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revision 1.1505 by jmc, Mon Sep 26 19:00:49 2011 UTC revision 1.1565 by jmc, Fri Dec 30 16:54:46 2011 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint63h (2011/12/30)
8    o pkg/offline:
9      - new S/R OFFLINE_RESET_PARMS for resetting main-model params (switch off flags);
10      - compute vertical velocity if not read from file (switch on exactConserv
11        & staggerTimeStep);
12      - fix output of ptracer monitor iter & time for default PTRACERS_monitorFreq.
13    o verification:
14      - update grid-files (in tutorial_held_suarez_cs/input and fizhi-cs-32x32x40/input)
15        with grid-angle generated using "utils/matlab/cs_grid/cubeCalcAngle.m":
16        fix Pb in yG definition @ 2 missing corners (previously yG was averaged);
17      - update output of exp. global_ocean.cs32x15.viscA4 after changing
18        grid-file angles (used here for coriolis-3d);
19      - remove (or gzip) few files not needed to run fizhi-cs experiments.
20    o pkg/exf (vertor interpolation):
21      - rotate vector component toward local grid-axis orientation using grid-angles
22        (stored in GRID.h) instead of locally computed rotation angle; keep old code
23        available with exf option EXF_USE_OLD_VEC_ROTATION (undef by default).
24    o pkg/seaice:
25      - allow to compile with exf options ALLOW_ATM_TEMP or ALLOW_DOWNWARD_RADIATION
26        undefined. Fix and remove the stop when ALLOW_RUNOFF is undefined.
27    o pkg/PKG_OPTIONS.h files:
28      - move #include "CPP_OPTIONS.h" just after #include "PACKAGES_CONFIG.h",
29        outside of the #ifdef ALLOW_THISPKG / #endif block.
30      - update verification/*/code/PKG_OPTIONS.h files.
31    o add a verification experiment (offline_exf_seaice/input.seaice) that test
32      the B-grid LSOR solver
33    o pkg/seaice: sort out emissivity and long wave radiation step 2:
34      - add emissivity for snow and ice as new run-time parameters
35        (unfortunately) that default to the corresponding exf values; this
36        changes results in most verification experiments so that for backward
37        compatibility these parameter have to be set explicitly to inconsistent
38        values (ugly);
39      - the exf-flag EXF_LWDOWN_WITH_EMISSIVITY then gets rid off the hard-wired
40        emissivities of 0.97 associated with lwdownloc in S/R seaice_solve4temp
41        until we agree how to handle this bug properly
42    o pkg/exf (interpolation):
43      - add a set of run-time param ({inputfield}_interpMethod), one for
44        each interpolated input field, to select the interpolation method
45        with a value of zero switching off the interpolation;
46      - print interpolation parameters to standard output;
47      - refine exf_check.F accordingly ; stop if USE_NO_INTERP_RUNOFF is defined
48        (to use instead runoff_interpMethod=0 in data.exf).
49      - simplify default setting of interpolation parameters (for all fields,
50        set position to match model grid cell-center position, leading to trivial
51        interpolation in case of regular Lat-Lon grid) and fix for the case of
52        non-uniform delY.
53    o pkg/exf/exf_radiation.F: add the factor ocean_emissivity to lwdown, for
54       within #ifdef EXF_LWDOWN_WITH_EMISSIVITY/#endif. Unless ocean_emissivity=1.
55       this factor is absolutely required, because the lw exitance (= out-going
56       long wave radiation) is emissivity*stefanBoltzmann*T^4 + rho*lwdown,
57       where the reflectivity rho = 1-emissivity for conservation reasons. Once
58       this is established, we can remove the CPP-Flag (if we want to).
59    o pkg/seaice:
60      - qualify a stop statement in S/R seaice_check: EXF_READ_EVAP and
61        ALLOW_BULKFORMULAE are only required if SEAICE_EXTERNAL_FLUXES is defined
62      - sort out emissivity and long wave radiation, step 1: make SEAICE_emissivity
63        what the name implies (and not emissivity*BoltzmannConstant), this means
64        the old default value of 5.5e-8 now means
65        5.5e-8/5.670e-8 = 0.97001763668430343479 as ocean_emissivity in
66        S/R exf_readparms
67      - FV-discretization of the B-grid LSOR solver, turn on with
68        SEAICE_LSRBNEW. This new solver also involves a slight re-organization
69        of the calling routine dynsolver, so that B and C-grid code look a
70        little more alike.
71      - fix index bugs in ostres.F (B-grid code)
72    o pkg/seaice/seaice_ocean_budget.F: change (unused) code to make it look better
73    o pkg/seaice/seaice_readparms.F: make ocean_emissivity*stefanBoltzmann the
74      default for SEAICE_emissivity, if useEXF; requires setting a wrong
75      parameter value in global_ocean.cs32x15/input.seaice/data.seaice for
76      backward compatiblity
77    o model/src: use sigmaR in calc_ivdc
78    
79    checkpoint63g (2011/12/16)
80    o pkg/seaice/seaice_growth.F:
81      fix heat conservation of the coupled ocean-seaice system.
82      when SEAICE_HEAT_CONSERV_FIX is defined, the mismatch of
83      solid vs liquid water treatment is resolved via QNET.
84    o pkg/seaice/seaice_growth.F:
85      add missing term for sublimation in saltFlux, which was breaking conservation.
86    o pkg/seaice/seaice_model.F:
87      Remove this patholigical case treatment in evolution branch,
88      where it is un-necessary and breaks conservation.
89      Update global_ocean.cs32x15/results accordingly for
90      output.seaice.txt output_adm.seaice.txt and output_adm.seaice_dynmix.txt
91    o model/src:
92      useRealFreshWaterFlux: remove masking of EmPmP (using maskInC) in
93      external_forcing_surf.F and apply mask directly in S/R SOLVE_FOR_PRESSURE.
94    o pkg/obcs:
95      modify Stevens boundary conditions so that S/R obcs_calc_stevens computes
96      tendency for temperature and salinity that is then applied to update
97      theta and salt in S/R obcs_apply_ts; this requires proper masking of all
98      horizontal advection and diffusion contributions on the boundary (in
99      S/Rs gad_advection, gad_calc_rhs, gmredi_rtransport, gmredi_calc_diff), and
100      removing the mask in S/R timestep_tracer. The advantage of this approach is
101      that the updated tracer values include contributions from the surface
102      forcing and vertical diffusion.
103      This modification changes exp4.stevens because of vertical diffusion.
104    o model/src:
105      change non-curvilinear grid setting to also work with exch2 + blank tiles:
106      - move delX,delY to new header file (SET_GRID.h) and adjust length to 1rst
107        face dimensions.
108      - new S/R INI_LOCAL_GRID to define model tile-local grid (using same units
109        as delX,delY) and called from S/R INI_CARTESIAN_GRID, INI_CYLINDER_GRID
110        and INI_SPHERICAL_POLAR_GRID.
111      change test-experiment global_ocean.90x40x15:
112      - split the domain in many more tiles (9x4 tiles of 10x10 each);
113      - switch to exch2 and remove 1 blank-tile (but only for MPI test).
114      - update results of both test (std & dwnslp).
115    o pkg/diagnostics/diagstat_calc.F: fix problem with non-initialised halos in
116       tmp-fields for TARGET_NEC_SX at the cost of extra loops and less vectorisation
117    o model/src:
118      - take sigma-coords related code out of update_etah.F into new S/R UPDATE_ETAWS
119        and fix initialisation when using sigma-coords.
120    o model/src:
121     - improve Gael's changes from Jan 14, 2011 "addition of an 'update' of hfacc etc.
122       to their current value at the beginning of forward_step.F": add a new run-time
123       switch "doResetHFactors" (default=false) and use it to do (or not) the resetting.
124     - set doResetHFactors=T in the following test exp:
125        global_ocean.90x40x15/input (rStar) & input.dwnslp (linFS),
126        global_ocean.cs32x15/input.seaice (rStar), hs94.cs-32x32x5/input.impIGW (linFS)
127        and tutorial_global_oce_in_p (nonLinFS in p)
128    o pkg/ecco
129      - added IES cost term
130    o verification/advect_xz
131      - scale down the depth by 1/100 (from 200 km to just 2.km)
132      - add secondary test using divergent flow, r-star and implicit vertical advection.
133      - add note (check_conserve_TS.txt) and matlab script to check global
134        conservation of T & S with NonLin-FreeSurf and Adams-Bashforth.
135    o pkg/rbcs:
136      - add missing relaxUFile & relaxVFile in namelist (in rbcs_readparms.F).
137    o pkg/obcs (Stevens BCs):
138      - fix various problems in the phase speed computations of the Stevens
139        boundary conditions:
140        - sign error for western and southern boundaries,
141        - time tendencies were underestimated by factor of dTracerLev and some just
142          zero (for multidim advection schemes) -> now estimate time tendencies
143          from difference between previous (n) time level and the one before (n-1);
144          this requires storing a field per tracer per boundary, also in the pickup
145          files.
146        - replace deltaTmom in cflMer/Zon computation with dTracerLev
147        - set default phase velocity to cflMer/Zon
148      - update verification experiment exp4.stevens
149    o pkg/generic_advdiff (implicit_r):
150      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
151        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
152      - fix implicit vertical diffusion or advection with NonLin FreeSurf
153        (was using current recip_hFacC instead of future recip_hFacC): set future
154        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
155        solver S/R ;
156      - fill diagnostics of vertical advective fluxes (computed from tendency)
157        when using implicit vert. advection;
158      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
159         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
160         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
161         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
162    o pkg/diagnostics:
163      - add diags for T & S tendency which goes through Adams-Bashforth.
164    
165    checkpoint63f (2011/11/30)
166    o pkg/obcs/obcs_calc_stevens.F:
167      - join some loops to reduce number of if-statements
168      - fix a bug in code for northern and southern boundaries.
169    o pkg/seaice/seaice_init_varia.F
170      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
171        caused zero ice-velocities for the B-grid code
172    o pkg/seaice/seaice_init_fixed.F
173      - fix a bug in the initialisation of the second metric terms
174        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
175      - this affects all seaice configurations with useCurviLinearGrid = .true.
176        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
177        = .true. (default)
178      - the only verification experiment affected is global_ocean.cs32x15:
179        icedyn, seaice, and seaice_dynmix (AD)
180    o pkg/thsice/thsice_diagnostics_state.F
181      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
182        not contain garbage that can lead to surprises in diagstats_calc.F
183    o model/src:
184      - move bi,bj loops inside INTEGR_CONTINUITY ;
185      - call INTEGR_CONTINUITY directly from forward_step.F
186        (previously called from momentum_correction_step.F)
187      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
188        forward_step.F and pkg/ecco/the_main_loop.F
189    o model/src/do_oceanic_phys.F:
190      - reset addMass to zero only if useICEFRONT ;
191      - separated k-loop for rhoInSitu calculation ;
192      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
193        and at constant T,S (= WdRHOdP);
194      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
195        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
196        transport of locally-referenced potential density);
197        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
198    o gluemnc:
199      - replace ncrcat with ncks when adding variables to *.glob.nc
200      - change the way variables without record dimensions are handled so that
201        files that have variables with and without record variables can be glued:
202        add a record dimension with a new unique name to be able to differentiate
203        between variable with and without a-prior record dimensions. Remove
204        this record dimension before adding the variable to the *.glob.nc file.
205        This procedure automatically works also for grid.*.nc files that do not
206        have any record dimension.
207    o verification/cpl_aim+ocn:
208      - generate new reference output on baudelaire (gfortran, mpich2) (previously
209        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
210    o pkg/obcs/obcs_calc_stevens.F:
211      - add code for northern and southern boundaries.
212      - reorder some loops to save some operations and so that drFBar can be scalar
213    o model/src:
214      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
215        truncation) and add diagnostics for Adams-Bashforth tendency increment.
216      - update test-exp. AD output:
217        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
218      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
219        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
220        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
221        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
222        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
223        tutorial_plume_on_slope.
224    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
225      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
226      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
227      does not even come with an F77 compiler anymore, this should not be
228      a limitation
229    
230    checkpoint63e (2011/11/06)
231    o pkg/seaice adjoint of LSR:
232      - substantially rework STORE dirs.
233      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
234        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
235        and only perform SOLV_MAX_FIXED adjoint iters.
236        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
237        always goes to same record, meaning that the last forward field will be
238        the one used in the adjoint - an approximation.
239      - now produces non-zero LSR-related gradients, and acceptable gradients for
240        An's zonal (x-z) test case (to be checked in)
241      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
242        (but these are screwed up by the thermodynamics in the first place);
243        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
244        output_adm.txt also reflects changes to seaice_lsr
245      - global_ocean.cs32x15:
246        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
247          (output_adm.seaice.txt was updated)
248        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
249          (output_adm.seaice_dynmix.txt)
250    o test-exp. exp4+stevens:
251      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
252    o pkg/seaice (lsr solver):
253      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
254        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
255      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
256      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
257        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
258      - compute (with new S/R) and print initial (+ free-driff sol. if available)
259        and final residual of linearised system.
260    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
261      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
262    o pkg/obcs: Stevens BCs (still only for east and west)
263      - fix Stevens BCs by using intermediate velocities of previous
264        time step as "baroclinic" contribution rather velocity of one grid cell
265        inside the boundaries; more consistent but makes the entire treatment
266        more complicated, requires new pickup files and two new S/Rs:
267        obcs_copy_uv_n and obcs_save_uv_n
268        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
269        (undefined by default)
270      - silently move computation of some grid factors into separate loops to
271        save some recomputations
272      - add a hack for non-linear free surface
273      - add a verification experiment to exp4 that tests this code
274    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
275    
276    checkpoint63d (2011/10/25)
277    o pkg/obcs + seaice-dynamics:
278      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
279        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
280        values (consistent with an implicit method).
281      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
282        return to older implementation (same results as before); note that none of
283        the "experimental" OBCS_SEAICE options are implemented in the new version.
284      - switch test exp. seaice_obcs to use new version (update output).
285    o pkg/seaice:
286      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
287      - add parenthesis in Water-Ice drag calculations (evp & lsr);
288      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
289        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
290      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
291        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
292    o pkg/layers:
293      - Include potential density as new coordinate (Thanks to David Munday)
294    o pkg/dic:
295      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
296        carbonate computation/output to CALC_PCO2_APPROX
297    o pkg/generic_advdiff
298      - make TAF generate code that vectorizes:
299        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
300    o model/src:
301      - improve vectorization also for adjoint code of
302        solve_tridiagonal and solve_pentadiagonal. As this requires up to
303        5 new 3D-fields, this code is only turned on for the combination of
304        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
305        for singular matrix check (only for TARGET_NEC_SX).
306      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
307        ALLOW_AUTODIFF. This flag now needs to be set outside of
308        solve_tri/pentadiagonal.F
309    o pkg/exf:
310      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
311        optional namelist EXF_NML_OBCS).
312      - add many debug-print (to trace down where pkg/cal error msg comes from)
313    o pkg/mom_vecinv/mom_vi_hdissip.F
314      - rearrange loops so that vectorization is improved and in particular
315        the adjoint routine vectorizes. The code is a little longer now, but I
316        think easier to read.
317        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
318    o pkg/seaice:
319      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
320    o pkg/exch2:
321      - alternative code (without tile x tile matrix) for cumulated (global) sum;
322        used as default; keep using matrix version in adjustment.cs-32x32x1.
323    o tools/build_options:
324      - after merging some MPI and/or multi-threads specific optfiles so that
325        the modified default optfile support both built (using genmake2 -mpi
326        for the MPI built, using genmake2 -omp for OpenMP built),
327        move now obsolete optfiles to tools/build_options/unsupported/
328       (add copy of email sent to support list in doc/optfiles_changes.txt)
329    
330    checkpoint63c (2011/09/28)
331    o pkg/ebm:
332      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
333        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
334  o pkg/seaice (SItracer pickup)  o pkg/seaice (SItracer pickup)
335  * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)  * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
336    To be done:    To be done:

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