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revision 1.1522 by mlosch, Wed Oct 26 09:30:32 2011 UTC revision 1.1572 by heimbach, Fri Jan 6 14:06:18 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 optim: make Makefile more robust (?)
8    o pkg/obcs:
9      * fix treatment of obcs_read_pickup for TAF
10    o pkg/shelfice:
11      * add missing initialisation of num_shifwflx
12      * new adjoint verification exp. for isomip
13      * change Prandtl and Schmidt numbers from generic formulations
14        (in terms of model diffus. and visc.) to separate runtime
15        parameters, with Holland and Jenkins (1999) default values.
16    o pkg/exf (interpolation):
17      - extended input field (2 rows) near the N & S poles:
18        * fill in with the symetric value (when even Nb of data in longitude)
19        * add average value at the poles only for scalar quantities ; for vector
20          component interpolation, skip the averaging and keep duplicated values,
21          unless the 2 components have same location (uvInterp=T) in which case
22          interpolate the 2 components together using S/R EXF_INTERP_UV.
23      - new S/R EXF_INTERP_UV to interpolate the 2 components of a vector field
24        together: this allows to account properly for local orientation when
25        averaging at N & S pole.
26      - add CPP option EXF_USE_OLD_INTERP_POLE to recover old results regarding
27        exf-interpolation near N & S poles. Undef by default.
28      - add debug check/print on 1rst iter if debugLevel >=2.
29    o pkg/exf:
30      - change masking flags definition (no longer "parameter"), put them in
31        common block and set them in S/R EXF_INIT_FIXED.
32      - change recognized masking flag from s,u,v to c,w,s since the mask
33        to use (maskC,W,S) depends on position on model grid and has little to
34        do with scalar/vector difference; fix masking if using P-coordinates.
35      - fix masking of wind-stress (was wrong if interpolated or read on A-grid)
36        and update results of exp. global_with_exf (x2).
37      - fix setting of zenith-angle table when SHORTWAVE_HEATING is undef.
38    o pkg/obcs
39      - S/R obcs_calc_stevens: fix a small bug (gammat -> gammas where appropriate)
40    o pkg/exf (interpolation):
41      - assume periodicity in X only if input field cover full longitude range.
42      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
43        and should vectorise).
44      - fix input lat of the 2 added row (in case we provide N.pole data).
45    
46    checkpoint63h (2011/12/30)
47    o pkg/seaice:
48      - change declaration of UVM from _RL to _RS in order to get B-grid
49        uIce,vIce monitor when _RS = real*4
50    o pkg/offline:
51      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
52      - compute vertical velocity if not read from file (switch on exactConserv
53        & staggerTimeStep);
54      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
55    o verification:
56      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
57        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
58        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
59      - update output of exp. global_ocean.cs32x15.viscA4 after changing
60        grid-file angles (used here for coriolis-3d);
61      - remove (or gzip) few files not needed to run fizhi-cs experiments.
62    o pkg/exf (vector interpolation):
63      - rotate vector component toward local grid-axis orientation using grid-angles
64        (stored in GRID.h) instead of locally computed rotation angle; keep old code
65        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
66    o pkg/seaice:
67      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
68        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
69    o pkg/PKG_OPTIONS.h files:
70      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
71        outside of the #ifdef ALLOW_THISPKG / #endif block.
72      - update verification/*/code/PKG_OPTIONS.h files.
73    o add a verification experiment (offline_exf_seaice/input.seaice) that test
74      the B-grid LSOR solver
75    o pkg/seaice: sort out emissivity and long wave radiation step 2:
76      - add emissivity for snow and ice as new run-time parameters
77        (unfortunately) that default to the corresponding exf values; this
78        changes results in most verification experiments so that for backward
79        compatibility these parameter have to be set explicitly to inconsistent
80        values (ugly);
81      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
82        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
83        until we agree how to handle this bug properly
84    o pkg/exf (interpolation):
85      - add a set of run-time param ({inputfield}_interpMethod), one for
86        each interpolated input field, to select the interpolation method
87        with a value of zero switching off the interpolation;
88      - print interpolation parameters to standard output;
89      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
90        (to use instead runoff_interpMethod=0 in data.exf).
91      - simplify default setting of interpolation parameters (for all fields,
92        set position to match model grid cell-center position, leading to trivial
93        interpolation in case of regular Lat-Lon grid) and fix for the case of
94        non-uniform delY.
95    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
96       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
97       this factor is absolutely required, because the lw exitance (= out-going
98       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
99       where the reflectivity rho = 1-emissivity for conservation reasons. Once
100       this is established, we can remove the CPP-Flag (if we want to).
101    o pkg/seaice:
102      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
103        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
104      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
105        what the name implies (and not emissivity*BoltzmannConstant), this means
106        the old default value of 5.5e-8 now means
107        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
108        S/R exf_readparms
109      - FV-discretization of the B-grid LSOR solver, turn on with
110        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
111        of the calling routine dynsolver, so that B and C-grid code look a
112        little more alike.
113      - fix index bugs in ostres.F (B-grid code)
114    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
115    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
116      default for SEAICE_emissivity, if useEXF; requires setting a wrong
117      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
118      backward compatiblity
119    o model/src: use sigmaR in calc_ivdc
120    
121    checkpoint63g (2011/12/16)
122    o pkg/seaice/seaice_growth.F:
123      fix heat conservation of the coupled ocean-seaice system.
124      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
125      solid vs liquid water treatment is resolved via QNET.
126    o pkg/seaice/seaice_growth.F:
127      add missing term for sublimation in saltFlux, which was breaking conservation.
128    o pkg/seaice/seaice_model.F:
129      Remove this patholigical case treatment in evolution branch,
130      where it is un-necessary and breaks conservation.
131      Update global_ocean.cs32x15/results accordingly for
132      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
133    o model/src:
134      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
135      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
136    o pkg/obcs:
137      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
138      tendency for temperature and salinity that is then applied to update
139      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
140      horizontal advection and diffusion contributions on the boundary (in
141      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
142      removing the mask in S/R timestep_tracer. The advantage of this approach is
143      that the updated tracer values include contributions from the surface
144      forcing and vertical diffusion.
145      This modification changes exp4.stevens because of vertical diffusion.
146    o model/src:
147      change non-curvilinear grid setting to also work with exch2 + blank tiles:
148      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
149        face dimensions.
150      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
151        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
152        and INI_SPHERICAL_POLAR_GRID.
153      change test-experiment global_ocean.90x40x15:
154      - split the domain in many more tiles (9x4 tiles of 10x10 each);
155      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
156      - update results of both test (std & dwnslp).
157    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
158       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
159    o model/src:
160      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
161        and fix initialisation when using sigma-coords.
162    o model/src:
163     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
164       to their current value at the beginning of forward_step.F": add a new run-time
165       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
166     - set doResetHFactors=T in the following test exp:
167        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
168        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
169        and tutorial_global_oce_in_p (nonLinFS in p)
170    o pkg/ecco
171      - added IES cost term
172    o verification/advect_xz
173      - scale down the depth by 1/100 (from 200 km to just 2.km)
174      - add secondary test using divergent flow, r-star and implicit vertical advection.
175      - add note (check_conserve_TS.txt) and matlab script to check global
176        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
177    o pkg/rbcs:
178      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
179    o pkg/obcs (Stevens BCs):
180      - fix various problems in the phase speed computations of the Stevens
181        boundary conditions:
182        - sign error for western and southern boundaries,
183        - time tendencies were underestimated by factor of dTracerLev and some just
184          zero (for multidim advection schemes) -> now estimate time tendencies
185          from difference between previous (n) time level and the one before (n-1);
186          this requires storing a field per tracer per boundary, also in the pickup
187          files.
188        - replace deltaTmom in cflMer/Zon computation with dTracerLev
189        - set default phase velocity to cflMer/Zon
190      - update verification experiment exp4.stevens
191    o pkg/generic_advdiff (implicit_r):
192      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
193        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
194      - fix implicit vertical diffusion or advection with NonLin FreeSurf
195        (was using current recip_hFacC instead of future recip_hFacC): set future
196        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
197        solver S/R ;
198      - fill diagnostics of vertical advective fluxes (computed from tendency)
199        when using implicit vert. advection;
200      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
201         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
202         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
203         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
204    o pkg/diagnostics:
205      - add diags for T & S tendency which goes through Adams-Bashforth.
206    
207    checkpoint63f (2011/11/30)
208    o pkg/obcs/obcs_calc_stevens.F:
209      - join some loops to reduce number of if-statements
210      - fix a bug in code for northern and southern boundaries.
211    o pkg/seaice/seaice_init_varia.F
212      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
213        caused zero ice-velocities for the B-grid code
214    o pkg/seaice/seaice_init_fixed.F
215      - fix a bug in the initialisation of the second metric terms
216        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
217      - this affects all seaice configurations with useCurviLinearGrid = .true.
218        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
219        = .true. (default)
220      - the only verification experiment affected is global_ocean.cs32x15:
221        icedyn, seaice, and seaice_dynmix (AD)
222    o pkg/thsice/thsice_diagnostics_state.F
223      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
224        not contain garbage that can lead to surprises in diagstats_calc.F
225    o model/src:
226      - move bi,bj loops inside INTEGR_CONTINUITY ;
227      - call INTEGR_CONTINUITY directly from forward_step.F
228        (previously called from momentum_correction_step.F)
229      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
230        forward_step.F and pkg/ecco/the_main_loop.F
231    o model/src/do_oceanic_phys.F:
232      - reset addMass to zero only if useICEFRONT ;
233      - separated k-loop for rhoInSitu calculation ;
234      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
235        and at constant T,S (= WdRHOdP);
236      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
237        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
238        transport of locally-referenced potential density);
239        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
240    o gluemnc:
241      - replace ncrcat with ncks when adding variables to *.glob.nc
242      - change the way variables without record dimensions are handled so that
243        files that have variables with and without record variables can be glued:
244        add a record dimension with a new unique name to be able to differentiate
245        between variable with and without a-prior record dimensions. Remove
246        this record dimension before adding the variable to the *.glob.nc file.
247        This procedure automatically works also for grid.*.nc files that do not
248        have any record dimension.
249    o verification/cpl_aim+ocn:
250      - generate new reference output on baudelaire (gfortran, mpich2) (previously
251        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
252    o pkg/obcs/obcs_calc_stevens.F:
253      - add code for northern and southern boundaries.
254      - reorder some loops to save some operations and so that drFBar can be scalar
255    o model/src:
256      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
257        truncation) and add diagnostics for Adams-Bashforth tendency increment.
258      - update test-exp. AD output:
259        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
260      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
261        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
262        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
263        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
264        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
265        tutorial_plume_on_slope.
266    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
267      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
268      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
269      does not even come with an F77 compiler anymore, this should not be
270      a limitation
271    
272    checkpoint63e (2011/11/06)
273    o pkg/seaice adjoint of LSR:
274      - substantially rework STORE dirs.
275      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
276        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
277        and only perform SOLV_MAX_FIXED adjoint iters.
278        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
279        always goes to same record, meaning that the last forward field will be
280        the one used in the adjoint - an approximation.
281      - now produces non-zero LSR-related gradients, and acceptable gradients for
282        An's zonal (x-z) test case (to be checked in)
283      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
284        (but these are screwed up by the thermodynamics in the first place);
285        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
286        output_adm.txt also reflects changes to seaice_lsr
287      - global_ocean.cs32x15:
288        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
289          (output_adm.seaice.txt was updated)
290        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
291          (output_adm.seaice_dynmix.txt)
292    o test-exp. exp4+stevens:
293      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
294    o pkg/seaice (lsr solver):
295      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
296        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
297      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
298      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
299        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
300      - compute (with new S/R) and print initial (+ free-driff sol. if available)
301        and final residual of linearised system.
302  o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity  o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
303    (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)    (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
304  o pkg/obcs: Stevens BCs (still only for east and west)  o pkg/obcs: Stevens BCs (still only for east and west)
305    - fix Stevens BCs by using intermediate velocities of previous    - fix Stevens BCs by using intermediate velocities of previous
306      time step as "baroclinic" contribution rather velocity of one grid cell      time step as "baroclinic" contribution rather velocity of one grid cell
307      inside the boundaries; more consistent but makes the entire treatment      inside the boundaries; more consistent but makes the entire treatment
308      more complicated, requires new pickup files and two new S/Rs:      more complicated, requires new pickup files and two new S/Rs:
309      obcs_copy_uv_n and obcs_save_uv_n      obcs_copy_uv_n and obcs_save_uv_n
310      keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY      keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
311      (undefined by default)      (undefined by default)
312    - silently move computation of some grid factors into separate loops to    - silently move computation of some grid factors into separate loops to
313      save some recomputations      save some recomputations
314    - add a hack for non-linear free surface    - add a hack for non-linear free surface
315    - add a verification experiment to exp4 that tests this code    - add a verification experiment to exp4 that tests this code

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