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revision 1.1787 by mlosch, Fri Dec 21 13:24:22 2012 UTC revision 1.1845 by jmc, Sun Mar 31 16:30:33 2013 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint64f (2013/03/31)
8    o verification/OpenAD:
9      - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
10    o verification/isomip, pkg/shelfice and OpenAD:
11      - add OpenAD setup to this exp and make shelfice package work with OpenAD
12    o verification/tutorial_global_oce_biogeo:
13      - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
14    o verification/offline_exf_seaice:
15      - replace adjoint experiment (now similar to fwd input.thermo/ setup).
16    o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
17      - add OpenAD setup to this exp and make ptracers package work with OpenAD
18    o pkg/seaice/seaice_evp.F:
19       mask the asymmetric contribution of the ice-ocean stress (when
20       the turningAngle is non-zero) over open water to avoid stripes
21       in the EVP-solutions after many EVP-substeps. This does not change
22       the verification experiment (because turningAngle=0 in that experiment),
23       but will affect other EVP solutions with turningAngle.ne.0
24    o verification, AD & TLM output:
25      - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
26        additions and multiplications which affect results at machine truncation
27        level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
28        lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
29        (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
30        digits of matching.
31    o pkg/seaice:
32       modify lsr-algorithm so that it vectorizes AND converges by using a
33       "zebra" method: split vector loop into two with step size 2; this
34       solves a general convergence problem for the JFNK solver on a vector
35       computer. It has the potential to even improve convergence for
36       non-vector machines, but it does change the results so it is turned
37       off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
38       SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
39    
40    checkpoint64e (2013/03/05)
41    o pkg/ecco and several verification experiments:
42       Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
43       from ecco package, and revert to unified routine in model/src/
44       Adjust verification experiments accordingly, especially gloal_oce_llc90
45       Should conclude long-standing work by Gael to reconsile the_main_loop with
46       ECCO and will enable OpenAD's revolve loop in ECCO setup.
47    o pkg/generic_advdiff:
48      - implement compressible flow method for multi-dim advection (similar to
49        gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
50        TAF generates many recomputations) to use it; no yet coded with implicit
51        vertical advection.
52      - change experiment advect_cs (new output) and advect_xy (same output)
53        to test compressible flow multi-dim advection.
54    o pkg/generic_advdiff:
55      - fix SOM advection for unusual cases (linear Free-Surf in r*, other
56        cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
57    o pkg/seaice:
58      - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
59        bug affects two verification experiments (lab_sea and lab_sea.hb87),
60        recover old (wrong) results by setting noSlipFac = 2. in
61        seaice_calc_strainrates.F;
62      - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
63      - add runtime parameter SEAICE_JFNKepsilon for that finite difference
64        gradient in the Jacobian times vector operation (s/r seaice_jacvec)
65      - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
66    o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
67      - new subroutines seaice_lsr_tridiagu/v
68      - introduce loop bounds i/jmin/max to be able to use a restricted
69        additive Schwarz method, but not used for now.
70      - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
71      - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
72    o OpenAD support
73       Reorganize S/R call for overall time-stepping loop to facilitate
74       OpenAD revolve loop replacement
75       (new S/R main_do_loop.F)
76    o model/src:
77      - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
78      - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
79        ADAMS_BASHFORTH2.
80    o pkg/cheapaml:
81      - add new parameter (default=F, same as before) to disable full domain
82        (including land) periodicity in X & Y dir.
83      - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
84        prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
85        into single S/R CHEAPAML_TIMESTEP.
86    
87    checkpoint64d (2013/02/17)
88    o pkg/monitor (angular momentum):
89      - do not add Eta contribution to the total AM if using rigid-lid;
90      - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
91      - horizontal discretisation: compute Zonal wind contribution separately for
92        each component (instead of from cell centered averaged) and use the 4
93        grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
94      - Check that AM is conserved with linear dynamics (momAdvection=F and linear
95        FreeSurf) if using vectorInvariant momentum.
96    o model/src (horizontal grid):
97      - move initialisation of all horizontal grid arrays to null value
98        from specific horizontal grid S/R to main S/R INI_GRID;
99      - add 2 new arrays to project model C-grid velocity on to zonal direction
100        (similar to AngleCosC & -AngleSinC but at U and V point location) and
101        compute them in S/R CALC_GRID_ANGLES.
102    o pkg/seaice: replace a hard coded parameter by a runtime parameter
103        SEAICE_JFNK_tolIter
104    o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
105        preconditioner for JFNK (run LSR into the overlaps as far as possible,
106        i.e OLx/y-2, but overwrite the solution in the overlaps)
107      - extend loop range in seaice_calc_viscosity
108      - add new parameters SEAICE_OLx/y (default = OLx/y-2)
109      - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
110      - slightly modify loops in tridiagonal solver lsr-preconditioner
111      - by default remove the extra exchange in seaice_preconditioner with a
112        replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
113      - modify offline_exf_seaice so that old results without RAS are reproduced
114        for output.dyn_jfnk.txt
115      in seaice_fgmres.F (unrelated to RAS)
116      - add a cpp-flag option for a re-ordered mapping (potentially more
117        efficient), but because this changes the results, turn it off by
118        default
119      - replace the save statement by local common blocks
120    o utils/matlab:
121      - fix tile-offset in rdmnc.m when output was produced using EXCH2.
122      - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
123        instead of local script "load_cs.m".
124    o pkg/seaice:
125      - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
126        to the scalarProductMetric and the unrolling. By chance this does not
127        change the verification experiment, because of the particular domain
128        decomposition
129    o pkg/diagnostics:
130      - change default missing_value from UNSET_RL to -999.
131    o pkg/layers: improve vectorization of layers_fluxcalc.F
132      - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
133        time spent in this routine by more than a factor of 3 on an NEC-SX8
134      - step 2: replace search algorithm by a bisection algorithm found in
135        Press et al. Numerical Recipes in Fortran. This algorithm can be
136        vectorized and finds the correct bin in approx. log2(Nlayers) steps.
137        For now, use this algorithm only for TARGET_NEC_SX defined.
138      - moved the search algorithm into a separate subroutine, that is kept
139        within the same file for automatic inlining.
140      - modified catching potential errors
141    o pkg/ecco:
142      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
143    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
144      - modifications for ALLOW_GENTIM2D_CONTROL
145      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
146      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
147      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
148      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
149    o model/src:
150      - account for moist thermodynamics in (dry) potential temperature equation;
151        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
152        and cpl_aim+ocn.
153      - also switch to standard compiler (gfortran, was using ifort previously)
154        for fizhi-cs experiments reference output.
155    o pkg/ctrl:
156      - 1st step toward generic time-varying control variable (2D) via CPP option
157        ALLOW_GENTIM2D_CONTROL
158      - note new namelist ctrl_nml_genarr in data.ctrl
159    o verification/global_ocean.cs32x15:
160      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
161        thsice calling sequence and update "output.icedyn.txt" output file.
162    o pkg/ptracers:
163      - from Ryan A.: code to allow to restart a tracer at regular time interval
164        specifying a reset frequency and a reset-phase (for each tracers).
165    o pkg/thsice:
166      - implement new sequence of calls for thsice+seaice:
167          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
168          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
169      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
170        in CPP_OPTIONS.h) to recover old sequence;
171      - update diagnostics for Intermediate State thsice diagnostics: now filled
172        just before advection (instead of just after advection in old sequence);
173      - update output of experiment offline_exf_seaice (standard test);
174      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
175        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
176    o pkg/aim_v23:
177      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
178      - use standard pkg/mdsio routines to read & write CO2 pickup file;
179      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
180      - Implement new sequence of calls for seaice advection (with thsice and
181        seaice diffusion): do ice advection after ice-Thermodynamic (previously
182        was done before); change aim_do_physics.F (split the bi,bj loops block);
183      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
184    o pkg/thsice:
185      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
186        where just seaice diffusion is used without seaice-dynamics.
187    
188    checkpoint64c (2013/01/18)
189    o pkg/seaice:
190      - add a parameter JFNKres_tFac that can replace JFNKres_t
191        (= JFNKres_tFac*JFNKresidual before JFNK solver)
192      - add a line search option to the JFNK solver
193      - move update of u/vIce and computation of initial residual into a separate
194        routine (same file); makes the code a little easier to read (?)
195      - the line search requires computation of the residual and for some reason
196        I cannot do the update of u/vIce at the beginning of the Newton loop
197        without changing the results, so we move computation of the new residual
198        also to the end of the Newton loop, even without the line search
199    o pkg/mdsio:
200      - write missing value (corresponding to undefined array value) to meta files;
201        skip this if missing value is one (UNSET_RL would be a better value for the
202        case of undefined missing value but it's current the default missing-value);
203        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
204    o pkg/exf & thsice:
205      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
206        diagnostics) even when SHORTWAVE_HEATING is #undef;
207    o verification/cfc_example:
208      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
209        illustrate how to use it).
210    o verification/offline_exf_seaice:
211      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
212        files to only one time-record.
213      in input.thermo: narrow the 2 bands of low initial ice-concentration near
214        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
215        snapshot output; same mcPheePiston value as in thsice with
216        surf-current=0.2m/s.
217      in input.thsice: similar set-up as in input.thermo (channel with same seaice
218        initial conditions).
219    o verification/cfc_example:
220      - update file "data" with more standard choice (default rotationPeriod,
221        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
222        set deltaTFreeSurf to deltaTtracer) and update the output.
223    o pkg/layers:
224      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
225      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
226    o verification/offline_exf_seaice:
227      - set all {field}period to zero for constant-in-time forcing (not tested
228        anywhere else).
229    o verification/offline_exf_seaice:
230      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
231      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
232    o model/src:
233      - implement Finite-Volume method for (hydrostatic) presure gradient
234        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
235    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
236      - In order to be compatible with the default EVP code, this requires changing
237        the EVP code around a little; and because any small change immediately
238        breaks the lab_sea.hb87 verification experiment, the reference output is
239        updated two times (each time the remaining aggrement was only 2 digits):
240        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
241        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
242        The adjoint test lab_sea.evp also needed to be updated.
243      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
244        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
245        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
246        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
247        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
248        kept obscure, because I need to test it a little more.
249    o pkg/cheapaml:
250      - fix few incorrect type (_RL/_RS) in subroutine calls.
251    o pkg/seaice:
252      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
253        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
254    o model/src:
255      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
256        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
257        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
258    o pkg/cheapaml:
259      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
260        update output of experiment cheapAML_box.
261      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
262        and set them only in one place (cheapaml_readparms.F).
263      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
264      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
265        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
266    o model/src/the_main_loop.F:
267      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
268    o pkg/seaice:
269      - remove legacy branch code.
270      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
271    o verification/*/code*/SEAICE_OPTIONS.h:
272      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
273        SEAICE_CAP_HEFF).
274    o pkg/cheapaml:
275      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
276        to load new forcing fields.
277      - add missing "_d 0" where it's needed; + some editing (improve indentation).
278      - remove switch to "-r8" compiler option (no longer needed) in verification
279        cheapAML_box, keep same output (small trucation error differences).
280    o verification/offline_exf_seaice:
281      - add thermodynamics only test.
282    o verification/cheapAML_box:
283      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
284        keep same output (same 14 digits for cg2d).
285      - switch on "-r8" compiler option (some numerical values are missing
286        the "_d 0") and update output (only 6 digits for cg2d were preserved).
287    
288    checkpoint64b (2012/12/24)
289    o pkg/cheapaml:
290      - remove un-used variables (Qnet,EmPmR) from pickup files.
291      - store tendency of advected variables into cheapaml pickup file
292        and fix the AB-2 restart.
293    o verification/offline_exf_seaice and lab_sea adjoint:
294      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
295      - switch to 4 time steps in offline, consistent with lab_sea.
296      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
297      - update results after change of experiment seaice.
298    o pkg/seaice:
299      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
300        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
301        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
302        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
303    o model/src:
304      - add run-time parameter to select CG2D solver minimum-residual solution
305        (in case of a poor convergence).
306  o pkg/seaice/seaice_lsr.F  o pkg/seaice/seaice_lsr.F
307    - move calculation of matrix coefficients into new    - move calculation of matrix coefficients into new
308      S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same      S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
309      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
310      in S/R SEAICE_PRECONDITIONER      in S/R SEAICE_PRECONDITIONER
311    - 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
312      is not used twice; this simplyfies the calculations, but since      is not used twice; this simplifies the calculations, but since
313      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
314      not tested in testreport---this does not affect the testreport results.      not tested in testreport---this does not affect the testreport results.
315  o verification/seaice_obcs:  o verification/seaice_obcs:
# Line 44  o pkg/seaice: Line 343  o pkg/seaice:
343    - add a verification experiment for JFNK in offline_exf_seaice    - add a verification experiment for JFNK in offline_exf_seaice
344  o verification:  o verification:
345    - change (for now, only fwd test) offline_exf_seaice experiment:    - change (for now, only fwd test) offline_exf_seaice experiment:
346      use a re-entrant channel with idealized costline (trapezoidal shape)      use a re-entrant channel with idealized coastline (trapezoidal shape)
347      at southern boundary to explore seaice dynamics and thermodynamics      at southern boundary to explore seaice dynamics and thermodynamics
348      with simple forcing. Main set-up has dynamics+thermo and SST relaxation;      with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
349      secondary test (input.thsice) use thermodynamics only with SST relaxation.      secondary test (input.thsice) use thermodynamics only with SST relaxation.

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