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revision 1.1513 by mlosch, Thu Oct 13 14:54:44 2011 UTC revision 1.1567 by jmc, Sun Jan 1 01:25:54 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 model/src:  o pkg/exf (interpolation):
8    - improve vectorization also for adjoint code of    - assume periodicity in X only if input field cover full longitude range.
9      - improve search for lat. index (supposed to be faster, in ~log2(ny) steps,
10        and should vectorise).
11      - fix input lat of the 2 added row (in case we provide N.pole data).
12    
13    checkpoint63h (2011/12/30)
14    o pkg/seaice:
15      - change declaration of UVM from _RL to _RS in order to get B-grid
16        uIce,vIce monitor when _RS = real*4
17    o pkg/offline:
18      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
19      - compute vertical velocity if not read from file (switch on exactConserv
20        & staggerTimeStep);
21      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
22    o verification:
23      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
24        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
25        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
26      - update output of exp. global_ocean.cs32x15.viscA4 after changing
27        grid-file angles (used here for coriolis-3d);
28      - remove (or gzip) few files not needed to run fizhi-cs experiments.
29    o pkg/exf (vector interpolation):
30      - rotate vector component toward local grid-axis orientation using grid-angles
31        (stored in GRID.h) instead of locally computed rotation angle; keep old code
32        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
33    o pkg/seaice:
34      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
35        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
36    o pkg/PKG_OPTIONS.h files:
37      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
38        outside of the #ifdef ALLOW_THISPKG / #endif block.
39      - update verification/*/code/PKG_OPTIONS.h files.
40    o add a verification experiment (offline_exf_seaice/input.seaice) that test
41      the B-grid LSOR solver
42    o pkg/seaice: sort out emissivity and long wave radiation step 2:
43      - add emissivity for snow and ice as new run-time parameters
44        (unfortunately) that default to the corresponding exf values; this
45        changes results in most verification experiments so that for backward
46        compatibility these parameter have to be set explicitly to inconsistent
47        values (ugly);
48      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
49        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
50        until we agree how to handle this bug properly
51    o pkg/exf (interpolation):
52      - add a set of run-time param ({inputfield}_interpMethod), one for
53        each interpolated input field, to select the interpolation method
54        with a value of zero switching off the interpolation;
55      - print interpolation parameters to standard output;
56      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
57        (to use instead runoff_interpMethod=0 in data.exf).
58      - simplify default setting of interpolation parameters (for all fields,
59        set position to match model grid cell-center position, leading to trivial
60        interpolation in case of regular Lat-Lon grid) and fix for the case of
61        non-uniform delY.
62    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
63       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
64       this factor is absolutely required, because the lw exitance (= out-going
65       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
66       where the reflectivity rho = 1-emissivity for conservation reasons. Once
67       this is established, we can remove the CPP-Flag (if we want to).
68    o pkg/seaice:
69      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
70        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
71      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
72        what the name implies (and not emissivity*BoltzmannConstant), this means
73        the old default value of 5.5e-8 now means
74        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
75        S/R exf_readparms
76      - FV-discretization of the B-grid LSOR solver, turn on with
77        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
78        of the calling routine dynsolver, so that B and C-grid code look a
79        little more alike.
80      - fix index bugs in ostres.F (B-grid code)
81    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
82    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
83      default for SEAICE_emissivity, if useEXF; requires setting a wrong
84      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
85      backward compatiblity
86    o model/src: use sigmaR in calc_ivdc
87    
88    checkpoint63g (2011/12/16)
89    o pkg/seaice/seaice_growth.F:
90      fix heat conservation of the coupled ocean-seaice system.
91      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
92      solid vs liquid water treatment is resolved via QNET.
93    o pkg/seaice/seaice_growth.F:
94      add missing term for sublimation in saltFlux, which was breaking conservation.
95    o pkg/seaice/seaice_model.F:
96      Remove this patholigical case treatment in evolution branch,
97      where it is un-necessary and breaks conservation.
98      Update global_ocean.cs32x15/results accordingly for
99      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
100    o model/src:
101      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
102      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
103    o pkg/obcs:
104      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
105      tendency for temperature and salinity that is then applied to update
106      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
107      horizontal advection and diffusion contributions on the boundary (in
108      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
109      removing the mask in S/R timestep_tracer. The advantage of this approach is
110      that the updated tracer values include contributions from the surface
111      forcing and vertical diffusion.
112      This modification changes exp4.stevens because of vertical diffusion.
113    o model/src:
114      change non-curvilinear grid setting to also work with exch2 + blank tiles:
115      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
116        face dimensions.
117      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
118        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
119        and INI_SPHERICAL_POLAR_GRID.
120      change test-experiment global_ocean.90x40x15:
121      - split the domain in many more tiles (9x4 tiles of 10x10 each);
122      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
123      - update results of both test (std & dwnslp).
124    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
125       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
126    o model/src:
127      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
128        and fix initialisation when using sigma-coords.
129    o model/src:
130     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
131       to their current value at the beginning of forward_step.F": add a new run-time
132       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
133     - set doResetHFactors=T in the following test exp:
134        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
135        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
136        and tutorial_global_oce_in_p (nonLinFS in p)
137    o pkg/ecco
138      - added IES cost term
139    o verification/advect_xz
140      - scale down the depth by 1/100 (from 200 km to just 2.km)
141      - add secondary test using divergent flow, r-star and implicit vertical advection.
142      - add note (check_conserve_TS.txt) and matlab script to check global
143        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
144    o pkg/rbcs:
145      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
146    o pkg/obcs (Stevens BCs):
147      - fix various problems in the phase speed computations of the Stevens
148        boundary conditions:
149        - sign error for western and southern boundaries,
150        - time tendencies were underestimated by factor of dTracerLev and some just
151          zero (for multidim advection schemes) -> now estimate time tendencies
152          from difference between previous (n) time level and the one before (n-1);
153          this requires storing a field per tracer per boundary, also in the pickup
154          files.
155        - replace deltaTmom in cflMer/Zon computation with dTracerLev
156        - set default phase velocity to cflMer/Zon
157      - update verification experiment exp4.stevens
158    o pkg/generic_advdiff (implicit_r):
159      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
160        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
161      - fix implicit vertical diffusion or advection with NonLin FreeSurf
162        (was using current recip_hFacC instead of future recip_hFacC): set future
163        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
164        solver S/R ;
165      - fill diagnostics of vertical advective fluxes (computed from tendency)
166        when using implicit vert. advection;
167      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
168         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
169         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
170         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
171    o pkg/diagnostics:
172      - add diags for T & S tendency which goes through Adams-Bashforth.
173    
174    checkpoint63f (2011/11/30)
175    o pkg/obcs/obcs_calc_stevens.F:
176      - join some loops to reduce number of if-statements
177      - fix a bug in code for northern and southern boundaries.
178    o pkg/seaice/seaice_init_varia.F
179      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
180        caused zero ice-velocities for the B-grid code
181    o pkg/seaice/seaice_init_fixed.F
182      - fix a bug in the initialisation of the second metric terms
183        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
184      - this affects all seaice configurations with useCurviLinearGrid = .true.
185        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
186        = .true. (default)
187      - the only verification experiment affected is global_ocean.cs32x15:
188        icedyn, seaice, and seaice_dynmix (AD)
189    o pkg/thsice/thsice_diagnostics_state.F
190      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
191        not contain garbage that can lead to surprises in diagstats_calc.F
192    o model/src:
193      - move bi,bj loops inside INTEGR_CONTINUITY ;
194      - call INTEGR_CONTINUITY directly from forward_step.F
195        (previously called from momentum_correction_step.F)
196      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
197        forward_step.F and pkg/ecco/the_main_loop.F
198    o model/src/do_oceanic_phys.F:
199      - reset addMass to zero only if useICEFRONT ;
200      - separated k-loop for rhoInSitu calculation ;
201      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
202        and at constant T,S (= WdRHOdP);
203      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
204        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
205        transport of locally-referenced potential density);
206        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
207    o gluemnc:
208      - replace ncrcat with ncks when adding variables to *.glob.nc
209      - change the way variables without record dimensions are handled so that
210        files that have variables with and without record variables can be glued:
211        add a record dimension with a new unique name to be able to differentiate
212        between variable with and without a-prior record dimensions. Remove
213        this record dimension before adding the variable to the *.glob.nc file.
214        This procedure automatically works also for grid.*.nc files that do not
215        have any record dimension.
216    o verification/cpl_aim+ocn:
217      - generate new reference output on baudelaire (gfortran, mpich2) (previously
218        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
219    o pkg/obcs/obcs_calc_stevens.F:
220      - add code for northern and southern boundaries.
221      - reorder some loops to save some operations and so that drFBar can be scalar
222    o model/src:
223      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
224        truncation) and add diagnostics for Adams-Bashforth tendency increment.
225      - update test-exp. AD output:
226        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
227      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
228        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
229        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
230        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
231        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
232        tutorial_plume_on_slope.
233    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
234      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
235      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
236      does not even come with an F77 compiler anymore, this should not be
237      a limitation
238    
239    checkpoint63e (2011/11/06)
240    o pkg/seaice adjoint of LSR:
241      - substantially rework STORE dirs.
242      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
243        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
244        and only perform SOLV_MAX_FIXED adjoint iters.
245        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
246        always goes to same record, meaning that the last forward field will be
247        the one used in the adjoint - an approximation.
248      - now produces non-zero LSR-related gradients, and acceptable gradients for
249        An's zonal (x-z) test case (to be checked in)
250      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
251        (but these are screwed up by the thermodynamics in the first place);
252        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
253        output_adm.txt also reflects changes to seaice_lsr
254      - global_ocean.cs32x15:
255        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
256          (output_adm.seaice.txt was updated)
257        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
258          (output_adm.seaice_dynmix.txt)
259    o test-exp. exp4+stevens:
260      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
261    o pkg/seaice (lsr solver):
262      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
263        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
264      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
265      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
266        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
267      - compute (with new S/R) and print initial (+ free-driff sol. if available)
268        and final residual of linearised system.
269    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
270      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
271    o pkg/obcs: Stevens BCs (still only for east and west)
272      - fix Stevens BCs by using intermediate velocities of previous
273        time step as "baroclinic" contribution rather velocity of one grid cell
274        inside the boundaries; more consistent but makes the entire treatment
275        more complicated, requires new pickup files and two new S/Rs:
276        obcs_copy_uv_n and obcs_save_uv_n
277        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
278        (undefined by default)
279      - silently move computation of some grid factors into separate loops to
280        save some recomputations
281      - add a hack for non-linear free surface
282      - add a verification experiment to exp4 that tests this code
283    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
284    
285    checkpoint63d (2011/10/25)
286    o pkg/obcs + seaice-dynamics:
287      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
288        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
289        values (consistent with an implicit method).
290      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
291        return to older implementation (same results as before); note that none of
292        the "experimental" OBCS_SEAICE options are implemented in the new version.
293      - switch test exp. seaice_obcs to use new version (update output).
294    o pkg/seaice:
295      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
296      - add parenthesis in Water-Ice drag calculations (evp & lsr);
297      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
298        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
299      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
300        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
301    o pkg/layers:
302      - Include potential density as new coordinate (Thanks to David Munday)
303    o pkg/dic:
304      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
305        carbonate computation/output to CALC_PCO2_APPROX
306    o pkg/generic_advdiff
307      - make TAF generate code that vectorizes:
308        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
309    o model/src:
310      - improve vectorization also for adjoint code of
311      solve_tridiagonal and solve_pentadiagonal. As this requires up to      solve_tridiagonal and solve_pentadiagonal. As this requires up to
312      5 new 3D-fields, this code is only turned on for the combination of      5 new 3D-fields, this code is only turned on for the combination of
313      ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX.      ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
314        for singular matrix check (only for TARGET_NEC_SX).
315    - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to    - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
316      ALLOW_AUTODIFF. This flag now needs to be set outside of      ALLOW_AUTODIFF. This flag now needs to be set outside of
317      solve_tri/pentadiagonal.F      solve_tri/pentadiagonal.F
318  o pkg/exf:  o pkg/exf:
319    - fix previous modif in exf_readparms.F (revision 1.66: treatment of    - fix previous modif in exf_readparms.F (revision 1.66: treatment of

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