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revision 1.1768 by mlosch, Wed Nov 14 16:43:38 2012 UTC revision 1.1836 by jmc, Mon Mar 4 19:08:25 2013 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/generic_advdiff:
8      - implement compressible flow method for multi-dim advection (similar to
9        gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
10        TAF generates many recomputations) to use it; no yet coded with implicit
11        vertical advection.
12      - change experiment advect_cs (new output) and advect_xy (same output)
13        to test compressible flow multi-dim advection.
14    o pkg/generic_advdiff:
15      - fix SOM advection for unusual cases (linear Free-Surf in r*, other
16        cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
17  o pkg/seaice:  o pkg/seaice:
18    - turn the LSR-relaxation parameters WFAU/V into runtime parameters    - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
19        bug affects two verification experiments (lab_sea and lab_sea.hb87),
20        recover old (wrong) results by setting noSlipFac = 2. in
21        seaice_calc_strainrates.F;
22      - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
23      - add runtime parameter SEAICE_JFNKepsilon for that finite difference
24        gradient in the Jacobian times vector operation (s/r seaice_jacvec)
25      - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
26    o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
27      - new subroutines seaice_lsr_tridiagu/v
28      - introduce loop bounds i/jmin/max to be able to use a restricted
29        additive Schwarz method, but not used for now.
30      - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
31      - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
32    o OpenAD support
33      Reorganize S/R call for overall time-stepping loop to facilitate
34      OpenAD revolve loop replacement
35      (new S/R main_do_loop.F)
36    o model/src:
37      - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
38      - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
39        ADAMS_BASHFORTH2.
40    o pkg/cheapaml:
41      - add new parameter (default=F, same as before) to disable full domain
42        (including land) periodicity in X & Y dir.
43      - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
44        prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
45        into single S/R CHEAPAML_TIMESTEP.
46    
47    checkpoint64d (2013/02/17)
48    o pkg/monitor (angular momentum):
49      - do not add Eta contribution to the total AM if using rigid-lid;
50      - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
51      - horizontal discretisation: compute Zonal wind contribution separately for
52        each component (instead of from cell centered averaged) and use the 4
53        grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
54      - Check that AM is conserved with linear dynamics (momAdvection=F and linear
55        FreeSurf) if using vectorInvariant momentum.
56    o model/src (horizontal grid):
57      - move initialisation of all horizontal grid arrays to null value
58        from specific horizontal grid S/R to main S/R INI_GRID;
59      - add 2 new arrays to project model C-grid velocity on to zonal direction
60        (similar to AngleCosC & -AngleSinC but at U and V point location) and
61        compute them in S/R CALC_GRID_ANGLES.
62    o pkg/seaice: replace a hard coded parameter by a runtime parameter
63        SEAICE_JFNK_tolIter
64    o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
65        preconditioner for JFNK (run LSR into the overlaps as far as possible,
66        i.e OLx/y-2, but overwrite the solution in the overlaps)
67      - extend loop range in seaice_calc_viscosity
68      - add new parameters SEAICE_OLx/y (default = OLx/y-2)
69      - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
70      - slightly modify loops in tridiagonal solver lsr-preconditioner
71      - by default remove the extra exchange in seaice_preconditioner with a
72        replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
73      - modify offline_exf_seaice so that old results without RAS are reproduced
74        for output.dyn_jfnk.txt
75      in seaice_fgmres.F (unrelated to RAS)
76      - add a cpp-flag option for a re-ordered mapping (potentially more
77        efficient), but because this changes the results, turn it off by
78        default
79      - replace the save statement by local common blocks
80    o utils/matlab:
81      - fix tile-offset in rdmnc.m when output was produced using EXCH2.
82      - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
83        instead of local script "load_cs.m".
84    o pkg/seaice:
85      - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
86        to the scalarProductMetric and the unrolling. By chance this does not
87        change the verification experiment, because of the particular domain
88        decomposition
89    o pkg/diagnostics:
90      - change default missing_value from UNSET_RL to -999.
91    o pkg/layers: improve vectorization of layers_fluxcalc.F
92      - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
93        time spent in this routine by more than a factor of 3 on an NEC-SX8
94      - step 2: replace search algorithm by a bisection algorithm found in
95        Press et al. Numerical Recipes in Fortran. This algorithm can be
96        vectorized and finds the correct bin in approx. log2(Nlayers) steps.
97        For now, use this algorithm only for TARGET_NEC_SX defined.
98      - moved the search algorithm into a separate subroutine, that is kept
99        within the same file for automatic inlining.
100      - modified catching potential errors
101    o pkg/ecco:
102      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
103    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
104      - modifications for ALLOW_GENTIM2D_CONTROL
105      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
106      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
107      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
108      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
109    o model/src:
110      - account for moist thermodynamics in (dry) potential temperature equation;
111        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
112        and cpl_aim+ocn.
113      - also switch to standard compiler (gfortran, was using ifort previously)
114        for fizhi-cs experiments reference output.
115    o pkg/ctrl:
116      - 1st step toward generic time-varying control variable (2D) via CPP option
117        ALLOW_GENTIM2D_CONTROL
118      - note new namelist ctrl_nml_genarr in data.ctrl
119    o verification/global_ocean.cs32x15:
120      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
121        thsice calling sequence and update "output.icedyn.txt" output file.
122    o pkg/ptracers:
123      - from Ryan A.: code to allow to restart a tracer at regular time interval
124        specifying a reset frequency and a reset-phase (for each tracers).
125    o pkg/thsice:
126      - implement new sequence of calls for thsice+seaice:
127          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
128          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
129      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
130        in CPP_OPTIONS.h) to recover old sequence;
131      - update diagnostics for Intermediate State thsice diagnostics: now filled
132        just before advection (instead of just after advection in old sequence);
133      - update output of experiment offline_exf_seaice (standard test);
134      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
135        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
136    o pkg/aim_v23:
137      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
138      - use standard pkg/mdsio routines to read & write CO2 pickup file;
139      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
140      - Implement new sequence of calls for seaice advection (with thsice and
141        seaice diffusion): do ice advection after ice-Thermodynamic (previously
142        was done before); change aim_do_physics.F (split the bi,bj loops block);
143      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
144    o pkg/thsice:
145      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
146        where just seaice diffusion is used without seaice-dynamics.
147    
148    checkpoint64c (2013/01/18)
149    o pkg/seaice:
150      - add a parameter JFNKres_tFac that can replace JFNKres_t
151        (= JFNKres_tFac*JFNKresidual before JFNK solver)
152      - add a line search option to the JFNK solver
153      - move update of u/vIce and computation of initial residual into a separate
154        routine (same file); makes the code a little easier to read (?)
155      - the line search requires computation of the residual and for some reason
156        I cannot do the update of u/vIce at the beginning of the Newton loop
157        without changing the results, so we move computation of the new residual
158        also to the end of the Newton loop, even without the line search
159    o pkg/mdsio:
160      - write missing value (corresponding to undefined array value) to meta files;
161        skip this if missing value is one (UNSET_RL would be a better value for the
162        case of undefined missing value but it's current the default missing-value);
163        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
164    o pkg/exf & thsice:
165      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
166        diagnostics) even when SHORTWAVE_HEATING is #undef;
167    o verification/cfc_example:
168      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
169        illustrate how to use it).
170    o verification/offline_exf_seaice:
171      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
172        files to only one time-record.
173      in input.thermo: narrow the 2 bands of low initial ice-concentration near
174        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
175        snapshot output; same mcPheePiston value as in thsice with
176        surf-current=0.2m/s.
177      in input.thsice: similar set-up as in input.thermo (channel with same seaice
178        initial conditions).
179    o verification/cfc_example:
180      - update file "data" with more standard choice (default rotationPeriod,
181        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
182        set deltaTFreeSurf to deltaTtracer) and update the output.
183    o pkg/layers:
184      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
185      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
186    o verification/offline_exf_seaice:
187      - set all {field}period to zero for constant-in-time forcing (not tested
188        anywhere else).
189    o verification/offline_exf_seaice:
190      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
191      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
192    o model/src:
193      - implement Finite-Volume method for (hydrostatic) presure gradient
194        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
195    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
196      - In order to be compatible with the default EVP code, this requires changing
197        the EVP code around a little; and because any small change immediately
198        breaks the lab_sea.hb87 verification experiment, the reference output is
199        updated two times (each time the remaining aggrement was only 2 digits):
200        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
201        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
202        The adjoint test lab_sea.evp also needed to be updated.
203      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
204        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
205        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
206        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
207        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
208        kept obscure, because I need to test it a little more.
209    o pkg/cheapaml:
210      - fix few incorrect type (_RL/_RS) in subroutine calls.
211    o pkg/seaice:
212      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
213        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
214    o model/src:
215      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
216        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
217        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
218    o pkg/cheapaml:
219      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
220        update output of experiment cheapAML_box.
221      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
222        and set them only in one place (cheapaml_readparms.F).
223      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
224      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
225        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
226    o model/src/the_main_loop.F:
227      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
228    o pkg/seaice:
229      - remove legacy branch code.
230      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
231    o verification/*/code*/SEAICE_OPTIONS.h:
232      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
233        SEAICE_CAP_HEFF).
234    o pkg/cheapaml:
235      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
236        to load new forcing fields.
237      - add missing "_d 0" where it's needed; + some editing (improve indentation).
238      - remove switch to "-r8" compiler option (no longer needed) in verification
239        cheapAML_box, keep same output (small trucation error differences).
240    o verification/offline_exf_seaice:
241      - add thermodynamics only test.
242    o verification/cheapAML_box:
243      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
244        keep same output (same 14 digits for cg2d).
245      - switch on "-r8" compiler option (some numerical values are missing
246        the "_d 0") and update output (only 6 digits for cg2d were preserved).
247    
248    checkpoint64b (2012/12/24)
249    o pkg/cheapaml:
250      - remove un-used variables (Qnet,EmPmR) from pickup files.
251      - store tendency of advected variables into cheapaml pickup file
252        and fix the AB-2 restart.
253    o verification/offline_exf_seaice and lab_sea adjoint:
254      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
255      - switch to 4 time steps in offline, consistent with lab_sea.
256      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
257      - update results after change of experiment seaice.
258    o pkg/seaice:
259      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
260        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
261        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
262        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
263    o model/src:
264      - add run-time parameter to select CG2D solver minimum-residual solution
265        (in case of a poor convergence).
266    o pkg/seaice/seaice_lsr.F
267      - move calculation of matrix coefficients into new
268        S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
269        file; the main purpose of this change is to be able to reuse the code
270        in S/R SEAICE_PRECONDITIONER
271      - modify the computation of the residual so that the mass of sea-ice
272        is not used twice; this simplifies the calculations, but since
273        the residual is never used except when LSR_mixIniGuess.ge.4---and this is
274        not tested in testreport---this does not affect the testreport results.
275    o verification/seaice_obcs:
276      - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
277        verification/lab_sea/input.salt_plume; changes results/output.txt*
278    o model/src:
279      - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
280    o pkg/seaice:
281      - improve description of parameters in seaice_fgmres.F and start
282        cleaning up the code
283      - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
284        second argument
285      - add a metric based on grid cell area to SEAICE_SCALPROD; update
286        results of offline_exf_seaice.dyn_jfnk
287      - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
288    o pkg/aim_v23:
289      - fix an other bug in dissipation heating (grid-cell area was missing).
290    o model/src + pkg/seaice:
291      - add global (multi-tile) linear solver for pair of tri-diagonal system
292        along X and Y lines, respectively for U and V component.
293        Note: 1) MPI and cube-exchange not yet coded.
294            2) probably not accurate for poorly conditioned / large size problem.
295      - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
296        default: not compiled and not used.
297    o pkg/seaice:
298      - first attempt at a multi-threaded fgmres solver for the JFNK solver:
299        introduce bi/bj loops and use global_sum_tile_rl instead of
300        mpi_allreduce in seaice_fgmres.F
301      - improve diagnostics output for fgmres solver (seaice_fgmres.F)
302      - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
303      - add a verification experiment for JFNK in offline_exf_seaice
304    o verification:
305      - change (for now, only fwd test) offline_exf_seaice experiment:
306        use a re-entrant channel with idealized coastline (trapezoidal shape)
307        at southern boundary to explore seaice dynamics and thermodynamics
308        with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
309        secondary test (input.thsice) use thermodynamics only with SST relaxation.
310      - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
311    o pkg/exf:
312      - disable "sstExtrapol" when Nr=1
313    o verification:
314      - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
315        to test pkg/cheapaml.
316    o pkg/aim_v23 & pkg/shap_filt:
317      - fix dissipation heating (erroneous gravity multiplication factor).
318    o pkg/seaice:
319      - remove unused field pressPre from jfnk solver
320      - rename two subroutines in seaice_preconditioner.F
321    o eesupp/src:
322       - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
323    o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
324       - remove wrong parts of the rhs and the lhs (were in there
325         because I did not understand the concept of this preconditioner)
326       - add an exchange between u- and v-sweep. This increases communication
327         by a factor of two but improves the convergence of jfnk. Ideally,
328         one would like the u- and v-sweep to be independent. So far within
329         undocumented ifdefs
330       - reorganize the extra computations for printing the residuals
331    o tools/genmake2:
332      - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
333        since it's not necessary (and was preventing to use MNC in some cases).
334    
335    checkpoint64a (2012/11/16)
336    o pkg/autodiff:
337      - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
338        autodiff_readparms.F no longer depends on calling order (within
339        packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
340        rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
341        and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
342    o pkg/obcs:
343      - adding tidal velocity forcing capability to obcs
344        for usage example, see verification/seaice_obcs/input.tides
345    o pkg/seaice:
346      - turn the LSR-relaxation parameters WFAU/V into runtime parameters
347      SEAICE_LSRrelaxU/V      SEAICE_LSRrelaxU/V
348      - introduce runtime parameter SEAICEetaZmethod (=0 by default)
349  o pkg/aim_v23:  o pkg/aim_v23:
350    - implement heating from friction (bottom friction and stratospheric drag).    - implement heating from friction (bottom friction and stratospheric drag).
351  o pkg/shap_filt:  o pkg/shap_filt:

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