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revision 1.1502 by jmc, Wed Sep 21 16:29:49 2011 UTC revision 1.1557 by jmc, Wed Dec 21 17:31:53 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 pkg/exf (interpolation):
8      - add a set of run-time param ({inputfield}_interpMethod), one for
9        each interpolated input field, to select the interpolation method
10        with a value of zero switching off the interpolation;
11      - print interpolation parameters to standard output;
12      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
13        (to use instead runoff_interpMethod=0 in data.exf).
14    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
15       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
16       this factor is absolutely required, because the lw exitance (= out-going
17       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
18       where the reflectivity rho = 1-emissivity for conservation reasons. Once
19       this is established, we can remove the CPP-Flag (if we want to).
20    o pkg/seaice:
21      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
22        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
23      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
24        what the name implies (and not emissivity*BoltzmannConstant), this means
25        the old default value of 5.5e-8 now means
26        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
27        S/R exf_readparms
28      - FV-discretization of the B-grid LSOR solver, turn on with
29        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
30        of the calling routine dynsolver, so that B and C-grid code look a
31        little more alike.
32      - fix index bugs in ostres.F (B-grid code)
33    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
34    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
35      default for SEAICE_emissivity, if useEXF; requires setting a wrong
36      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
37      backward compatiblity
38    o model/src: use sigmaR in calc_ivdc
39    
40    checkpoint63g (2011/12/16)
41    o pkg/seaice/seaice_growth.F:
42      fix heat conservation of the coupled ocean-seaice system.
43      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
44      solid vs liquid water treatment is resolved via QNET.
45    o pkg/seaice/seaice_growth.F:
46      add missing term for sublimation in saltFlux, which was breaking conservation.
47    o pkg/seaice/seaice_model.F:
48      Remove this patholigical case treatment in evolution branch,
49      where it is un-necessary and breaks conservation.
50      Update global_ocean.cs32x15/results accordingly for
51      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
52    o model/src:
53      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
54      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
55    o pkg/obcs:
56      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
57      tendency for temperature and salinity that is then applied to update
58      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
59      horizontal advection and diffusion contributions on the boundary (in
60      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
61      removing the mask in S/R timestep_tracer. The advantage of this approach is
62      that the updated tracer values include contributions from the surface
63      forcing and vertical diffusion.
64      This modification changes exp4.stevens because of vertical diffusion.
65    o model/src:
66      change non-curvilinear grid setting to also work with exch2 + blank tiles:
67      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
68        face dimensions.
69      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
70        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
71        and INI_SPHERICAL_POLAR_GRID.
72      change test-experiment global_ocean.90x40x15:
73      - split the domain in many more tiles (9x4 tiles of 10x10 each);
74      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
75      - update results of both test (std & dwnslp).
76    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
77       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
78    o model/src:
79      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
80        and fix initialisation when using sigma-coords.
81    o model/src:
82     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
83       to their current value at the beginning of forward_step.F": add a new run-time
84       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
85     - set doResetHFactors=T in the following test exp:
86        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
87        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
88        and tutorial_global_oce_in_p (nonLinFS in p)
89    o pkg/ecco
90      - added IES cost term
91    o verification/advect_xz
92      - scale down the depth by 1/100 (from 200 km to just 2.km)
93      - add secondary test using divergent flow, r-star and implicit vertical advection.
94      - add note (check_conserve_TS.txt) and matlab script to check global
95        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
96    o pkg/rbcs:
97      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
98    o pkg/obcs (Stevens BCs):
99      - fix various problems in the phase speed computations of the Stevens
100        boundary conditions:
101        - sign error for western and southern boundaries,
102        - time tendencies were underestimated by factor of dTracerLev and some just
103          zero (for multidim advection schemes) -> now estimate time tendencies
104          from difference between previous (n) time level and the one before (n-1);
105          this requires storing a field per tracer per boundary, also in the pickup
106          files.
107        - replace deltaTmom in cflMer/Zon computation with dTracerLev
108        - set default phase velocity to cflMer/Zon
109      - update verification experiment exp4.stevens
110    o pkg/generic_advdiff (implicit_r):
111      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
112        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
113      - fix implicit vertical diffusion or advection with NonLin FreeSurf
114        (was using current recip_hFacC instead of future recip_hFacC): set future
115        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
116        solver S/R ;
117      - fill diagnostics of vertical advective fluxes (computed from tendency)
118        when using implicit vert. advection;
119      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
120         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
121         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
122         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
123    o pkg/diagnostics:
124      - add diags for T & S tendency which goes through Adams-Bashforth.
125    
126    checkpoint63f (2011/11/30)
127    o pkg/obcs/obcs_calc_stevens.F:
128      - join some loops to reduce number of if-statements
129      - fix a bug in code for northern and southern boundaries.
130    o pkg/seaice/seaice_init_varia.F
131      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
132        caused zero ice-velocities for the B-grid code
133    o pkg/seaice/seaice_init_fixed.F
134      - fix a bug in the initialisation of the second metric terms
135        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
136      - this affects all seaice configurations with useCurviLinearGrid = .true.
137        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
138        = .true. (default)
139      - the only verification experiment affected is global_ocean.cs32x15:
140        icedyn, seaice, and seaice_dynmix (AD)
141    o pkg/thsice/thsice_diagnostics_state.F
142      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
143        not contain garbage that can lead to surprises in diagstats_calc.F
144    o model/src:
145      - move bi,bj loops inside INTEGR_CONTINUITY ;
146      - call INTEGR_CONTINUITY directly from forward_step.F
147        (previously called from momentum_correction_step.F)
148      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
149        forward_step.F and pkg/ecco/the_main_loop.F
150    o model/src/do_oceanic_phys.F:
151      - reset addMass to zero only if useICEFRONT ;
152      - separated k-loop for rhoInSitu calculation ;
153      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
154        and at constant T,S (= WdRHOdP);
155      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
156        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
157        transport of locally-referenced potential density);
158        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
159    o gluemnc:
160      - replace ncrcat with ncks when adding variables to *.glob.nc
161      - change the way variables without record dimensions are handled so that
162        files that have variables with and without record variables can be glued:
163        add a record dimension with a new unique name to be able to differentiate
164        between variable with and without a-prior record dimensions. Remove
165        this record dimension before adding the variable to the *.glob.nc file.
166        This procedure automatically works also for grid.*.nc files that do not
167        have any record dimension.
168    o verification/cpl_aim+ocn:
169      - generate new reference output on baudelaire (gfortran, mpich2) (previously
170        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
171    o pkg/obcs/obcs_calc_stevens.F:
172      - add code for northern and southern boundaries.
173      - reorder some loops to save some operations and so that drFBar can be scalar
174    o model/src:
175      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
176        truncation) and add diagnostics for Adams-Bashforth tendency increment.
177      - update test-exp. AD output:
178        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
179      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
180        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
181        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
182        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
183        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
184        tutorial_plume_on_slope.
185    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
186      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
187      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
188      does not even come with an F77 compiler anymore, this should not be
189      a limitation
190    
191    checkpoint63e (2011/11/06)
192    o pkg/seaice adjoint of LSR:
193      - substantially rework STORE dirs.
194      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
195        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
196        and only perform SOLV_MAX_FIXED adjoint iters.
197        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
198        always goes to same record, meaning that the last forward field will be
199        the one used in the adjoint - an approximation.
200      - now produces non-zero LSR-related gradients, and acceptable gradients for
201        An's zonal (x-z) test case (to be checked in)
202      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
203        (but these are screwed up by the thermodynamics in the first place);
204        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
205        output_adm.txt also reflects changes to seaice_lsr
206      - global_ocean.cs32x15:
207        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
208          (output_adm.seaice.txt was updated)
209        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
210          (output_adm.seaice_dynmix.txt)
211    o test-exp. exp4+stevens:
212      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
213    o pkg/seaice (lsr solver):
214      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
215        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
216      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
217      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
218        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
219      - compute (with new S/R) and print initial (+ free-driff sol. if available)
220        and final residual of linearised system.
221    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
222      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
223    o pkg/obcs: Stevens BCs (still only for east and west)
224      - fix Stevens BCs by using intermediate velocities of previous
225        time step as "baroclinic" contribution rather velocity of one grid cell
226        inside the boundaries; more consistent but makes the entire treatment
227        more complicated, requires new pickup files and two new S/Rs:
228        obcs_copy_uv_n and obcs_save_uv_n
229        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
230        (undefined by default)
231      - silently move computation of some grid factors into separate loops to
232        save some recomputations
233      - add a hack for non-linear free surface
234      - add a verification experiment to exp4 that tests this code
235    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
236    
237    checkpoint63d (2011/10/25)
238    o pkg/obcs + seaice-dynamics:
239      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
240        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
241        values (consistent with an implicit method).
242      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
243        return to older implementation (same results as before); note that none of
244        the "experimental" OBCS_SEAICE options are implemented in the new version.
245      - switch test exp. seaice_obcs to use new version (update output).
246    o pkg/seaice:
247      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
248      - add parenthesis in Water-Ice drag calculations (evp & lsr);
249      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
250        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
251      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
252        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
253    o pkg/layers:
254      - Include potential density as new coordinate (Thanks to David Munday)
255    o pkg/dic:
256      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
257        carbonate computation/output to CALC_PCO2_APPROX
258    o pkg/generic_advdiff
259      - make TAF generate code that vectorizes:
260        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
261    o model/src:
262      - improve vectorization also for adjoint code of
263        solve_tridiagonal and solve_pentadiagonal. As this requires up to
264        5 new 3D-fields, this code is only turned on for the combination of
265        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
266        for singular matrix check (only for TARGET_NEC_SX).
267      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
268        ALLOW_AUTODIFF. This flag now needs to be set outside of
269        solve_tri/pentadiagonal.F
270    o pkg/exf:
271      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
272        optional namelist EXF_NML_OBCS).
273      - add many debug-print (to trace down where pkg/cal error msg comes from)
274    o pkg/mom_vecinv/mom_vi_hdissip.F
275      - rearrange loops so that vectorization is improved and in particular
276        the adjoint routine vectorizes. The code is a little longer now, but I
277        think easier to read.
278        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
279    o pkg/seaice:
280      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
281    o pkg/exch2:
282      - alternative code (without tile x tile matrix) for cumulated (global) sum;
283        used as default; keep using matrix version in adjustment.cs-32x32x1.
284    o tools/build_options:
285      - after merging some MPI and/or multi-threads specific optfiles so that
286        the modified default optfile support both built (using genmake2 -mpi
287        for the MPI built, using genmake2 -omp for OpenMP built),
288        move now obsolete optfiles to tools/build_options/unsupported/
289       (add copy of email sent to support list in doc/optfiles_changes.txt)
290    
291    checkpoint63c (2011/09/28)
292    o pkg/ebm:
293      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
294        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
295    o pkg/seaice (SItracer pickup)
296    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
297      To be done:
298      - thorough testing of missing fields in S/R seaice_read_pickup
299      - thorough matching between generic tracers and specific fields used
300        (e.g. volume-weighted age, area-weighted age, salinity, ...)
301    o pkg/grdchk:
302      - all procs calculate and print finite-difference gradient (for testreport)
303      - change description output used by testreport;
304      - AD testing: also compare and report Finite-difference gradient;
305        => update all output_adm*.txt
306    o test exp. global_ocean_ebm:
307      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
308        and turn on exactConserve; update (fwd) output.
309    o pkg/seaice (LSR):
310      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
311      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
312        * identical results with non-CS topology (but save up to half of EXCH calls)
313        * no much changes in cs-32 verification tests since no ice at face edges
314         (differences due to convergence criteria, since nb of iterations changed)
315        * expect some differences on lat-lon-cap grid.
316        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
317  o pkg/exch2:  o pkg/exch2:
318    - 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
319      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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