCS_SEAICE.h
686       Note: OBCS_PARAMS.h & OBCS_GRID.h can be included without OBCS_OPTIONS.h
687         (contain no conditional statement which depends on OBCS options).
688      - move "useOBCSYearlyFields" from "data.obcs" (hold in OBCS_PARAMS.h)
689        to parameter file "data.exf", namelist EXF_NML_OBCS (in EXF_PARAM.h).
690    o ctrl, cost, grdchk & autodiff pkgs:
691      - make options file more standard (like other {PKG}_OPTIONS.h file but
692        with AD_CONFIG.h); clean-up some of the included header files.
693    o pkg/obcs:
694      - do not mask tracer when applying OB (tracer == 0 could generate problems)
695      - apply tracer OB values to tracer field only at OB location (instead of
696        over a band of OLx width)
697      - clean-up obcs_apply_w.F & obcs_apply_eta.F (since less calls to these S/R)
698      - remove OBCS_MULTIDIM_OLD_VERSION code in gad_advection.F and remove
699        obcs_apply_tloc.F & obcs_apply_sloc.F
700    o obcs in model/src:
701      - call OBCS_APPLY_W only if NonHydrostatic.
702      - call OBCS_APPLY_ETA only if NonLinFreeSurf.
703      - reset dEtaHdt and wVel to zero outside OB interior region ;
704      - leave tracer unchanged outside OB interior region: This has no effect
705        on the solution but just to prevent unrealistic tracer value outside OB.
706      - zero out velocity outside OB interior region: This has no effect on
707        the solution but just to prevent unrealistic velocity outside OB.
708    o obcs and non-lin free-surf:
709       move call to OBCS_APPLY_R_STAR from update_r_star.F to calc_r_star.F
710       and call to OBCS_APPLY_SURF_DR from update_surf_dr.F to calc_surf_dr.F
711       + add argument "etaFld" to OBCS_APPLY_R_STAR & OBCS_APPLY_SURF_DR:
712       this fixes missing EXCH + get consistent eta OB value (+ fix restart).
713       update results of test-exp. exp4(nlfs).
714    o exp4 (nlfs) test-exp:
715       use OBC for Eta at Western & Eastern OB (to test prescribing Eta
716       with NonLin-FreeSurf); update output.nlfs.txt
717    o obcs and 2d/3d solver norm:
718       use interior masks (maskInC) to cancel out cg2d & cg3d matrix coeff at OB
719       and outside OB interior region (will allow to place OB further inside the
720       domain). Depending on the domain, can affects cg2d-Norm (previous
721       cancellation outside OB was only partial), e.g. in exp4 & obcs_ctrl,
722       and cg3d-Norm (previous Norm was computed before canceling OB terms),
723       e.g. in tutorial_plume_on_slope.
724      - update output of exp.: exp4 (x2), obcs_ctrl and tutorial_plume_on_slope.
725    o pkg rbcs:
726      - split RBCS.h into 3 files: RBCS_SIZE.h, RBCS_PARAMS.h & RBCS_FIELDS.h
727      - add capability to apply relaxation to horizontal velocity uVel & vVel.
728    o pkg/grdchk: add gradient check for control variable xx_shifwflx
729    o pkg/shelfice/shelfice_init_fixed.F
730      fix CPP-flag combinations
731    o pkg/seaice: Merge iceage code of Pierre Rampal
732      * update/change/correct ice age calculations
733      * add age updates for pathological cases
734      Probably needs more testing...
735    
736    checkpoint62x (2011/05/13)
737    o pkg/mom_vecinv:
738       high-order vorticity scheme: use interior masks (maskInW & S)
739       to zero-out (outside OB) gradient of vorticity.
740    o verification exp.:
741       turn on "useEnergyConservingCoriolis" (better discretisation) in exp.
742       hs94.128x64x5 and seaice_obcs ; update results.
743    o pkg/obcs:
744      fix bug in OBeta for YZ sections in obcs_exf_load.F
745    o pkg/ctrl, pkg/shelfice, and optim:
746      - add new control variable xx_shifwflx (fresh water flux underneath ice
747        shelves). This is almost as tedious as obcs-ctrl, because the
748        variables needs its own mask.
749      - add a cost function term that penalizes the deviation of xx_shifwflx
750        from the first guess (zero) in analogy to other control variables
751    o pkg/shelfice:
752      - start basic adjoint
753    o pkg/ctrl:
754      - remove extra 2D field "for good measure" when initializing in
755        ctrl_set_globfld_[xy/xz/yz].F
756    - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec    - replace hard coded precision 32 (a bug) in ctrl_map_ini_gen by ctrlprec
757    - improve error messages in ctrl_set_unpack_*    - improve error messages in ctrl_set_unpack_*
758  o OBC implementation in momentum:  o OBC implementation in momentum:
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