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revision 1.1788 by jmc, Sat Dec 22 00:41:09 2012 UTC revision 1.1843 by gforget, Mon Mar 25 21:41:47 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 verification/offline_exf_seaice: replace adjoint experiment.
8    o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
9      - add OpenAD setup to this exp and make ptracers package work with OpenAD
10    o pkg/seaice/seaice_evp.F: mask the asymmetric contribution of the ice-ocean
11      stress (when the turningAngle is non-zero) over open water to avoid
12      stripes in the EVP-solutions after many EVP-substeps. This does not change
13      the verification experiment (because turningAngle=0 in that experiment), but
14      will affect other EVP solutions with turningAngle.ne.0
15    o verification, AD & TLM output:
16      - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
17        additions and multiplications which affect results at machine truncation
18        level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
19        lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
20        (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
21        digits of matching.
22    o pkg/seaice:
23       modify lsr-algorithm so that it vectorizes AND converges by using a
24       "zebra" method: split vector loop into two with step size 2; this
25       solves a general convergence problem for the JFNK solver on a vector
26       computer. It has the potential to even improve convergence for
27       non-vector machines, but it does change the results so it is turned
28       off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
29       SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
30    
31    checkpoint64e (2013/03/05)
32    o pkg/ecco and several verification experiments:
33       Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
34       from ecco package, and revert to unified routine in model/src/
35       Adjust verification experiments accordingly, especially gloal_oce_llc90
36       Should conclude long-standing work by Gael to reconsile the_main_loop with
37       ECCO and will enable OpenAD's revolve loop in ECCO setup.
38    o pkg/generic_advdiff:
39      - implement compressible flow method for multi-dim advection (similar to
40        gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
41        TAF generates many recomputations) to use it; no yet coded with implicit
42        vertical advection.
43      - change experiment advect_cs (new output) and advect_xy (same output)
44        to test compressible flow multi-dim advection.
45    o pkg/generic_advdiff:
46      - fix SOM advection for unusual cases (linear Free-Surf in r*, other
47        cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
48    o pkg/seaice:
49      - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
50        bug affects two verification experiments (lab_sea and lab_sea.hb87),
51        recover old (wrong) results by setting noSlipFac = 2. in
52        seaice_calc_strainrates.F;
53      - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
54      - add runtime parameter SEAICE_JFNKepsilon for that finite difference
55        gradient in the Jacobian times vector operation (s/r seaice_jacvec)
56      - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
57    o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
58      - new subroutines seaice_lsr_tridiagu/v
59      - introduce loop bounds i/jmin/max to be able to use a restricted
60        additive Schwarz method, but not used for now.
61      - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
62      - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
63    o OpenAD support
64       Reorganize S/R call for overall time-stepping loop to facilitate
65       OpenAD revolve loop replacement
66       (new S/R main_do_loop.F)
67    o model/src:
68      - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
69      - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
70        ADAMS_BASHFORTH2.
71    o pkg/cheapaml:
72      - add new parameter (default=F, same as before) to disable full domain
73        (including land) periodicity in X & Y dir.
74      - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
75        prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
76        into single S/R CHEAPAML_TIMESTEP.
77    
78    checkpoint64d (2013/02/17)
79    o pkg/monitor (angular momentum):
80      - do not add Eta contribution to the total AM if using rigid-lid;
81      - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
82      - horizontal discretisation: compute Zonal wind contribution separately for
83        each component (instead of from cell centered averaged) and use the 4
84        grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
85      - Check that AM is conserved with linear dynamics (momAdvection=F and linear
86        FreeSurf) if using vectorInvariant momentum.
87    o model/src (horizontal grid):
88      - move initialisation of all horizontal grid arrays to null value
89        from specific horizontal grid S/R to main S/R INI_GRID;
90      - add 2 new arrays to project model C-grid velocity on to zonal direction
91        (similar to AngleCosC & -AngleSinC but at U and V point location) and
92        compute them in S/R CALC_GRID_ANGLES.
93    o pkg/seaice: replace a hard coded parameter by a runtime parameter
94        SEAICE_JFNK_tolIter
95    o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
96        preconditioner for JFNK (run LSR into the overlaps as far as possible,
97        i.e OLx/y-2, but overwrite the solution in the overlaps)
98      - extend loop range in seaice_calc_viscosity
99      - add new parameters SEAICE_OLx/y (default = OLx/y-2)
100      - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
101      - slightly modify loops in tridiagonal solver lsr-preconditioner
102      - by default remove the extra exchange in seaice_preconditioner with a
103        replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
104      - modify offline_exf_seaice so that old results without RAS are reproduced
105        for output.dyn_jfnk.txt
106      in seaice_fgmres.F (unrelated to RAS)
107      - add a cpp-flag option for a re-ordered mapping (potentially more
108        efficient), but because this changes the results, turn it off by
109        default
110      - replace the save statement by local common blocks
111    o utils/matlab:
112      - fix tile-offset in rdmnc.m when output was produced using EXCH2.
113      - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
114        instead of local script "load_cs.m".
115    o pkg/seaice:
116      - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
117        to the scalarProductMetric and the unrolling. By chance this does not
118        change the verification experiment, because of the particular domain
119        decomposition
120    o pkg/diagnostics:
121      - change default missing_value from UNSET_RL to -999.
122    o pkg/layers: improve vectorization of layers_fluxcalc.F
123      - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
124        time spent in this routine by more than a factor of 3 on an NEC-SX8
125      - step 2: replace search algorithm by a bisection algorithm found in
126        Press et al. Numerical Recipes in Fortran. This algorithm can be
127        vectorized and finds the correct bin in approx. log2(Nlayers) steps.
128        For now, use this algorithm only for TARGET_NEC_SX defined.
129      - moved the search algorithm into a separate subroutine, that is kept
130        within the same file for automatic inlining.
131      - modified catching potential errors
132    o pkg/ecco:
133      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
134    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
135      - modifications for ALLOW_GENTIM2D_CONTROL
136      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
137      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
138      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
139      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
140    o model/src:
141      - account for moist thermodynamics in (dry) potential temperature equation;
142        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
143        and cpl_aim+ocn.
144      - also switch to standard compiler (gfortran, was using ifort previously)
145        for fizhi-cs experiments reference output.
146    o pkg/ctrl:
147      - 1st step toward generic time-varying control variable (2D) via CPP option
148        ALLOW_GENTIM2D_CONTROL
149      - note new namelist ctrl_nml_genarr in data.ctrl
150    o verification/global_ocean.cs32x15:
151      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
152        thsice calling sequence and update "output.icedyn.txt" output file.
153    o pkg/ptracers:
154      - from Ryan A.: code to allow to restart a tracer at regular time interval
155        specifying a reset frequency and a reset-phase (for each tracers).
156    o pkg/thsice:
157      - implement new sequence of calls for thsice+seaice:
158          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
159          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
160      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
161        in CPP_OPTIONS.h) to recover old sequence;
162      - update diagnostics for Intermediate State thsice diagnostics: now filled
163        just before advection (instead of just after advection in old sequence);
164      - update output of experiment offline_exf_seaice (standard test);
165      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
166        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
167    o pkg/aim_v23:
168      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
169      - use standard pkg/mdsio routines to read & write CO2 pickup file;
170      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
171      - Implement new sequence of calls for seaice advection (with thsice and
172        seaice diffusion): do ice advection after ice-Thermodynamic (previously
173        was done before); change aim_do_physics.F (split the bi,bj loops block);
174      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
175    o pkg/thsice:
176      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
177        where just seaice diffusion is used without seaice-dynamics.
178    
179    checkpoint64c (2013/01/18)
180    o pkg/seaice:
181      - add a parameter JFNKres_tFac that can replace JFNKres_t
182        (= JFNKres_tFac*JFNKresidual before JFNK solver)
183      - add a line search option to the JFNK solver
184      - move update of u/vIce and computation of initial residual into a separate
185        routine (same file); makes the code a little easier to read (?)
186      - the line search requires computation of the residual and for some reason
187        I cannot do the update of u/vIce at the beginning of the Newton loop
188        without changing the results, so we move computation of the new residual
189        also to the end of the Newton loop, even without the line search
190    o pkg/mdsio:
191      - write missing value (corresponding to undefined array value) to meta files;
192        skip this if missing value is one (UNSET_RL would be a better value for the
193        case of undefined missing value but it's current the default missing-value);
194        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
195    o pkg/exf & thsice:
196      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
197        diagnostics) even when SHORTWAVE_HEATING is #undef;
198    o verification/cfc_example:
199      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
200        illustrate how to use it).
201    o verification/offline_exf_seaice:
202      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
203        files to only one time-record.
204      in input.thermo: narrow the 2 bands of low initial ice-concentration near
205        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
206        snapshot output; same mcPheePiston value as in thsice with
207        surf-current=0.2m/s.
208      in input.thsice: similar set-up as in input.thermo (channel with same seaice
209        initial conditions).
210    o verification/cfc_example:
211      - update file "data" with more standard choice (default rotationPeriod,
212        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
213        set deltaTFreeSurf to deltaTtracer) and update the output.
214    o pkg/layers:
215      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
216      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
217    o verification/offline_exf_seaice:
218      - set all {field}period to zero for constant-in-time forcing (not tested
219        anywhere else).
220    o verification/offline_exf_seaice:
221      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
222      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
223    o model/src:
224      - implement Finite-Volume method for (hydrostatic) presure gradient
225        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
226    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
227      - In order to be compatible with the default EVP code, this requires changing
228        the EVP code around a little; and because any small change immediately
229        breaks the lab_sea.hb87 verification experiment, the reference output is
230        updated two times (each time the remaining aggrement was only 2 digits):
231        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
232        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
233        The adjoint test lab_sea.evp also needed to be updated.
234      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
235        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
236        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
237        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
238        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
239        kept obscure, because I need to test it a little more.
240    o pkg/cheapaml:
241      - fix few incorrect type (_RL/_RS) in subroutine calls.
242    o pkg/seaice:
243      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
244        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
245    o model/src:
246      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
247        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
248        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
249    o pkg/cheapaml:
250      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
251        update output of experiment cheapAML_box.
252      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
253        and set them only in one place (cheapaml_readparms.F).
254      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
255      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
256        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
257    o model/src/the_main_loop.F:
258      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
259    o pkg/seaice:
260      - remove legacy branch code.
261      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
262    o verification/*/code*/SEAICE_OPTIONS.h:
263      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
264        SEAICE_CAP_HEFF).
265    o pkg/cheapaml:
266      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
267        to load new forcing fields.
268      - add missing "_d 0" where it's needed; + some editing (improve indentation).
269      - remove switch to "-r8" compiler option (no longer needed) in verification
270        cheapAML_box, keep same output (small trucation error differences).
271    o verification/offline_exf_seaice:
272      - add thermodynamics only test.
273    o verification/cheapAML_box:
274      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
275        keep same output (same 14 digits for cg2d).
276      - switch on "-r8" compiler option (some numerical values are missing
277        the "_d 0") and update output (only 6 digits for cg2d were preserved).
278    
279    checkpoint64b (2012/12/24)
280    o pkg/cheapaml:
281      - remove un-used variables (Qnet,EmPmR) from pickup files.
282      - store tendency of advected variables into cheapaml pickup file
283        and fix the AB-2 restart.
284    o verification/offline_exf_seaice and lab_sea adjoint:
285      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
286      - switch to 4 time steps in offline, consistent with lab_sea.
287      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
288      - update results after change of experiment seaice.
289    o pkg/seaice:
290      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
291        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
292        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
293        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
294  o model/src:  o model/src:
295    - add run-time parameter to select CG2D solver minimum-residual solution    - add run-time parameter to select CG2D solver minimum-residual solution
296      (in case of a poor convergence).      (in case of a poor convergence).
# Line 13  o pkg/seaice/seaice_lsr.F Line 300  o pkg/seaice/seaice_lsr.F
300      file; the main purpose of this change is to be able to reuse the code      file; the main purpose of this change is to be able to reuse the code
301      in S/R SEAICE_PRECONDITIONER      in S/R SEAICE_PRECONDITIONER
302    - modify the computation of the residual so that the mass of sea-ice    - modify the computation of the residual so that the mass of sea-ice
303      is not used twice; this simplyfies the calculations, but since      is not used twice; this simplifies the calculations, but since
304      the residual is never used except when LSR_mixIniGuess.ge.4---and this is      the residual is never used except when LSR_mixIniGuess.ge.4---and this is
305      not tested in testreport---this does not affect the testreport results.      not tested in testreport---this does not affect the testreport results.
306  o verification/seaice_obcs:  o verification/seaice_obcs:
# Line 47  o pkg/seaice: Line 334  o pkg/seaice:
334    - add a verification experiment for JFNK in offline_exf_seaice    - add a verification experiment for JFNK in offline_exf_seaice
335  o verification:  o verification:
336    - change (for now, only fwd test) offline_exf_seaice experiment:    - change (for now, only fwd test) offline_exf_seaice experiment:
337      use a re-entrant channel with idealized costline (trapezoidal shape)      use a re-entrant channel with idealized coastline (trapezoidal shape)
338      at southern boundary to explore seaice dynamics and thermodynamics      at southern boundary to explore seaice dynamics and thermodynamics
339      with simple forcing. Main set-up has dynamics+thermo and SST relaxation;      with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
340      secondary test (input.thsice) use thermodynamics only with SST relaxation.      secondary test (input.thsice) use thermodynamics only with SST relaxation.

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