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revision 1.1484 by jmc, Mon Aug 1 20:47:39 2011 UTC revision 1.1587 by jmc, Thu Feb 2 02:06:32 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/seaice/seaice_solve4temp.F (SOLVE4TEMP_LEGACY undef):
8      - remove from F_ia (and from it's derivative dFiDTs1) the contribution of
9        conductive heat flux F_c , and add it explicitly when updating tsurf as
10        solution of: Fc = Fia + d/dT(Fia - Fc) *delta.tsurf
11        so that now F_ia has a consistent meaning through the entire routine.
12        This causes differences at truncation level: update output of fwd exp.
13        global_ocean.cs32x15.seaice.
14    o pkg/seaice:
15      - lots of editing/cleaning in seaice_solve4temp.F + better documentation
16        of arrays, sign/direction of fluxes; no effect on results.
17      - replace hard coded 273.16 (=previous value of celsius2K) by celsius2K
18        in seaice_budget_ocean.F & seaice_solve4temp.F (SOLVE4TEMP_LEGACY part);
19        note: this should have been done before changing celsius2K default.
20      - to keep results unchanged, add back old value of celsius2K in verification
21        exp. input*/data : lab_sea (AD), offline_exf_seaice (fwd+AD) & seaice_obcs
22      - replace hard coded seawater freezing temp in seaice_solve4temp.F (part
23        SOLVE4TEMP_LEGACY) of 271.20 (=previous value of celsius2K + default
24        value of SEAICE_freeze) by celsius2K+SEAICE_freeze so that seawater
25        freezing temp is consistent with value in seaice_growth.F ; this causes
26        differences at machine truncation level: update lab_sea AD output (3/4).
27    o pkg/seaice:
28      - mask (in exf_init_fixed.F) atemp,aqh,evap,precip,runoff,lwflx,areamask
29        and climsst/sss even when using seaice (to prevent calculation that might
30        use SST on land); does not affect any verification exp.
31      - apply mask to taux,tauy (in seaice_get_dynforcing.F); update output
32        of lab_sea.fd & lab_sea.hb87 and global_ocean.cs32x15.seaice_dynmix.
33    o pkg/seaice/seaice_growth.F: add mask to avoid non-zero ice thickness
34      over land (non-legacy code)
35    o vectorize salt_plume package:
36      - add extra code to salt_plume_frac and salt_plume_tendency_apply_s
37      - this code computes plumebk everywhere (also over land), thus requires
38        code to avoid divisions by zero and catch the case of kLev=Nr.
39      - efficiency of salt_plume_frac is still sub-optimal
40    o tools (genmake2):
41      - fix makefile NAME specification (option: -makefile NAME) by adding
42        "-f $MAKEFILE" in few places where it was missing including makedepend
43        command (contribution from Paul).
44    
45    checkpoint63i (2012/01/24)
46    o model/src:
47      - add factorized versions of some EOS code to find_rho.F,
48        define USE_FACTORIZED_EOS to turn it on (default for TARGET_NEC_SX)
49    o model/src:
50      - add celsius2K to namelist PARM01; remove unused recip_rhoNil from PARAMS.h;
51      - change default celsius2K from 273.16 to 273.15
52      - to keep results unchanged, add back old value of celsius2K in verification
53        exp. input*/data : aim.5l_cs, 1D_ocean_ice_column, lab_sea (fwd),
54         global_ocean.cs32x15(seaice) & cpl_aim+ocn(input_atm).
55    o model/src: add a little initialisation trick to find_rho.F and find_alpha.F
56      to make TAF generate vectorizable code
57    o pkg/seaice/seaice_evp.F: add code (copied from CICE) that avoids underflows.
58       Turn on by defining SEAICE_EVP_ELIMINATE_UNDERFLOWS. Most compilers
59       have flags that do this more efficiently.
60    o pkg/diagnostics/diagstats_calc.F
61      - for TARGET_NEC_SX fix the treatment of the scaling factor tmpFac=scaleFact
62    o pkg/obcs (with exch2):
63      - derive OB indices in overlap region from OB-InsideMask (in obcs_init_fixed.F)
64        and remove code (in obcs_readparms.F) which was based on EXCH of indices
65        (through buffer) and did not account for exch2 (e.g., CS-grid) topology.
66    o pkg/exf and seaice exp:
67      - change offline_exf_seaice.seaicetd test exp. to use default DIFF1 value (=0)
68        so that switching off area & heff advection flags does not affect results.
69      - change default EXF_LWDOWN_WITH_EMISSIVITY to #define in EXF_OPTIONS.h
70      - keep exp. seaice_obcs & 1D_ocean_ice_column(ad) unchanged (using #undef
71        EXF_LWDOWN_WITH_EMISSIVITY) and, using pkg/exf default emissivities, update
72        results of verification experiments: 1D_ocean_ice_column(fwd),
73        global_ocean.cs32x15.seaice(fwd+ad) & seaice_dynmix(ad), lab_sea (all 8)
74        and offline_exf_seaice (all 4).
75    o pkg/seaice:
76      - remove array YNEG, RIVER, TMIX (replaced by local var) from common block;
77        remove also areaNm1 & hEffNm1 when SEAICE_GROWTH_LEGACY is undef.
78      - fix bug: areaNm1 & hEffNm1 are needed in seaice_growth (SEAICE_GROWTH_LEGACY)
79        but were not filled when resp. SEAICEadvArea=F & SEAICEadvHeff=F and
80        not multi-dim advection;
81      - fix seaice_growth.F to compile with both SEAICE_GROWTH_LEGACY and
82        SHORTWAVE_HEATING #undef.
83    o optim: make Makefile more robust (?)
84    o pkg/obcs:
85      * fix treatment of obcs_read_pickup for TAF
86    o pkg/shelfice:
87      * add missing initialisation of num_shifwflx
88      * new adjoint verification exp. for isomip
89      * change Prandtl and Schmidt numbers from generic formulations
90        (in terms of model diffus. and visc.) to separate runtime
91        parameters, with Holland and Jenkins (1999) default values.
92    o pkg/exf (interpolation):
93      - extended input field (2 rows) near the N & S poles:
94        * fill in with the symetric value (when even Nb of data in longitude)
95        * add average value at the poles only for scalar quantities ; for vector
96          component interpolation, skip the averaging and keep duplicated values,
97          unless the 2 components have same location (uvInterp=T) in which case
98          interpolate the 2 components together using S/R EXF_INTERP_UV.
99      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
100        together: this allows to account properly for local orientation when
101        averaging at N & S pole.
102      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
103        exf-interpolation near N & S poles. Undef by default.
104      - add debug check/print on 1rst iter if debugLevel >=2.
105    o pkg/exf:
106      - change masking flags definition (no longer "parameter"), put them in
107        common block and set them in S/R EXF_INIT_FIXED.
108      - change recognized masking flag from s,u,v to c,w,s since the mask
109        to use (maskC,W,S) depends on position on model grid and has little to
110        do with scalar/vector difference; fix masking if using P-coordinates.
111      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
112        and update results of exp. global_with_exf (x2).
113      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
114    o pkg/obcs
115      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
116    o pkg/exf (interpolation):
117      - assume periodicity in X only if input field cover full longitude range.
118      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
119        and should vectorise).
120      - fix input lat of the 2 added row (in case we provide N.pole data).
121    
122    checkpoint63h (2011/12/30)
123    o pkg/seaice:
124      - change declaration of UVM from _RL to _RS in order to get B-grid
125        uIce,vIce monitor when _RS = real*4
126    o pkg/offline:
127      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
128      - compute vertical velocity if not read from file (switch on exactConserv
129        & staggerTimeStep);
130      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
131    o verification:
132      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
133        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
134        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
135      - update output of exp. global_ocean.cs32x15.viscA4 after changing
136        grid-file angles (used here for coriolis-3d);
137      - remove (or gzip) few files not needed to run fizhi-cs experiments.
138    o pkg/exf (vector interpolation):
139      - rotate vector component toward local grid-axis orientation using grid-angles
140        (stored in GRID.h) instead of locally computed rotation angle; keep old code
141        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
142    o pkg/seaice:
143      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
144        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
145    o pkg/PKG_OPTIONS.h files:
146      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
147        outside of the #ifdef ALLOW_THISPKG / #endif block.
148      - update verification/*/code/PKG_OPTIONS.h files.
149    o add a verification experiment (offline_exf_seaice/input.seaice) that test
150      the B-grid LSOR solver
151    o pkg/seaice: sort out emissivity and long wave radiation step 2:
152      - add emissivity for snow and ice as new run-time parameters
153        (unfortunately) that default to the corresponding exf values; this
154        changes results in most verification experiments so that for backward
155        compatibility these parameter have to be set explicitly to inconsistent
156        values (ugly);
157      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
158        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
159        until we agree how to handle this bug properly
160    o pkg/exf (interpolation):
161      - add a set of run-time param ({inputfield}_interpMethod), one for
162        each interpolated input field, to select the interpolation method
163        with a value of zero switching off the interpolation;
164      - print interpolation parameters to standard output;
165      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
166        (to use instead runoff_interpMethod=0 in data.exf).
167      - simplify default setting of interpolation parameters (for all fields,
168        set position to match model grid cell-center position, leading to trivial
169        interpolation in case of regular Lat-Lon grid) and fix for the case of
170        non-uniform delY.
171    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
172       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
173       this factor is absolutely required, because the lw exitance (= out-going
174       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
175       where the reflectivity rho = 1-emissivity for conservation reasons. Once
176       this is established, we can remove the CPP-Flag (if we want to).
177    o pkg/seaice:
178      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
179        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
180      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
181        what the name implies (and not emissivity*BoltzmannConstant), this means
182        the old default value of 5.5e-8 now means
183        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
184        S/R exf_readparms
185      - FV-discretization of the B-grid LSOR solver, turn on with
186        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
187        of the calling routine dynsolver, so that B and C-grid code look a
188        little more alike.
189      - fix index bugs in ostres.F (B-grid code)
190    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
191    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
192      default for SEAICE_emissivity, if useEXF; requires setting a wrong
193      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
194      backward compatiblity
195    o model/src: use sigmaR in calc_ivdc
196    
197    checkpoint63g (2011/12/16)
198    o pkg/seaice/seaice_growth.F:
199      fix heat conservation of the coupled ocean-seaice system.
200      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
201      solid vs liquid water treatment is resolved via QNET.
202    o pkg/seaice/seaice_growth.F:
203      add missing term for sublimation in saltFlux, which was breaking conservation.
204    o pkg/seaice/seaice_model.F:
205      Remove this patholigical case treatment in evolution branch,
206      where it is un-necessary and breaks conservation.
207      Update global_ocean.cs32x15/results accordingly for
208      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
209    o model/src:
210      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
211      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
212    o pkg/obcs:
213      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
214      tendency for temperature and salinity that is then applied to update
215      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
216      horizontal advection and diffusion contributions on the boundary (in
217      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
218      removing the mask in S/R timestep_tracer. The advantage of this approach is
219      that the updated tracer values include contributions from the surface
220      forcing and vertical diffusion.
221      This modification changes exp4.stevens because of vertical diffusion.
222    o model/src:
223      change non-curvilinear grid setting to also work with exch2 + blank tiles:
224      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
225        face dimensions.
226      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
227        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
228        and INI_SPHERICAL_POLAR_GRID.
229      change test-experiment global_ocean.90x40x15:
230      - split the domain in many more tiles (9x4 tiles of 10x10 each);
231      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
232      - update results of both test (std & dwnslp).
233    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
234       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
235    o model/src:
236      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
237        and fix initialisation when using sigma-coords.
238    o model/src:
239     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
240       to their current value at the beginning of forward_step.F": add a new run-time
241       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
242     - set doResetHFactors=T in the following test exp:
243        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
244        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
245        and tutorial_global_oce_in_p (nonLinFS in p)
246    o pkg/ecco
247      - added IES cost term
248    o verification/advect_xz
249      - scale down the depth by 1/100 (from 200 km to just 2.km)
250      - add secondary test using divergent flow, r-star and implicit vertical advection.
251      - add note (check_conserve_TS.txt) and matlab script to check global
252        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
253    o pkg/rbcs:
254      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
255    o pkg/obcs (Stevens BCs):
256      - fix various problems in the phase speed computations of the Stevens
257        boundary conditions:
258        - sign error for western and southern boundaries,
259        - time tendencies were underestimated by factor of dTracerLev and some just
260          zero (for multidim advection schemes) -> now estimate time tendencies
261          from difference between previous (n) time level and the one before (n-1);
262          this requires storing a field per tracer per boundary, also in the pickup
263          files.
264        - replace deltaTmom in cflMer/Zon computation with dTracerLev
265        - set default phase velocity to cflMer/Zon
266      - update verification experiment exp4.stevens
267    o pkg/generic_advdiff (implicit_r):
268      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
269        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
270      - fix implicit vertical diffusion or advection with NonLin FreeSurf
271        (was using current recip_hFacC instead of future recip_hFacC): set future
272        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
273        solver S/R ;
274      - fill diagnostics of vertical advective fluxes (computed from tendency)
275        when using implicit vert. advection;
276      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
277         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
278         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
279         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
280    o pkg/diagnostics:
281      - add diags for T & S tendency which goes through Adams-Bashforth.
282    
283    checkpoint63f (2011/11/30)
284    o pkg/obcs/obcs_calc_stevens.F:
285      - join some loops to reduce number of if-statements
286      - fix a bug in code for northern and southern boundaries.
287    o pkg/seaice/seaice_init_varia.F
288      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
289        caused zero ice-velocities for the B-grid code
290    o pkg/seaice/seaice_init_fixed.F
291      - fix a bug in the initialisation of the second metric terms
292        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
293      - this affects all seaice configurations with useCurviLinearGrid = .true.
294        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
295        = .true. (default)
296      - the only verification experiment affected is global_ocean.cs32x15:
297        icedyn, seaice, and seaice_dynmix (AD)
298    o pkg/thsice/thsice_diagnostics_state.F
299      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
300        not contain garbage that can lead to surprises in diagstats_calc.F
301    o model/src:
302      - move bi,bj loops inside INTEGR_CONTINUITY ;
303      - call INTEGR_CONTINUITY directly from forward_step.F
304        (previously called from momentum_correction_step.F)
305      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
306        forward_step.F and pkg/ecco/the_main_loop.F
307    o model/src/do_oceanic_phys.F:
308      - reset addMass to zero only if useICEFRONT ;
309      - separated k-loop for rhoInSitu calculation ;
310      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
311        and at constant T,S (= WdRHOdP);
312      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
313        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
314        transport of locally-referenced potential density);
315        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
316    o gluemnc:
317      - replace ncrcat with ncks when adding variables to *.glob.nc
318      - change the way variables without record dimensions are handled so that
319        files that have variables with and without record variables can be glued:
320        add a record dimension with a new unique name to be able to differentiate
321        between variable with and without a-prior record dimensions. Remove
322        this record dimension before adding the variable to the *.glob.nc file.
323        This procedure automatically works also for grid.*.nc files that do not
324        have any record dimension.
325    o verification/cpl_aim+ocn:
326      - generate new reference output on baudelaire (gfortran, mpich2) (previously
327        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
328    o pkg/obcs/obcs_calc_stevens.F:
329      - add code for northern and southern boundaries.
330      - reorder some loops to save some operations and so that drFBar can be scalar
331    o model/src:
332      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
333        truncation) and add diagnostics for Adams-Bashforth tendency increment.
334      - update test-exp. AD output:
335        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
336      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
337        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
338        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
339        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
340        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
341        tutorial_plume_on_slope.
342    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
343      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
344      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
345      does not even come with an F77 compiler anymore, this should not be
346      a limitation
347    
348    checkpoint63e (2011/11/06)
349    o pkg/seaice adjoint of LSR:
350      - substantially rework STORE dirs.
351      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
352        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
353        and only perform SOLV_MAX_FIXED adjoint iters.
354        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
355        always goes to same record, meaning that the last forward field will be
356        the one used in the adjoint - an approximation.
357      - now produces non-zero LSR-related gradients, and acceptable gradients for
358        An's zonal (x-z) test case (to be checked in)
359      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
360        (but these are screwed up by the thermodynamics in the first place);
361        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
362        output_adm.txt also reflects changes to seaice_lsr
363      - global_ocean.cs32x15:
364        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
365          (output_adm.seaice.txt was updated)
366        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
367          (output_adm.seaice_dynmix.txt)
368    o test-exp. exp4+stevens:
369      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
370    o pkg/seaice (lsr solver):
371      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
372        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
373      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
374      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
375        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
376      - compute (with new S/R) and print initial (+ free-driff sol. if available)
377        and final residual of linearised system.
378    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
379      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
380    o pkg/obcs: Stevens BCs (still only for east and west)
381      - fix Stevens BCs by using intermediate velocities of previous
382        time step as "baroclinic" contribution rather velocity of one grid cell
383        inside the boundaries; more consistent but makes the entire treatment
384        more complicated, requires new pickup files and two new S/Rs:
385        obcs_copy_uv_n and obcs_save_uv_n
386        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
387        (undefined by default)
388      - silently move computation of some grid factors into separate loops to
389        save some recomputations
390      - add a hack for non-linear free surface
391      - add a verification experiment to exp4 that tests this code
392    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
393    
394    checkpoint63d (2011/10/25)
395    o pkg/obcs + seaice-dynamics:
396      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
397        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
398        values (consistent with an implicit method).
399      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
400        return to older implementation (same results as before); note that none of
401        the "experimental" OBCS_SEAICE options are implemented in the new version.
402      - switch test exp. seaice_obcs to use new version (update output).
403    o pkg/seaice:
404      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
405      - add parenthesis in Water-Ice drag calculations (evp & lsr);
406      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
407        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
408      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
409        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
410    o pkg/layers:
411      - Include potential density as new coordinate (Thanks to David Munday)
412    o pkg/dic:
413      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
414        carbonate computation/output to CALC_PCO2_APPROX
415    o pkg/generic_advdiff
416      - make TAF generate code that vectorizes:
417        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
418    o model/src:
419      - improve vectorization also for adjoint code of
420        solve_tridiagonal and solve_pentadiagonal. As this requires up to
421        5 new 3D-fields, this code is only turned on for the combination of
422        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
423        for singular matrix check (only for TARGET_NEC_SX).
424      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
425        ALLOW_AUTODIFF. This flag now needs to be set outside of
426        solve_tri/pentadiagonal.F
427    o pkg/exf:
428      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
429        optional namelist EXF_NML_OBCS).
430      - add many debug-print (to trace down where pkg/cal error msg comes from)
431    o pkg/mom_vecinv/mom_vi_hdissip.F
432      - rearrange loops so that vectorization is improved and in particular
433        the adjoint routine vectorizes. The code is a little longer now, but I
434        think easier to read.
435        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
436    o pkg/seaice:
437      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
438    o pkg/exch2:
439      - alternative code (without tile x tile matrix) for cumulated (global) sum;
440        used as default; keep using matrix version in adjustment.cs-32x32x1.
441    o tools/build_options:
442      - after merging some MPI and/or multi-threads specific optfiles so that
443        the modified default optfile support both built (using genmake2 -mpi
444        for the MPI built, using genmake2 -omp for OpenMP built),
445        move now obsolete optfiles to tools/build_options/unsupported/
446       (add copy of email sent to support list in doc/optfiles_changes.txt)
447    
448    checkpoint63c (2011/09/28)
449    o pkg/ebm:
450      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
451        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
452    o pkg/seaice (SItracer pickup)
453    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
454      To be done:
455      - thorough testing of missing fields in S/R seaice_read_pickup
456      - thorough matching between generic tracers and specific fields used
457        (e.g. volume-weighted age, area-weighted age, salinity, ...)
458    o pkg/grdchk:
459      - all procs calculate and print finite-difference gradient (for testreport)
460      - change description output used by testreport;
461      - AD testing: also compare and report Finite-difference gradient;
462        => update all output_adm*.txt
463    o test exp. global_ocean_ebm:
464      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
465        and turn on exactConserve; update (fwd) output.
466    o pkg/seaice (LSR):
467      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
468      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
469        * identical results with non-CS topology (but save up to half of EXCH calls)
470        * no much changes in cs-32 verification tests since no ice at face edges
471         (differences due to convergence criteria, since nb of iterations changed)
472        * expect some differences on lat-lon-cap grid.
473        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
474    o pkg/exch2:
475      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
476        many tiles); until alternative coding is added, just add a stop.
477    o pkg/kpp:
478      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
479        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
480    o optfiles:
481      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
482        into corresponding standard one, which now support different build:
483        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
484      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
485    o pkg/obcs (seaice):
486      - add missing EXCH for uIce,vIce after applying OBCS;
487      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
488        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
489        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
490      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
491      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
492        and eedata.mth for MPI and mutlti-threaded testing.
493    o pkg/flt:
494      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
495      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
496      - fix pickup and trajectories + profiles output with multi-threads;
497      - add parameter to select group of fields to write along trajectory and
498        profile (default unchanged);
499      - only call PORT_RAND* function when flt_noise <> 0;
500      - add multi-threaded test for verification exp. flt_example.
501    o eesupp/src:
502      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
503      - USE_OMP_THREADING: check that number of threads (from eedata) matches
504        actual number (from env.var. setting).
505    o pkg/ebm:
506      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
507      - add multi-threaded test for verification exp. global_ocean_ebm
508    
509    checkpoint63b (2011/08/29)
510    o pkg/ebm:
511      - fix sign of runoff;
512      - update directly forcing fields (Qnet,EmPmR) to use standard
513        external_forcing_surf.F (remove ebm_forcing_surf.F);
514      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
515      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
516        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
517      - update global_ocean_ebm parameters file data and update output (fwd+ad).
518    o verification/matrix_example:
519      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
520        MPI and mutlti-threaded testing.
521    o pkg/matrix:
522      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
523      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
524      - fix for multi-threaded (remove DATA statement);
525      - use standard DIFFERENT_MULTIPLE function;
526      - add MATRIX_OPTIONS.h
527    o verification/matrix_example:
528       To allow to split the domain in several tiles, change the domain size
529        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
530        Western side) of land points.
531    o (*_)write_pickup:
532      - fix few bugs in mypackage_read/write_pickup.F
533      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
534        array of length 1 (was caught by compiler syntax-check).
535    o pkg/diagnostics (velocity potential solver):
536      - fix initialisation of main diagonal matrix (for overlap values)
537    o tools/build_options:
538      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
539        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
540      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
541        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
542        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
543        and use "-devel" testreport option for standard testing on baudelaire.
544    o pkg/grdchk:
545      - Assume that all gradient-check position are within the same tile
546        corresponding to global indices (iGloTile,jGloTile) and that
547        positions (i,j indices or nbeg) are local to this tile;
548      - set tile local-indices and proc. number according to tile global-indices;
549      - remove grdchkwhichproc from namelist (retired param);
550      - send adjoint gradient to all procs so that all procs print it to STDOUT;
551      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
552    o adding package bbl (Bottom Boundary Layer)
553      description in MITgcm/pkg/bbl/bbl_description.tex
554      example/test experiment in MITgcm_contrib/bbl
555    o adjoint verifications
556      - changed 5 experiments to multi-tiles
557        * global_ocean.90x40x15
558        * obcs_ctrl
559        * offline_exf_seaice
560        * tutorial_dic_adjoffline
561        * tutorial_tracer_adjsens
562        changed reference output for those that crossed tile boundaries
563        (changed choices of gradient check positions)
564      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
565      - temporary bug fix in grdchk_loc.F for obcs
566    o genmake2 & testreport
567      - add target "obj" (just for OBJFILES files) to Makefile;
568      - add option to specify FEXTRAFLAGS on command line.
569    o pkg/mypackage:
570      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
571    
572    checkpoint63a (2011/08/02)
573  o pkg/diagnostics (velocity potential):  o pkg/diagnostics (velocity potential):
574    - fix velocity-potential calculation when using OBCS: balance net inflow    - fix velocity-potential calculation when using OBCS: balance net inflow
575      at each level (new S/R OBCS_DIAG_BALANCE).      at each level (new S/R OBCS_DIAG_BALANCE).
# Line 54  o pkg/gmredi: Line 620  o pkg/gmredi:
620     Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),     Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
621     and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)     and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
622    
623  checkpoint63 (2011/07/11)  checkpoint63  (2011/07/11)
624  o pkg/exch2:  o pkg/exch2:
625   - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h   - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
626   - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the   - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
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