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revision 1.1502 by jmc, Wed Sep 21 16:29:49 2011 UTC revision 1.1560 by mlosch, Thu Dec 22 15:38:56 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 add a verification experiment (offline_exf_seaice/input.seaice) that test
8      the B-grid LSOR solver
9    o pkg/seaice: sort out emissivity and long wave radiation step 2:
10      - add emissivity for snow and ice as new run-time parameters
11        (unfortunately) that default to the corresponding exf values; this
12        changes results in most verification experiments so that for backward
13        compatibility these parameter have to be set explicitly to inconsistent
14        values (ugly);
15      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
16        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
17        until we agree how to handle this bug properly
18    o pkg/exf (interpolation):
19      - add a set of run-time param ({inputfield}_interpMethod), one for
20        each interpolated input field, to select the interpolation method
21        with a value of zero switching off the interpolation;
22      - print interpolation parameters to standard output;
23      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
24        (to use instead runoff_interpMethod=0 in data.exf).
25      - simplify default setting of interpolation parameters (for all fields,
26        set position to match model grid cell-center position, leading to trivial
27        interpolation in case of regular Lat-Lon grid) and fix for the case of
28        non-uniform delY.
29    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
30       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
31       this factor is absolutely required, because the lw exitance (= out-going
32       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
33       where the reflectivity rho = 1-emissivity for conservation reasons. Once
34       this is established, we can remove the CPP-Flag (if we want to).
35    o pkg/seaice:
36      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
37        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
38      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
39        what the name implies (and not emissivity*BoltzmannConstant), this means
40        the old default value of 5.5e-8 now means
41        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
42        S/R exf_readparms
43      - FV-discretization of the B-grid LSOR solver, turn on with
44        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
45        of the calling routine dynsolver, so that B and C-grid code look a
46        little more alike.
47      - fix index bugs in ostres.F (B-grid code)
48    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
49    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
50      default for SEAICE_emissivity, if useEXF; requires setting a wrong
51      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
52      backward compatiblity
53    o model/src: use sigmaR in calc_ivdc
54    
55    checkpoint63g (2011/12/16)
56    o pkg/seaice/seaice_growth.F:
57      fix heat conservation of the coupled ocean-seaice system.
58      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
59      solid vs liquid water treatment is resolved via QNET.
60    o pkg/seaice/seaice_growth.F:
61      add missing term for sublimation in saltFlux, which was breaking conservation.
62    o pkg/seaice/seaice_model.F:
63      Remove this patholigical case treatment in evolution branch,
64      where it is un-necessary and breaks conservation.
65      Update global_ocean.cs32x15/results accordingly for
66      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
67    o model/src:
68      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
69      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
70    o pkg/obcs:
71      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
72      tendency for temperature and salinity that is then applied to update
73      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
74      horizontal advection and diffusion contributions on the boundary (in
75      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
76      removing the mask in S/R timestep_tracer. The advantage of this approach is
77      that the updated tracer values include contributions from the surface
78      forcing and vertical diffusion.
79      This modification changes exp4.stevens because of vertical diffusion.
80    o model/src:
81      change non-curvilinear grid setting to also work with exch2 + blank tiles:
82      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
83        face dimensions.
84      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
85        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
86        and INI_SPHERICAL_POLAR_GRID.
87      change test-experiment global_ocean.90x40x15:
88      - split the domain in many more tiles (9x4 tiles of 10x10 each);
89      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
90      - update results of both test (std & dwnslp).
91    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
92       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
93    o model/src:
94      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
95        and fix initialisation when using sigma-coords.
96    o model/src:
97     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
98       to their current value at the beginning of forward_step.F": add a new run-time
99       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
100     - set doResetHFactors=T in the following test exp:
101        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
102        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
103        and tutorial_global_oce_in_p (nonLinFS in p)
104    o pkg/ecco
105      - added IES cost term
106    o verification/advect_xz
107      - scale down the depth by 1/100 (from 200 km to just 2.km)
108      - add secondary test using divergent flow, r-star and implicit vertical advection.
109      - add note (check_conserve_TS.txt) and matlab script to check global
110        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
111    o pkg/rbcs:
112      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
113    o pkg/obcs (Stevens BCs):
114      - fix various problems in the phase speed computations of the Stevens
115        boundary conditions:
116        - sign error for western and southern boundaries,
117        - time tendencies were underestimated by factor of dTracerLev and some just
118          zero (for multidim advection schemes) -> now estimate time tendencies
119          from difference between previous (n) time level and the one before (n-1);
120          this requires storing a field per tracer per boundary, also in the pickup
121          files.
122        - replace deltaTmom in cflMer/Zon computation with dTracerLev
123        - set default phase velocity to cflMer/Zon
124      - update verification experiment exp4.stevens
125    o pkg/generic_advdiff (implicit_r):
126      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
127        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
128      - fix implicit vertical diffusion or advection with NonLin FreeSurf
129        (was using current recip_hFacC instead of future recip_hFacC): set future
130        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
131        solver S/R ;
132      - fill diagnostics of vertical advective fluxes (computed from tendency)
133        when using implicit vert. advection;
134      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
135         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
136         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
137         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
138    o pkg/diagnostics:
139      - add diags for T & S tendency which goes through Adams-Bashforth.
140    
141    checkpoint63f (2011/11/30)
142    o pkg/obcs/obcs_calc_stevens.F:
143      - join some loops to reduce number of if-statements
144      - fix a bug in code for northern and southern boundaries.
145    o pkg/seaice/seaice_init_varia.F
146      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
147        caused zero ice-velocities for the B-grid code
148    o pkg/seaice/seaice_init_fixed.F
149      - fix a bug in the initialisation of the second metric terms
150        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
151      - this affects all seaice configurations with useCurviLinearGrid = .true.
152        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
153        = .true. (default)
154      - the only verification experiment affected is global_ocean.cs32x15:
155        icedyn, seaice, and seaice_dynmix (AD)
156    o pkg/thsice/thsice_diagnostics_state.F
157      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
158        not contain garbage that can lead to surprises in diagstats_calc.F
159    o model/src:
160      - move bi,bj loops inside INTEGR_CONTINUITY ;
161      - call INTEGR_CONTINUITY directly from forward_step.F
162        (previously called from momentum_correction_step.F)
163      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
164        forward_step.F and pkg/ecco/the_main_loop.F
165    o model/src/do_oceanic_phys.F:
166      - reset addMass to zero only if useICEFRONT ;
167      - separated k-loop for rhoInSitu calculation ;
168      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
169        and at constant T,S (= WdRHOdP);
170      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
171        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
172        transport of locally-referenced potential density);
173        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
174    o gluemnc:
175      - replace ncrcat with ncks when adding variables to *.glob.nc
176      - change the way variables without record dimensions are handled so that
177        files that have variables with and without record variables can be glued:
178        add a record dimension with a new unique name to be able to differentiate
179        between variable with and without a-prior record dimensions. Remove
180        this record dimension before adding the variable to the *.glob.nc file.
181        This procedure automatically works also for grid.*.nc files that do not
182        have any record dimension.
183    o verification/cpl_aim+ocn:
184      - generate new reference output on baudelaire (gfortran, mpich2) (previously
185        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
186    o pkg/obcs/obcs_calc_stevens.F:
187      - add code for northern and southern boundaries.
188      - reorder some loops to save some operations and so that drFBar can be scalar
189    o model/src:
190      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
191        truncation) and add diagnostics for Adams-Bashforth tendency increment.
192      - update test-exp. AD output:
193        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
194      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
195        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
196        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
197        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
198        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
199        tutorial_plume_on_slope.
200    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
201      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
202      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
203      does not even come with an F77 compiler anymore, this should not be
204      a limitation
205    
206    checkpoint63e (2011/11/06)
207    o pkg/seaice adjoint of LSR:
208      - substantially rework STORE dirs.
209      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
210        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
211        and only perform SOLV_MAX_FIXED adjoint iters.
212        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
213        always goes to same record, meaning that the last forward field will be
214        the one used in the adjoint - an approximation.
215      - now produces non-zero LSR-related gradients, and acceptable gradients for
216        An's zonal (x-z) test case (to be checked in)
217      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
218        (but these are screwed up by the thermodynamics in the first place);
219        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
220        output_adm.txt also reflects changes to seaice_lsr
221      - global_ocean.cs32x15:
222        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
223          (output_adm.seaice.txt was updated)
224        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
225          (output_adm.seaice_dynmix.txt)
226    o test-exp. exp4+stevens:
227      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
228    o pkg/seaice (lsr solver):
229      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
230        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
231      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
232      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
233        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
234      - compute (with new S/R) and print initial (+ free-driff sol. if available)
235        and final residual of linearised system.
236    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
237      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
238    o pkg/obcs: Stevens BCs (still only for east and west)
239      - fix Stevens BCs by using intermediate velocities of previous
240        time step as "baroclinic" contribution rather velocity of one grid cell
241        inside the boundaries; more consistent but makes the entire treatment
242        more complicated, requires new pickup files and two new S/Rs:
243        obcs_copy_uv_n and obcs_save_uv_n
244        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
245        (undefined by default)
246      - silently move computation of some grid factors into separate loops to
247        save some recomputations
248      - add a hack for non-linear free surface
249      - add a verification experiment to exp4 that tests this code
250    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
251    
252    checkpoint63d (2011/10/25)
253    o pkg/obcs + seaice-dynamics:
254      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
255        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
256        values (consistent with an implicit method).
257      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
258        return to older implementation (same results as before); note that none of
259        the "experimental" OBCS_SEAICE options are implemented in the new version.
260      - switch test exp. seaice_obcs to use new version (update output).
261    o pkg/seaice:
262      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
263      - add parenthesis in Water-Ice drag calculations (evp & lsr);
264      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
265        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
266      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
267        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
268    o pkg/layers:
269      - Include potential density as new coordinate (Thanks to David Munday)
270    o pkg/dic:
271      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
272        carbonate computation/output to CALC_PCO2_APPROX
273    o pkg/generic_advdiff
274      - make TAF generate code that vectorizes:
275        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
276    o model/src:
277      - improve vectorization also for adjoint code of
278        solve_tridiagonal and solve_pentadiagonal. As this requires up to
279        5 new 3D-fields, this code is only turned on for the combination of
280        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
281        for singular matrix check (only for TARGET_NEC_SX).
282      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
283        ALLOW_AUTODIFF. This flag now needs to be set outside of
284        solve_tri/pentadiagonal.F
285    o pkg/exf:
286      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
287        optional namelist EXF_NML_OBCS).
288      - add many debug-print (to trace down where pkg/cal error msg comes from)
289    o pkg/mom_vecinv/mom_vi_hdissip.F
290      - rearrange loops so that vectorization is improved and in particular
291        the adjoint routine vectorizes. The code is a little longer now, but I
292        think easier to read.
293        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
294    o pkg/seaice:
295      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
296    o pkg/exch2:
297      - alternative code (without tile x tile matrix) for cumulated (global) sum;
298        used as default; keep using matrix version in adjustment.cs-32x32x1.
299    o tools/build_options:
300      - after merging some MPI and/or multi-threads specific optfiles so that
301        the modified default optfile support both built (using genmake2 -mpi
302        for the MPI built, using genmake2 -omp for OpenMP built),
303        move now obsolete optfiles to tools/build_options/unsupported/
304       (add copy of email sent to support list in doc/optfiles_changes.txt)
305    
306    checkpoint63c (2011/09/28)
307    o pkg/ebm:
308      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
309        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
310    o pkg/seaice (SItracer pickup)
311    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
312      To be done:
313      - thorough testing of missing fields in S/R seaice_read_pickup
314      - thorough matching between generic tracers and specific fields used
315        (e.g. volume-weighted age, area-weighted age, salinity, ...)
316    o pkg/grdchk:
317      - all procs calculate and print finite-difference gradient (for testreport)
318      - change description output used by testreport;
319      - AD testing: also compare and report Finite-difference gradient;
320        => update all output_adm*.txt
321    o test exp. global_ocean_ebm:
322      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
323        and turn on exactConserve; update (fwd) output.
324    o pkg/seaice (LSR):
325      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
326      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
327        * identical results with non-CS topology (but save up to half of EXCH calls)
328        * no much changes in cs-32 verification tests since no ice at face edges
329         (differences due to convergence criteria, since nb of iterations changed)
330        * expect some differences on lat-lon-cap grid.
331        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
332  o pkg/exch2:  o pkg/exch2:
333    - add new CPP option to disable Cumul-Sum matrix (to save storage when using    - add new CPP option to disable Cumul-Sum matrix (to save storage when using
334      many tiles); until alternative coding is added, just add a stop.      many tiles); until alternative coding is added, just add a stop.

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