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revision 1.1455 by gforget, Wed Jun 15 01:31:34 2011 UTC revision 1.1519 by jmc, Tue Oct 25 12:35:08 2011 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint63d (2011/10/25)
8    o pkg/obcs + seaice-dynamics:
9      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
10        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
11        values (consistent with an implicit method).
12      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
13        return to older implementation (same results as before); note that none of
14        the "experimental" OBCS_SEAICE options are implemented in the new version.
15      - switch test exp. seaice_obcs to use new version (update output).
16    o pkg/seaice:
17      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
18      - add parenthesis in Water-Ice drag calculations (evp & lsr);
19      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
20        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
21      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
22        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
23    o pkg/layers:
24      - Include potential density as new coordinate (Thanks to David Munday)
25    o pkg/dic:
26      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
27        carbonate computation/output to CALC_PCO2_APPROX
28    o pkg/generic_advdiff
29      - make TAF generate code that vectorizes:
30        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
31    o model/src:
32      - improve vectorization also for adjoint code of
33        solve_tridiagonal and solve_pentadiagonal. As this requires up to
34        5 new 3D-fields, this code is only turned on for the combination of
35        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
36        for singular matrix check (only for TARGET_NEC_SX).
37      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
38        ALLOW_AUTODIFF. This flag now needs to be set outside of
39        solve_tri/pentadiagonal.F
40    o pkg/exf:
41      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
42        optional namelist EXF_NML_OBCS).
43      - add many debug-print (to trace down where pkg/cal error msg comes from)
44    o pkg/mom_vecinv/mom_vi_hdissip.F
45      - rearrange loops so that vectorization is improved and in particular
46        the adjoint routine vectorizes. The code is a little longer now, but I
47        think easier to read.
48        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
49    o pkg/seaice:
50      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
51    o pkg/exch2:
52      - alternative code (without tile x tile matrix) for cumulated (global) sum;
53        used as default; keep using matrix version in adjustment.cs-32x32x1.
54    o tools/build_options:
55      - after merging some MPI and/or multi-threads specific optfiles so that
56        the modified default optfile support both built (using genmake2 -mpi
57        for the MPI built, using genmake2 -omp for OpenMP built),
58        move now obsolete optfiles to tools/build_options/unsupported/
59       (add copy of email sent to support list in doc/optfiles_changes.txt)
60    
61    checkpoint63c (2011/09/28)
62    o pkg/ebm:
63      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
64        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
65    o pkg/seaice (SItracer pickup)
66    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
67      To be done:
68      - thorough testing of missing fields in S/R seaice_read_pickup
69      - thorough matching between generic tracers and specific fields used
70        (e.g. volume-weighted age, area-weighted age, salinity, ...)
71    o pkg/grdchk:
72      - all procs calculate and print finite-difference gradient (for testreport)
73      - change description output used by testreport;
74      - AD testing: also compare and report Finite-difference gradient;
75        => update all output_adm*.txt
76    o test exp. global_ocean_ebm:
77      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
78        and turn on exactConserve; update (fwd) output.
79    o pkg/seaice (LSR):
80      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
81      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
82        * identical results with non-CS topology (but save up to half of EXCH calls)
83        * no much changes in cs-32 verification tests since no ice at face edges
84         (differences due to convergence criteria, since nb of iterations changed)
85        * expect some differences on lat-lon-cap grid.
86        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
87    o pkg/exch2:
88      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
89        many tiles); until alternative coding is added, just add a stop.
90    o pkg/kpp:
91      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
92        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
93    o optfiles:
94      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
95        into corresponding standard one, which now support different build:
96        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
97      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
98    o pkg/obcs (seaice):
99      - add missing EXCH for uIce,vIce after applying OBCS;
100      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
101        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
102        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
103      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
104      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
105        and eedata.mth for MPI and mutlti-threaded testing.
106    o pkg/flt:
107      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
108      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
109      - fix pickup and trajectories + profiles output with multi-threads;
110      - add parameter to select group of fields to write along trajectory and
111        profile (default unchanged);
112      - only call PORT_RAND* function when flt_noise <> 0;
113      - add multi-threaded test for verification exp. flt_example.
114    o eesupp/src:
115      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
116      - USE_OMP_THREADING: check that number of threads (from eedata) matches
117        actual number (from env.var. setting).
118    o pkg/ebm:
119      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
120      - add multi-threaded test for verification exp. global_ocean_ebm
121    
122    checkpoint63b (2011/08/29)
123    o pkg/ebm:
124      - fix sign of runoff;
125      - update directly forcing fields (Qnet,EmPmR) to use standard
126        external_forcing_surf.F (remove ebm_forcing_surf.F);
127      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
128      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
129        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
130      - update global_ocean_ebm parameters file data and update output (fwd+ad).
131    o verification/matrix_example:
132      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
133        MPI and mutlti-threaded testing.
134    o pkg/matrix:
135      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
136      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
137      - fix for multi-threaded (remove DATA statement);
138      - use standard DIFFERENT_MULTIPLE function;
139      - add MATRIX_OPTIONS.h
140    o verification/matrix_example:
141       To allow to split the domain in several tiles, change the domain size
142        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
143        Western side) of land points.
144    o (*_)write_pickup:
145      - fix few bugs in mypackage_read/write_pickup.F
146      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
147        array of length 1 (was caught by compiler syntax-check).
148    o pkg/diagnostics (velocity potential solver):
149      - fix initialisation of main diagonal matrix (for overlap values)
150    o tools/build_options:
151      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
152        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
153      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
154        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
155        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
156        and use "-devel" testreport option for standard testing on baudelaire.
157    o pkg/grdchk:
158      - Assume that all gradient-check position are within the same tile
159        corresponding to global indices (iGloTile,jGloTile) and that
160        positions (i,j indices or nbeg) are local to this tile;
161      - set tile local-indices and proc. number according to tile global-indices;
162      - remove grdchkwhichproc from namelist (retired param);
163      - send adjoint gradient to all procs so that all procs print it to STDOUT;
164      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
165    o adding package bbl (Bottom Boundary Layer)
166      description in MITgcm/pkg/bbl/bbl_description.tex
167      example/test experiment in MITgcm_contrib/bbl
168    o adjoint verifications
169      - changed 5 experiments to multi-tiles
170        * global_ocean.90x40x15
171        * obcs_ctrl
172        * offline_exf_seaice
173        * tutorial_dic_adjoffline
174        * tutorial_tracer_adjsens
175        changed reference output for those that crossed tile boundaries
176        (changed choices of gradient check positions)
177      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
178      - temporary bug fix in grdchk_loc.F for obcs
179    o genmake2 & testreport
180      - add target "obj" (just for OBJFILES files) to Makefile;
181      - add option to specify FEXTRAFLAGS on command line.
182    o pkg/mypackage:
183      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
184    
185    checkpoint63a (2011/08/02)
186    o pkg/diagnostics (velocity potential):
187      - fix velocity-potential calculation when using OBCS: balance net inflow
188        at each level (new S/R OBCS_DIAG_BALANCE).
189      - fix some of the problems with OBCS in stream-function calculation.
190    o pkg/exf/exf_readparms.F
191      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
192        EXF_NML_OBCS) more consistent, so that you need not have these lists
193        in data.exf when they are not used.
194    o optim/optim_readdata.F:
195      - add some output about obcs variables that might help debugging
196      - add a check about nvarlength
197    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
198    o pkg/diagnostics (velocity potential):
199      - fix mask for OBCS (still problems in stream-function with OBCS);
200      - add specific parameter (default = main code CG2D params) for solver;
201      - in case of poor convergence, use solution corresponding to lowest residual.
202    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
203      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
204      and should be avoided where possible.
205    o model/src (rStar):
206      - include r* effect on reference-state (PhiRef) in totPhiHyd
207        (so that it's really the potential anomaly at the cell center);
208        affect solution only if z* with full pressure in EOS.
209      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
210        update output (because of z* in totPhiHyd and viscA4 changes);
211      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
212        @ constant r) until interpolation at constant r is implemented.
213    o pkg/diagnostics
214      - fix RCENTER diagnostics in case cell center is not at interface middle
215    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
216      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
217      that THETA and SALT are "conservative temperature" and "absolute
218      salinity"
219    o pkg/ctrl
220      - fix computation of endrec in s/r ctrl_init_rec
221      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
222    o pkg/seaice/seaice_growth.F
223      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
224        remove then obsolete STORE directives
225      - fix STORE directives for tice and tices, so that only the
226        appropriate part of the fields are stored (and not the entire
227        field); update global_ocean.cs32x15.seaice AD output.
228      - cosmetic changes: adjust CPP flags and indentation for better
229        legibilty
230    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
231      Chris Wilson)
232    o pkg/gmredi:
233       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
234       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
235    
236    checkpoint63  (2011/07/11)
237    o pkg/exch2:
238     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
239     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
240       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
241       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
242    o pkg/diagnostics:
243     - deal with pairs of post-processed diags which are computed together; in
244       particular, re-order list of diags within 1 file to save 2nd computation.
245     - add S/R to compute velocity stream-function (called after velocity-potential
246       calculation) from divergence free transport -> new diagnostics "PsiVEL".
247     - add parameter to select grid-point location where PsiVEL == 0.
248    o eesupp/src:
249       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
250       (specific S/R needed with exch2 topology - for now, just print an error msg)
251    o pkg/shelfice
252     - Implement friction velocity-dependent transfer coefficients following
253       Holland and Jenkins, JPO, 1999
254       Original code by M. Losch with small modifs.
255       Enable with CPP option SHI_ALLOW_GAMMAFRICT
256       and runtime flag SHELFICEuseGammaFrict
257    o verification lab_sea & global_ocean.cs32x15:
258     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
259       does not miss some dependencies (but is slower) and also works with many files
260       (default makedepend limitation for AD built).
261     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
262    o pkg/diagnostics:
263     - add run-time parameter "useMissingValue" (def=False) to fill land-point
264        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
265       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
266     - Extend the use of "missing_value" setting from data.diagnostics for the case
267       of counter-diagnostics (where fraction-weight is zero). This applies both to
268       MNC and MDS output files.
269    o pkg/seaice/seaice_growth.F:
270      - add 'a priori' cap of latent heat flux based on actual mass considerations
271        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
272        non-legacy seaice_solve4temp.
273      - add diagnostic of the residual sublimation freshwater flux (the freshwater
274        flux taken from the ocean if the total actual latent heat fluxes exceed
275        the maximum)
276      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
277       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
278      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
279       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
280      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
281      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
282    o verification 1D_ocean_ice_column:
283       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
284       update results
285    o pkg/diagnostics:
286     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
287       which are not filled-up but computed from other diags ; In this case, the mate
288       diag points to the primary (filled-up) diag to used for post processing.
289     - Update Velocity-potential computation using post-processed diag framework.
290     ==> Change the ordering of fields and time-periods in MDS output file
291       when using periodic averaging: now writes one time record with the full set
292       of fields for this time period, then the next time reccord (it used to be
293       one field with the full set of time records then the next field).
294         Note: this is now similar to NetCDF (MNC) output file. <==
295    
296    checkpoint62z (2011/06/21)
297    o adjoint monitor:
298     - Add adjoint monitor output for packages exf, seaice
299       and update relevant testreport output
300  o pkg/seaice:  o pkg/seaice:
301   - re-order diags inits so that they appear in order in available_diagnostics.log   - re-order diags inits so that they appear in order in available_diagnostics.log
302   - added diags: hsnow thermo. rates of change, area preceeding ridiging process,   - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
# Line 11  o pkg/seaice: Line 304  o pkg/seaice:
304   - modified diag: SIdA; output actual effect, as the description states.   - modified diag: SIdA; output actual effect, as the description states.
305   - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.   - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
306   - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.   - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
307     (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;     (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
308      and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)      and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
309   - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.   - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
310   - added diagnostics for seaice genereic tracers (SItr*).   - added diagnostics for seaice generic tracers (SItr*).
311   - added SItrUnit and SItrNameLong run time param (for SItr* diags).   - added SItrUnit and SItrNameLong run time param (for SItr* diags).
312   - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.   - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
313     I. Fenty: 18-Jun-2011:
314     Minor changes to seaice package:
315     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
316        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
317       - Differentiated "regularization variables" from "floor variables"
318        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
319        * hiceMin became SEAICE_hice_reg (old hiceMin)
320          (with _reg meaning regularization variable)
321       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
322        so as to ensure energy conservation when going between phases
323      - A22 was not used anywhere
324     2) Changed regularization procedure for heffActual and hsnowActual to ensure
325        well-boundedness and smooth adjoint in seaice_growth.F
326     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
327        because the old regularization always set heffActual >= 0.05 cm
328     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
329        on AREA when HEFF > 0.
330      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
331        requiring that DISABLE_AREA_FLOOR *not* be defined
332     Affected verifications:
333      - 1D_ocean_ice_column (output.txt output_adm.txt)
334      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
335  o pkg/diagnostics:  o pkg/diagnostics:
336    - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).    - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
337    - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument    - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
# Line 24  o pkg/diagnostics: Line 339  o pkg/diagnostics:
339    - add pieces of code to compute velocity potential at each level (new diagnostics    - add pieces of code to compute velocity potential at each level (new diagnostics
340      PhiVEL, works only when UVELMASS & VVELMASS are also turned on);      PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
341      for now, using same params as CG2D (target-resisual, max Nb of iter ...).      for now, using same params as CG2D (target-resisual, max Nb of iter ...).
342      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
343        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
344        and in diagnostics_fract_fill.F (do not need a valid pointer for the
345        diagnostics counter-mate); check that definition of counter-diagnostic
346        includes a valid counter-mate (in diagnostics_set_levels.F).
347  o model/src (rStar):  o model/src (rStar):
348    - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);    - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
349      affect solution only if z* with full pressure in EOS;      affect solution only if z* with full pressure in EOS;

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