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revision 1.1445 by gforget, Fri May 27 23:28:39 2011 UTC revision 1.1569 by jmc, Tue Jan 3 18:11:55 2012 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/exf:
8      - change masking flags definition (no longer "parameter"), put them in
9        common block and set them in S/R EXF_INIT_FIXED.
10      - change recognized masking flag from s,u,v to c,w,s since the mask
11        to use (maskC,W,S) depends on position on model grid and has little to
12        do with scalar/vector difference; fix masking if using P-coordinates.
13      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
14        and update results of exp. global_with_exf (x2).
15      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
16    o pkg/obcs
17      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
18    o pkg/exf (interpolation):
19      - assume periodicity in X only if input field cover full longitude range.
20      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
21        and should vectorise).
22      - fix input lat of the 2 added row (in case we provide N.pole data).
23    
24    checkpoint63h (2011/12/30)
25    o pkg/seaice:
26      - change declaration of UVM from _RL to _RS in order to get B-grid
27        uIce,vIce monitor when _RS = real*4
28    o pkg/offline:
29      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
30      - compute vertical velocity if not read from file (switch on exactConserv
31        & staggerTimeStep);
32      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
33    o verification:
34      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
35        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
36        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
37      - update output of exp. global_ocean.cs32x15.viscA4 after changing
38        grid-file angles (used here for coriolis-3d);
39      - remove (or gzip) few files not needed to run fizhi-cs experiments.
40    o pkg/exf (vector interpolation):
41      - rotate vector component toward local grid-axis orientation using grid-angles
42        (stored in GRID.h) instead of locally computed rotation angle; keep old code
43        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
44    o pkg/seaice:
45      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
46        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
47    o pkg/PKG_OPTIONS.h files:
48      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
49        outside of the #ifdef ALLOW_THISPKG / #endif block.
50      - update verification/*/code/PKG_OPTIONS.h files.
51    o add a verification experiment (offline_exf_seaice/input.seaice) that test
52      the B-grid LSOR solver
53    o pkg/seaice: sort out emissivity and long wave radiation step 2:
54      - add emissivity for snow and ice as new run-time parameters
55        (unfortunately) that default to the corresponding exf values; this
56        changes results in most verification experiments so that for backward
57        compatibility these parameter have to be set explicitly to inconsistent
58        values (ugly);
59      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
60        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
61        until we agree how to handle this bug properly
62    o pkg/exf (interpolation):
63      - add a set of run-time param ({inputfield}_interpMethod), one for
64        each interpolated input field, to select the interpolation method
65        with a value of zero switching off the interpolation;
66      - print interpolation parameters to standard output;
67      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
68        (to use instead runoff_interpMethod=0 in data.exf).
69      - simplify default setting of interpolation parameters (for all fields,
70        set position to match model grid cell-center position, leading to trivial
71        interpolation in case of regular Lat-Lon grid) and fix for the case of
72        non-uniform delY.
73    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
74       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
75       this factor is absolutely required, because the lw exitance (= out-going
76       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
77       where the reflectivity rho = 1-emissivity for conservation reasons. Once
78       this is established, we can remove the CPP-Flag (if we want to).
79    o pkg/seaice:
80      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
81        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
82      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
83        what the name implies (and not emissivity*BoltzmannConstant), this means
84        the old default value of 5.5e-8 now means
85        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
86        S/R exf_readparms
87      - FV-discretization of the B-grid LSOR solver, turn on with
88        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
89        of the calling routine dynsolver, so that B and C-grid code look a
90        little more alike.
91      - fix index bugs in ostres.F (B-grid code)
92    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
93    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
94      default for SEAICE_emissivity, if useEXF; requires setting a wrong
95      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
96      backward compatiblity
97    o model/src: use sigmaR in calc_ivdc
98    
99    checkpoint63g (2011/12/16)
100    o pkg/seaice/seaice_growth.F:
101      fix heat conservation of the coupled ocean-seaice system.
102      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
103      solid vs liquid water treatment is resolved via QNET.
104    o pkg/seaice/seaice_growth.F:
105      add missing term for sublimation in saltFlux, which was breaking conservation.
106    o pkg/seaice/seaice_model.F:
107      Remove this patholigical case treatment in evolution branch,
108      where it is un-necessary and breaks conservation.
109      Update global_ocean.cs32x15/results accordingly for
110      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
111    o model/src:
112      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
113      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
114    o pkg/obcs:
115      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
116      tendency for temperature and salinity that is then applied to update
117      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
118      horizontal advection and diffusion contributions on the boundary (in
119      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
120      removing the mask in S/R timestep_tracer. The advantage of this approach is
121      that the updated tracer values include contributions from the surface
122      forcing and vertical diffusion.
123      This modification changes exp4.stevens because of vertical diffusion.
124    o model/src:
125      change non-curvilinear grid setting to also work with exch2 + blank tiles:
126      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
127        face dimensions.
128      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
129        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
130        and INI_SPHERICAL_POLAR_GRID.
131      change test-experiment global_ocean.90x40x15:
132      - split the domain in many more tiles (9x4 tiles of 10x10 each);
133      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
134      - update results of both test (std & dwnslp).
135    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
136       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
137    o model/src:
138      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
139        and fix initialisation when using sigma-coords.
140    o model/src:
141     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
142       to their current value at the beginning of forward_step.F": add a new run-time
143       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
144     - set doResetHFactors=T in the following test exp:
145        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
146        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
147        and tutorial_global_oce_in_p (nonLinFS in p)
148    o pkg/ecco
149      - added IES cost term
150    o verification/advect_xz
151      - scale down the depth by 1/100 (from 200 km to just 2.km)
152      - add secondary test using divergent flow, r-star and implicit vertical advection.
153      - add note (check_conserve_TS.txt) and matlab script to check global
154        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
155    o pkg/rbcs:
156      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
157    o pkg/obcs (Stevens BCs):
158      - fix various problems in the phase speed computations of the Stevens
159        boundary conditions:
160        - sign error for western and southern boundaries,
161        - time tendencies were underestimated by factor of dTracerLev and some just
162          zero (for multidim advection schemes) -> now estimate time tendencies
163          from difference between previous (n) time level and the one before (n-1);
164          this requires storing a field per tracer per boundary, also in the pickup
165          files.
166        - replace deltaTmom in cflMer/Zon computation with dTracerLev
167        - set default phase velocity to cflMer/Zon
168      - update verification experiment exp4.stevens
169    o pkg/generic_advdiff (implicit_r):
170      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
171        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
172      - fix implicit vertical diffusion or advection with NonLin FreeSurf
173        (was using current recip_hFacC instead of future recip_hFacC): set future
174        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
175        solver S/R ;
176      - fill diagnostics of vertical advective fluxes (computed from tendency)
177        when using implicit vert. advection;
178      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
179         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
180         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
181         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
182    o pkg/diagnostics:
183      - add diags for T & S tendency which goes through Adams-Bashforth.
184    
185    checkpoint63f (2011/11/30)
186    o pkg/obcs/obcs_calc_stevens.F:
187      - join some loops to reduce number of if-statements
188      - fix a bug in code for northern and southern boundaries.
189    o pkg/seaice/seaice_init_varia.F
190      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
191        caused zero ice-velocities for the B-grid code
192    o pkg/seaice/seaice_init_fixed.F
193      - fix a bug in the initialisation of the second metric terms
194        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
195      - this affects all seaice configurations with useCurviLinearGrid = .true.
196        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
197        = .true. (default)
198      - the only verification experiment affected is global_ocean.cs32x15:
199        icedyn, seaice, and seaice_dynmix (AD)
200    o pkg/thsice/thsice_diagnostics_state.F
201      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
202        not contain garbage that can lead to surprises in diagstats_calc.F
203    o model/src:
204      - move bi,bj loops inside INTEGR_CONTINUITY ;
205      - call INTEGR_CONTINUITY directly from forward_step.F
206        (previously called from momentum_correction_step.F)
207      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
208        forward_step.F and pkg/ecco/the_main_loop.F
209    o model/src/do_oceanic_phys.F:
210      - reset addMass to zero only if useICEFRONT ;
211      - separated k-loop for rhoInSitu calculation ;
212      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
213        and at constant T,S (= WdRHOdP);
214      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
215        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
216        transport of locally-referenced potential density);
217        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
218    o gluemnc:
219      - replace ncrcat with ncks when adding variables to *.glob.nc
220      - change the way variables without record dimensions are handled so that
221        files that have variables with and without record variables can be glued:
222        add a record dimension with a new unique name to be able to differentiate
223        between variable with and without a-prior record dimensions. Remove
224        this record dimension before adding the variable to the *.glob.nc file.
225        This procedure automatically works also for grid.*.nc files that do not
226        have any record dimension.
227    o verification/cpl_aim+ocn:
228      - generate new reference output on baudelaire (gfortran, mpich2) (previously
229        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
230    o pkg/obcs/obcs_calc_stevens.F:
231      - add code for northern and southern boundaries.
232      - reorder some loops to save some operations and so that drFBar can be scalar
233    o model/src:
234      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
235        truncation) and add diagnostics for Adams-Bashforth tendency increment.
236      - update test-exp. AD output:
237        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
238      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
239        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
240        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
241        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
242        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
243        tutorial_plume_on_slope.
244    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
245      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
246      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
247      does not even come with an F77 compiler anymore, this should not be
248      a limitation
249    
250    checkpoint63e (2011/11/06)
251    o pkg/seaice adjoint of LSR:
252      - substantially rework STORE dirs.
253      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
254        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
255        and only perform SOLV_MAX_FIXED adjoint iters.
256        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
257        always goes to same record, meaning that the last forward field will be
258        the one used in the adjoint - an approximation.
259      - now produces non-zero LSR-related gradients, and acceptable gradients for
260        An's zonal (x-z) test case (to be checked in)
261      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
262        (but these are screwed up by the thermodynamics in the first place);
263        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
264        output_adm.txt also reflects changes to seaice_lsr
265      - global_ocean.cs32x15:
266        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
267          (output_adm.seaice.txt was updated)
268        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
269          (output_adm.seaice_dynmix.txt)
270    o test-exp. exp4+stevens:
271      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
272    o pkg/seaice (lsr solver):
273      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
274        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
275      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
276      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
277        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
278      - compute (with new S/R) and print initial (+ free-driff sol. if available)
279        and final residual of linearised system.
280    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
281      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
282    o pkg/obcs: Stevens BCs (still only for east and west)
283      - fix Stevens BCs by using intermediate velocities of previous
284        time step as "baroclinic" contribution rather velocity of one grid cell
285        inside the boundaries; more consistent but makes the entire treatment
286        more complicated, requires new pickup files and two new S/Rs:
287        obcs_copy_uv_n and obcs_save_uv_n
288        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
289        (undefined by default)
290      - silently move computation of some grid factors into separate loops to
291        save some recomputations
292      - add a hack for non-linear free surface
293      - add a verification experiment to exp4 that tests this code
294    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
295    
296    checkpoint63d (2011/10/25)
297    o pkg/obcs + seaice-dynamics:
298      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
299        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
300        values (consistent with an implicit method).
301      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
302        return to older implementation (same results as before); note that none of
303        the "experimental" OBCS_SEAICE options are implemented in the new version.
304      - switch test exp. seaice_obcs to use new version (update output).
305    o pkg/seaice:
306      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
307      - add parenthesis in Water-Ice drag calculations (evp & lsr);
308      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
309        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
310      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
311        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
312    o pkg/layers:
313      - Include potential density as new coordinate (Thanks to David Munday)
314    o pkg/dic:
315      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
316        carbonate computation/output to CALC_PCO2_APPROX
317    o pkg/generic_advdiff
318      - make TAF generate code that vectorizes:
319        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
320    o model/src:
321      - improve vectorization also for adjoint code of
322        solve_tridiagonal and solve_pentadiagonal. As this requires up to
323        5 new 3D-fields, this code is only turned on for the combination of
324        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
325        for singular matrix check (only for TARGET_NEC_SX).
326      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
327        ALLOW_AUTODIFF. This flag now needs to be set outside of
328        solve_tri/pentadiagonal.F
329    o pkg/exf:
330      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
331        optional namelist EXF_NML_OBCS).
332      - add many debug-print (to trace down where pkg/cal error msg comes from)
333    o pkg/mom_vecinv/mom_vi_hdissip.F
334      - rearrange loops so that vectorization is improved and in particular
335        the adjoint routine vectorizes. The code is a little longer now, but I
336        think easier to read.
337        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
338    o pkg/seaice:
339      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
340    o pkg/exch2:
341      - alternative code (without tile x tile matrix) for cumulated (global) sum;
342        used as default; keep using matrix version in adjustment.cs-32x32x1.
343    o tools/build_options:
344      - after merging some MPI and/or multi-threads specific optfiles so that
345        the modified default optfile support both built (using genmake2 -mpi
346        for the MPI built, using genmake2 -omp for OpenMP built),
347        move now obsolete optfiles to tools/build_options/unsupported/
348       (add copy of email sent to support list in doc/optfiles_changes.txt)
349    
350    checkpoint63c (2011/09/28)
351    o pkg/ebm:
352      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
353        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
354    o pkg/seaice (SItracer pickup)
355    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
356      To be done:
357      - thorough testing of missing fields in S/R seaice_read_pickup
358      - thorough matching between generic tracers and specific fields used
359        (e.g. volume-weighted age, area-weighted age, salinity, ...)
360    o pkg/grdchk:
361      - all procs calculate and print finite-difference gradient (for testreport)
362      - change description output used by testreport;
363      - AD testing: also compare and report Finite-difference gradient;
364        => update all output_adm*.txt
365    o test exp. global_ocean_ebm:
366      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
367        and turn on exactConserve; update (fwd) output.
368    o pkg/seaice (LSR):
369      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
370      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
371        * identical results with non-CS topology (but save up to half of EXCH calls)
372        * no much changes in cs-32 verification tests since no ice at face edges
373         (differences due to convergence criteria, since nb of iterations changed)
374        * expect some differences on lat-lon-cap grid.
375        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
376    o pkg/exch2:
377      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
378        many tiles); until alternative coding is added, just add a stop.
379    o pkg/kpp:
380      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
381        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
382    o optfiles:
383      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
384        into corresponding standard one, which now support different build:
385        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
386      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
387    o pkg/obcs (seaice):
388      - add missing EXCH for uIce,vIce after applying OBCS;
389      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
390        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
391        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
392      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
393      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
394        and eedata.mth for MPI and mutlti-threaded testing.
395    o pkg/flt:
396      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
397      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
398      - fix pickup and trajectories + profiles output with multi-threads;
399      - add parameter to select group of fields to write along trajectory and
400        profile (default unchanged);
401      - only call PORT_RAND* function when flt_noise <> 0;
402      - add multi-threaded test for verification exp. flt_example.
403    o eesupp/src:
404      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
405      - USE_OMP_THREADING: check that number of threads (from eedata) matches
406        actual number (from env.var. setting).
407    o pkg/ebm:
408      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
409      - add multi-threaded test for verification exp. global_ocean_ebm
410    
411    checkpoint63b (2011/08/29)
412    o pkg/ebm:
413      - fix sign of runoff;
414      - update directly forcing fields (Qnet,EmPmR) to use standard
415        external_forcing_surf.F (remove ebm_forcing_surf.F);
416      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
417      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
418        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
419      - update global_ocean_ebm parameters file data and update output (fwd+ad).
420    o verification/matrix_example:
421      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
422        MPI and mutlti-threaded testing.
423    o pkg/matrix:
424      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
425      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
426      - fix for multi-threaded (remove DATA statement);
427      - use standard DIFFERENT_MULTIPLE function;
428      - add MATRIX_OPTIONS.h
429    o verification/matrix_example:
430       To allow to split the domain in several tiles, change the domain size
431        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
432        Western side) of land points.
433    o (*_)write_pickup:
434      - fix few bugs in mypackage_read/write_pickup.F
435      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
436        array of length 1 (was caught by compiler syntax-check).
437    o pkg/diagnostics (velocity potential solver):
438      - fix initialisation of main diagonal matrix (for overlap values)
439    o tools/build_options:
440      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
441        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
442      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
443        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
444        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
445        and use "-devel" testreport option for standard testing on baudelaire.
446    o pkg/grdchk:
447      - Assume that all gradient-check position are within the same tile
448        corresponding to global indices (iGloTile,jGloTile) and that
449        positions (i,j indices or nbeg) are local to this tile;
450      - set tile local-indices and proc. number according to tile global-indices;
451      - remove grdchkwhichproc from namelist (retired param);
452      - send adjoint gradient to all procs so that all procs print it to STDOUT;
453      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
454    o adding package bbl (Bottom Boundary Layer)
455      description in MITgcm/pkg/bbl/bbl_description.tex
456      example/test experiment in MITgcm_contrib/bbl
457    o adjoint verifications
458      - changed 5 experiments to multi-tiles
459        * global_ocean.90x40x15
460        * obcs_ctrl
461        * offline_exf_seaice
462        * tutorial_dic_adjoffline
463        * tutorial_tracer_adjsens
464        changed reference output for those that crossed tile boundaries
465        (changed choices of gradient check positions)
466      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
467      - temporary bug fix in grdchk_loc.F for obcs
468    o genmake2 & testreport
469      - add target "obj" (just for OBJFILES files) to Makefile;
470      - add option to specify FEXTRAFLAGS on command line.
471    o pkg/mypackage:
472      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
473    
474    checkpoint63a (2011/08/02)
475    o pkg/diagnostics (velocity potential):
476      - fix velocity-potential calculation when using OBCS: balance net inflow
477        at each level (new S/R OBCS_DIAG_BALANCE).
478      - fix some of the problems with OBCS in stream-function calculation.
479    o pkg/exf/exf_readparms.F
480      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
481        EXF_NML_OBCS) more consistent, so that you need not have these lists
482        in data.exf when they are not used.
483    o optim/optim_readdata.F:
484      - add some output about obcs variables that might help debugging
485      - add a check about nvarlength
486    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
487    o pkg/diagnostics (velocity potential):
488      - fix mask for OBCS (still problems in stream-function with OBCS);
489      - add specific parameter (default = main code CG2D params) for solver;
490      - in case of poor convergence, use solution corresponding to lowest residual.
491    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
492      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
493      and should be avoided where possible.
494    o model/src (rStar):
495      - include r* effect on reference-state (PhiRef) in totPhiHyd
496        (so that it's really the potential anomaly at the cell center);
497        affect solution only if z* with full pressure in EOS.
498      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
499        update output (because of z* in totPhiHyd and viscA4 changes);
500      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
501        @ constant r) until interpolation at constant r is implemented.
502    o pkg/diagnostics
503      - fix RCENTER diagnostics in case cell center is not at interface middle
504    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
505      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
506      that THETA and SALT are "conservative temperature" and "absolute
507      salinity"
508    o pkg/ctrl
509      - fix computation of endrec in s/r ctrl_init_rec
510      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
511    o pkg/seaice/seaice_growth.F
512      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
513        remove then obsolete STORE directives
514      - fix STORE directives for tice and tices, so that only the
515        appropriate part of the fields are stored (and not the entire
516        field); update global_ocean.cs32x15.seaice AD output.
517      - cosmetic changes: adjust CPP flags and indentation for better
518        legibilty
519    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
520      Chris Wilson)
521    o pkg/gmredi:
522       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
523       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
524    
525    checkpoint63  (2011/07/11)
526    o pkg/exch2:
527     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
528     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
529       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
530       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
531    o pkg/diagnostics:
532     - deal with pairs of post-processed diags which are computed together; in
533       particular, re-order list of diags within 1 file to save 2nd computation.
534     - add S/R to compute velocity stream-function (called after velocity-potential
535       calculation) from divergence free transport -> new diagnostics "PsiVEL".
536     - add parameter to select grid-point location where PsiVEL == 0.
537    o eesupp/src:
538       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
539       (specific S/R needed with exch2 topology - for now, just print an error msg)
540    o pkg/shelfice
541     - Implement friction velocity-dependent transfer coefficients following
542       Holland and Jenkins, JPO, 1999
543       Original code by M. Losch with small modifs.
544       Enable with CPP option SHI_ALLOW_GAMMAFRICT
545       and runtime flag SHELFICEuseGammaFrict
546    o verification lab_sea & global_ocean.cs32x15:
547     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
548       does not miss some dependencies (but is slower) and also works with many files
549       (default makedepend limitation for AD built).
550     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
551    o pkg/diagnostics:
552     - add run-time parameter "useMissingValue" (def=False) to fill land-point
553        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
554       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
555     - Extend the use of "missing_value" setting from data.diagnostics for the case
556       of counter-diagnostics (where fraction-weight is zero). This applies both to
557       MNC and MDS output files.
558    o pkg/seaice/seaice_growth.F:
559      - add 'a priori' cap of latent heat flux based on actual mass considerations
560        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
561        non-legacy seaice_solve4temp.
562      - add diagnostic of the residual sublimation freshwater flux (the freshwater
563        flux taken from the ocean if the total actual latent heat fluxes exceed
564        the maximum)
565      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
566       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
567      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
568       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
569      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
570      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
571    o verification 1D_ocean_ice_column:
572       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
573       update results
574    o pkg/diagnostics:
575     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
576       which are not filled-up but computed from other diags ; In this case, the mate
577       diag points to the primary (filled-up) diag to used for post processing.
578     - Update Velocity-potential computation using post-processed diag framework.
579     ==> Change the ordering of fields and time-periods in MDS output file
580       when using periodic averaging: now writes one time record with the full set
581       of fields for this time period, then the next time reccord (it used to be
582       one field with the full set of time records then the next field).
583         Note: this is now similar to NetCDF (MNC) output file. <==
584    
585    checkpoint62z (2011/06/21)
586    o adjoint monitor:
587     - Add adjoint monitor output for packages exf, seaice
588       and update relevant testreport output
589    o pkg/seaice:
590     - re-order diags inits so that they appear in order in available_diagnostics.log
591     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
592       area/heff/hsnow preceeding thermodynamic growth/melt.
593     - modified diag: SIdA; output actual effect, as the description states.
594     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
595     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
596       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
597        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
598     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
599     - added diagnostics for seaice generic tracers (SItr*).
600     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
601     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
602     I. Fenty: 18-Jun-2011:
603     Minor changes to seaice package:
604     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
605        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
606       - Differentiated "regularization variables" from "floor variables"
607        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
608        * hiceMin became SEAICE_hice_reg (old hiceMin)
609          (with _reg meaning regularization variable)
610       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
611        so as to ensure energy conservation when going between phases
612      - A22 was not used anywhere
613     2) Changed regularization procedure for heffActual and hsnowActual to ensure
614        well-boundedness and smooth adjoint in seaice_growth.F
615     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
616        because the old regularization always set heffActual >= 0.05 cm
617     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
618        on AREA when HEFF > 0.
619      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
620        requiring that DISABLE_AREA_FLOOR *not* be defined
621     Affected verifications:
622      - 1D_ocean_ice_column (output.txt output_adm.txt)
623      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
624    o pkg/diagnostics:
625      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
626      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
627        (was _RL, now integer) with option = 0 to retrieve all levels.
628      - add pieces of code to compute velocity potential at each level (new diagnostics
629        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
630        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
631      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
632        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
633        and in diagnostics_fract_fill.F (do not need a valid pointer for the
634        diagnostics counter-mate); check that definition of counter-diagnostic
635        includes a valid counter-mate (in diagnostics_set_levels.F).
636    o model/src (rStar):
637      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
638        affect solution only if z* with full pressure in EOS;
639        update output of test-exp global_ocean.90x40x15.
640    o pkg/seaice:
641      - introduce siEps=1e-5 parameter
642      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
643      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
644      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
645        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
646        as well as ice cover age and ridging index (attached to AREA).
647        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
648        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
649        Up to SItrMaxNum=3 tracers can be used simultaneously.
650    o pkg/salt_plume:
651      -introduce SPsalFRAC run time parameter that sets the fraction of the
652       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
653       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
654    o model debug options:
655      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
656        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
657      - Refine debug-msg printing selection (3 new levels):
658        debugMode  : controls printing of debug messages (sequence of S/R calls).
659        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
660         debLevZero =  0 ; /* level of disabled aux. msg printing */
661         debLevA =  1 ; /* level of minimum  aux. msg printing */
662         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
663         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
664         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
665         debLevE =  5 ; /* level of extensive debug printing */
666        New debugLevel default: with default debugMode value (=F),
667          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
668          and if debugMode=T, default debugLevel = 4 (debLevD).
669        Relation with previous settings:
670         debLevB (=2) corresponds to former debLevA (=1)
671         debLevD (=4) corresponds to former debLevB (=2)
672        Note:
673         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
674         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
675            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
676      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
677        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
678    o pkg/obcs:
679      - change OBCSfixTopo default from True to False (should not change the results);
680        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
681    o pkg/thsice:
682      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
683        2nd layer seaice sublimation (unlikely to happen)
684      - use Interior mask for OBCS in thsice_advection.F (similar to what is
685        done in gad_advection & seaice_advection).
686    o adjoint:
687      bug fix spotted by Gael Forget:
688      seaice_advection and thsice_advection still had
689      legacy CPP options to avoid CS corner updates for adjoint
690    o pkg/seaice:
691      => Change some of the defaults (2011/05/29):
692         - change SEAICEuseFluxForm default (from False to True)
693         - change DIFF1 default (from 0.004 m/s to 0. m/s)
694         And print warnings if DIFF1 is not set in data.seaice and centered
695          avection scheme is used without any diffusion.
696      also:
697      - fix seaice_diffusion calls in default AdvScheme part of seaice_advdiff.F;
698      - set SEAICEdiffKh[] default in the same way as SEAICEadvSch[]
699      - stop if DIFF1<>0 with SEAICEadvScheme <> 2, if DIFF1<>0 with any
700        other non-zero SEAICEdiffKh[] diffusivity, if SEAICEadvSalt=T with
701        #undef SEAICE_VARIABLE_SALINITY, if SEAICEadvAge=T with #undef SEAICE_AGE.
702      update results of test exp.:
703         lab_sea: output.fd (switch to AdvScheme=33 with diffKh=20)
704             output.hb87, output_adm.evp (SEAICEuseFluxForm=T and diffKh=200)
705             output_adm.noseaicedyn (SEAICEuseFluxForm=T)
706         offline_exf_seaice: output.seaicetd, output_adm (SEAICEuseFluxForm=T)
707         seaice_obcs: output (SEAICEuseFluxForm=T)
708      and prescribe old default for SEAICEuseFluxForm (=F) and DIFF1 (=0.004)
709          for standard fwd & AD lab_sea tests (to keep the same output).
710  o pkg/seaice/seaice_growth.F:  o pkg/seaice/seaice_growth.F:
711    - use Ian Fenty's capping formulas for actual ice    - use Ian Fenty's capping formulas for actual ice
712    thickness thoughout EVOLUTION branch.    thickness thoughout EVOLUTION branch.
713    - put treatment pathological case #2) in CPP brackets    - put treatment pathological case #2) in CPP brackets
714    (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).    (ALLOW_AVOID_INFINITESIMAL_AREA, undef by default).
715    - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.      - update global_ocean.cs32x15 and 1D_ocean_ice_colum results accordingly.
716  o pkg/seaice:  o pkg/seaice:
717    - seaice_diffusion.F : remove the min(DX,DY) factor permanently;    - seaice_diffusion.F : remove the min(DX,DY) factor permanently;
718    pass the Laplacian diffusivity (in m/s2) diffKh as a parameter;    pass the Laplacian diffusivity (in m^2/s) diffKh as a parameter;
719    also pass fac as a param, which can be 1. (to update the tendency    also pass fac as a param, which can be 1. (to update the tendency
720    field) or the time step (to update the field itself).    field) or the time step (to update the field itself).
721    - seaice_advdiff.F: for multidim, call seaice_diffusion with    - seaice_advdiff.F: for multidim, call seaice_diffusion with
722    e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call    e.g. SEAICEdiffKhHeff and with fac=1; for single-dim, call
723    seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.    seaice_diffusion with e.g. SEAICEdiffKhHeff and with fac=time step.
724    - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :    - SEAICE_PARAMS.h, seaice_readparms.F, seaice_check.F :
725    hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.    hooks to handle SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.
   - note: if any of SEAICEdiffKhHeff, SEAICEdiffKhArea, etc.  
   is specified to be >0, then DIFF1 is set to 0.  
726  o pkg/seaice:  o pkg/seaice:
727    diffusion with centered advection scheme (diffus.F & advect.F):    diffusion with centered advection scheme (diffus.F & advect.F):
728    - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)    - simplify S/R DIFFUS (put deltaT & DIFF1 factor outside, move EXCH outside)
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