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revision 1.1783 by mlosch, Mon Dec 17 15:38:59 2012 UTC revision 1.1842 by jahn, Mon Mar 25 16:30:52 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/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
8      - add OpenAD setup to this exp and make ptracers package work with OpenAD
9    o pkg/seaice/seaice_evp.F: mask the asymmetric contribution of the ice-ocean
10      stress (when the turningAngle is non-zero) over open water to avoid
11      stripes in the EVP-solutions after many EVP-substeps. This does not change
12      the verification experiment (because turningAngle=0 in that experiment), but
13      will affect other EVP solutions with turningAngle.ne.0
14    o verification, AD & TLM output:
15      - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
16        additions and multiplications which affect results at machine truncation
17        level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
18        lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
19        (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
20        digits of matching.
21    o pkg/seaice:
22       modify lsr-algorithm so that it vectorizes AND converges by using a
23       "zebra" method: split vector loop into two with step size 2; this
24       solves a general convergence problem for the JFNK solver on a vector
25       computer. It has the potential to even improve convergence for
26       non-vector machines, but it does change the results so it is turned
27       off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
28       SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
29    
30    checkpoint64e (2013/03/05)
31    o pkg/ecco and several verification experiments:
32       Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
33       from ecco package, and revert to unified routine in model/src/
34       Adjust verification experiments accordingly, especially gloal_oce_llc90
35       Should conclude long-standing work by Gael to reconsile the_main_loop with
36       ECCO and will enable OpenAD's revolve loop in ECCO setup.
37    o pkg/generic_advdiff:
38      - implement compressible flow method for multi-dim advection (similar to
39        gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
40        TAF generates many recomputations) to use it; no yet coded with implicit
41        vertical advection.
42      - change experiment advect_cs (new output) and advect_xy (same output)
43        to test compressible flow multi-dim advection.
44    o pkg/generic_advdiff:
45      - fix SOM advection for unusual cases (linear Free-Surf in r*, other
46        cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
47    o pkg/seaice:
48      - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
49        bug affects two verification experiments (lab_sea and lab_sea.hb87),
50        recover old (wrong) results by setting noSlipFac = 2. in
51        seaice_calc_strainrates.F;
52      - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
53      - add runtime parameter SEAICE_JFNKepsilon for that finite difference
54        gradient in the Jacobian times vector operation (s/r seaice_jacvec)
55      - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
56    o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
57      - new subroutines seaice_lsr_tridiagu/v
58      - introduce loop bounds i/jmin/max to be able to use a restricted
59        additive Schwarz method, but not used for now.
60      - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
61      - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
62    o OpenAD support
63       Reorganize S/R call for overall time-stepping loop to facilitate
64       OpenAD revolve loop replacement
65       (new S/R main_do_loop.F)
66    o model/src:
67      - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
68      - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
69        ADAMS_BASHFORTH2.
70    o pkg/cheapaml:
71      - add new parameter (default=F, same as before) to disable full domain
72        (including land) periodicity in X & Y dir.
73      - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
74        prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
75        into single S/R CHEAPAML_TIMESTEP.
76    
77    checkpoint64d (2013/02/17)
78    o pkg/monitor (angular momentum):
79      - do not add Eta contribution to the total AM if using rigid-lid;
80      - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
81      - horizontal discretisation: compute Zonal wind contribution separately for
82        each component (instead of from cell centered averaged) and use the 4
83        grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
84      - Check that AM is conserved with linear dynamics (momAdvection=F and linear
85        FreeSurf) if using vectorInvariant momentum.
86    o model/src (horizontal grid):
87      - move initialisation of all horizontal grid arrays to null value
88        from specific horizontal grid S/R to main S/R INI_GRID;
89      - add 2 new arrays to project model C-grid velocity on to zonal direction
90        (similar to AngleCosC & -AngleSinC but at U and V point location) and
91        compute them in S/R CALC_GRID_ANGLES.
92    o pkg/seaice: replace a hard coded parameter by a runtime parameter
93        SEAICE_JFNK_tolIter
94    o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
95        preconditioner for JFNK (run LSR into the overlaps as far as possible,
96        i.e OLx/y-2, but overwrite the solution in the overlaps)
97      - extend loop range in seaice_calc_viscosity
98      - add new parameters SEAICE_OLx/y (default = OLx/y-2)
99      - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
100      - slightly modify loops in tridiagonal solver lsr-preconditioner
101      - by default remove the extra exchange in seaice_preconditioner with a
102        replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
103      - modify offline_exf_seaice so that old results without RAS are reproduced
104        for output.dyn_jfnk.txt
105      in seaice_fgmres.F (unrelated to RAS)
106      - add a cpp-flag option for a re-ordered mapping (potentially more
107        efficient), but because this changes the results, turn it off by
108        default
109      - replace the save statement by local common blocks
110    o utils/matlab:
111      - fix tile-offset in rdmnc.m when output was produced using EXCH2.
112      - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
113        instead of local script "load_cs.m".
114    o pkg/seaice:
115      - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
116        to the scalarProductMetric and the unrolling. By chance this does not
117        change the verification experiment, because of the particular domain
118        decomposition
119    o pkg/diagnostics:
120      - change default missing_value from UNSET_RL to -999.
121    o pkg/layers: improve vectorization of layers_fluxcalc.F
122      - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
123        time spent in this routine by more than a factor of 3 on an NEC-SX8
124      - step 2: replace search algorithm by a bisection algorithm found in
125        Press et al. Numerical Recipes in Fortran. This algorithm can be
126        vectorized and finds the correct bin in approx. log2(Nlayers) steps.
127        For now, use this algorithm only for TARGET_NEC_SX defined.
128      - moved the search algorithm into a separate subroutine, that is kept
129        within the same file for automatic inlining.
130      - modified catching potential errors
131    o pkg/ecco:
132      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
133    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
134      - modifications for ALLOW_GENTIM2D_CONTROL
135      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
136      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
137      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
138      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
139    o model/src:
140      - account for moist thermodynamics in (dry) potential temperature equation;
141        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
142        and cpl_aim+ocn.
143      - also switch to standard compiler (gfortran, was using ifort previously)
144        for fizhi-cs experiments reference output.
145    o pkg/ctrl:
146      - 1st step toward generic time-varying control variable (2D) via CPP option
147        ALLOW_GENTIM2D_CONTROL
148      - note new namelist ctrl_nml_genarr in data.ctrl
149    o verification/global_ocean.cs32x15:
150      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
151        thsice calling sequence and update "output.icedyn.txt" output file.
152    o pkg/ptracers:
153      - from Ryan A.: code to allow to restart a tracer at regular time interval
154        specifying a reset frequency and a reset-phase (for each tracers).
155    o pkg/thsice:
156      - implement new sequence of calls for thsice+seaice:
157          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
158          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
159      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
160        in CPP_OPTIONS.h) to recover old sequence;
161      - update diagnostics for Intermediate State thsice diagnostics: now filled
162        just before advection (instead of just after advection in old sequence);
163      - update output of experiment offline_exf_seaice (standard test);
164      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
165        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
166    o pkg/aim_v23:
167      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
168      - use standard pkg/mdsio routines to read & write CO2 pickup file;
169      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
170      - Implement new sequence of calls for seaice advection (with thsice and
171        seaice diffusion): do ice advection after ice-Thermodynamic (previously
172        was done before); change aim_do_physics.F (split the bi,bj loops block);
173      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
174    o pkg/thsice:
175      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
176        where just seaice diffusion is used without seaice-dynamics.
177    
178    checkpoint64c (2013/01/18)
179    o pkg/seaice:
180      - add a parameter JFNKres_tFac that can replace JFNKres_t
181        (= JFNKres_tFac*JFNKresidual before JFNK solver)
182      - add a line search option to the JFNK solver
183      - move update of u/vIce and computation of initial residual into a separate
184        routine (same file); makes the code a little easier to read (?)
185      - the line search requires computation of the residual and for some reason
186        I cannot do the update of u/vIce at the beginning of the Newton loop
187        without changing the results, so we move computation of the new residual
188        also to the end of the Newton loop, even without the line search
189    o pkg/mdsio:
190      - write missing value (corresponding to undefined array value) to meta files;
191        skip this if missing value is one (UNSET_RL would be a better value for the
192        case of undefined missing value but it's current the default missing-value);
193        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
194    o pkg/exf & thsice:
195      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
196        diagnostics) even when SHORTWAVE_HEATING is #undef;
197    o verification/cfc_example:
198      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
199        illustrate how to use it).
200    o verification/offline_exf_seaice:
201      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
202        files to only one time-record.
203      in input.thermo: narrow the 2 bands of low initial ice-concentration near
204        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
205        snapshot output; same mcPheePiston value as in thsice with
206        surf-current=0.2m/s.
207      in input.thsice: similar set-up as in input.thermo (channel with same seaice
208        initial conditions).
209    o verification/cfc_example:
210      - update file "data" with more standard choice (default rotationPeriod,
211        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
212        set deltaTFreeSurf to deltaTtracer) and update the output.
213    o pkg/layers:
214      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
215      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
216    o verification/offline_exf_seaice:
217      - set all {field}period to zero for constant-in-time forcing (not tested
218        anywhere else).
219    o verification/offline_exf_seaice:
220      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
221      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
222    o model/src:
223      - implement Finite-Volume method for (hydrostatic) presure gradient
224        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
225    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
226      - In order to be compatible with the default EVP code, this requires changing
227        the EVP code around a little; and because any small change immediately
228        breaks the lab_sea.hb87 verification experiment, the reference output is
229        updated two times (each time the remaining aggrement was only 2 digits):
230        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
231        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
232        The adjoint test lab_sea.evp also needed to be updated.
233      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
234        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
235        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
236        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
237        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
238        kept obscure, because I need to test it a little more.
239    o pkg/cheapaml:
240      - fix few incorrect type (_RL/_RS) in subroutine calls.
241    o pkg/seaice:
242      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
243        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
244    o model/src:
245      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
246        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
247        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
248    o pkg/cheapaml:
249      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
250        update output of experiment cheapAML_box.
251      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
252        and set them only in one place (cheapaml_readparms.F).
253      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
254      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
255        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
256    o model/src/the_main_loop.F:
257      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
258    o pkg/seaice:
259      - remove legacy branch code.
260      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
261    o verification/*/code*/SEAICE_OPTIONS.h:
262      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
263        SEAICE_CAP_HEFF).
264    o pkg/cheapaml:
265      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
266        to load new forcing fields.
267      - add missing "_d 0" where it's needed; + some editing (improve indentation).
268      - remove switch to "-r8" compiler option (no longer needed) in verification
269        cheapAML_box, keep same output (small trucation error differences).
270    o verification/offline_exf_seaice:
271      - add thermodynamics only test.
272    o verification/cheapAML_box:
273      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
274        keep same output (same 14 digits for cg2d).
275      - switch on "-r8" compiler option (some numerical values are missing
276        the "_d 0") and update output (only 6 digits for cg2d were preserved).
277    
278    checkpoint64b (2012/12/24)
279    o pkg/cheapaml:
280      - remove un-used variables (Qnet,EmPmR) from pickup files.
281      - store tendency of advected variables into cheapaml pickup file
282        and fix the AB-2 restart.
283    o verification/offline_exf_seaice and lab_sea adjoint:
284      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
285      - switch to 4 time steps in offline, consistent with lab_sea.
286      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
287      - update results after change of experiment seaice.
288    o pkg/seaice:
289      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
290        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
291        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
292        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
293    o model/src:
294      - add run-time parameter to select CG2D solver minimum-residual solution
295        (in case of a poor convergence).
296    o pkg/seaice/seaice_lsr.F
297      - move calculation of matrix coefficients into new
298        S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
299        file; the main purpose of this change is to be able to reuse the code
300        in S/R SEAICE_PRECONDITIONER
301      - modify the computation of the residual so that the mass of sea-ice
302        is not used twice; this simplifies the calculations, but since
303        the residual is never used except when LSR_mixIniGuess.ge.4---and this is
304        not tested in testreport---this does not affect the testreport results.
305    o verification/seaice_obcs:
306      - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
307        verification/lab_sea/input.salt_plume; changes results/output.txt*
308    o model/src:
309      - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
310  o pkg/seaice:  o pkg/seaice:
311    - improve description of parameters in seaice_fgmres.F and start    - improve description of parameters in seaice_fgmres.F and start
312      cleaning up the code      cleaning up the code
313    - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of    - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
314      second argument      second argument
315    - add a metric based on grid cell area to SEAICE_SCALPROD; update    - add a metric based on grid cell area to SEAICE_SCALPROD; update
316      results of offline_exf_seaice.dyn_jfnk      results of offline_exf_seaice.dyn_jfnk
# Line 30  o pkg/seaice: Line 333  o pkg/seaice:
333    - add a verification experiment for JFNK in offline_exf_seaice    - add a verification experiment for JFNK in offline_exf_seaice
334  o verification:  o verification:
335    - change (for now, only fwd test) offline_exf_seaice experiment:    - change (for now, only fwd test) offline_exf_seaice experiment:
336      use a re-entrant channel with idealized costline (trapezoidal shape)      use a re-entrant channel with idealized coastline (trapezoidal shape)
337      at southern boundary to explore seaice dynamics and thermodynamics      at southern boundary to explore seaice dynamics and thermodynamics
338      with simple forcing. Main set-up has dynamics+thermo and SST relaxation;      with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
339      secondary test (input.thsice) use thermodynamics only with SST relaxation.      secondary test (input.thsice) use thermodynamics only with SST relaxation.

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