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revision 1.1791 by jmc, Mon Dec 24 15:55:10 2012 UTC revision 1.1855 by jmc, Thu Apr 11 20:53:23 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/shelfice:
8      - allow to specify the Ice-Shelf mass per unit area (instead of
9        shelficeLoadAnomaly) and do the conversion from one to the other
10      - move loading from file of shelficeLoadAnomaly from SHELFICE_INIT_VARIA
11        to SHELFICE_INIT_FIXED: (a) avoid some TAF recompution issues and
12        (b) will be loaded in time (before calling INI_PRESSURE) in case it is
13        needed in phi0surf for initial pressure calculation when useDynP_inEos_Zc
14      - update isomip experiment forward output (get machine truncation error
15        from conversion shelficeLoadAnomaly -> shelficeMass -> shelficeLoadAnomaly)
16    o verification/offline_exf_seaice:
17      revise data.seaice in input.thermo and input_ad and update results accordingly
18        HO = 0.2, SEAICE_areaLossFormula = 2,
19        SEAICE_growMeltByConv = .TRUE.,
20        SEAICE_doOpenWaterMelt = .TRUE.,
21      Improve consistency with input.thsice and fix the spurious 500m ice corners
22    o verification/global_ocean.cs32x15:
23      - set Energy Reference Level to liq. water @ 0 degC: temp_EvPrRn=0.,
24        in icedyn (thsice+seaice-dyn) test and update output.
25    o verification/offline_exf_seaice:
26      - adjust list of tested variables (with testreport) and update
27        standard test output with better slection of monitored fields.
28    o pkg/cd_code:
29      - swtich off Adams-Bashforth on the 1rst iteration. Update output of
30        experiment lab_sea.hb87
31    o tools/genmake2:
32      - change default makedepend from the system default to tools/xmakedepend:
33        When no makedepend is specified, select tools/xmakedepend it the test pass,
34        otherwise select the system default (if exist and pass the test) or
35        try to build cyrus-makedepend ; stop if none of the 3 works.
36    o pkg/exf & pkg/thsice:
37      - In case Energy-Reference-Level (ERL) is used (temp_EvPrRn=0), account
38        for energy content of Precip + RunOff & Evap. Assumes:
39       1) Rain has same temp as Air.
40       2) Snow has no heat capacity (consistent with seaice & thsice pkgs)
41       3) Run-Off comes at the temp of surface water (with same Cp)
42       4) Evap over ocean is released to the Atmos @ surf-temp (=SST); should be
43        put directly into Latent Heat flux & should use water-vapor heat capacity.
44       5) Evap over snow/seaice (pkg/thsice) assumes constant Lf+Lv (consistent
45        with snow having no Cp) => water vapor is released to Atmos @ 0^oC (=ERL).
46    o pkg/seaice: simplify the use of CPP flags in JFNK-related files
47        (compile when SEAICE_ALLOW_JFNK is defined)
48    o pkg/thsice:
49      - fix oceanic flux diagnostics & timeave (left from new sequence of calls
50        implementation): move THSICE_AVE call after the advection (called directly
51        from thsice_do_advect.F).
52    o verification/global_ocean.90x40x15 and OpenAD:
53      New experiment for OpenAD is identical to the one in input_ad except that
54        multiDimAdvection=.FALSE.,
55      There is still an issue with this.
56    o pkg/thsice:
57      - account for ice velocity (ocean relative velocity) in turbulent heat flux
58        at the base of the ice; update output of global_ocean.cs32x15 (icedyn)
59        and offline_exf_seaice (main test).
60    
61    checkpoint64f (2013/03/31)
62    o verification/OpenAD:
63      - new (smaller, without OAD_DEBUG) output_oadm.txt generated using gfortran.
64    o verification/isomip, pkg/shelfice and OpenAD:
65      - add OpenAD setup to this exp and make shelfice package work with OpenAD
66    o verification/tutorial_global_oce_biogeo:
67      - update AD and TLM output after turning off ALLOW_FE (in DIC_OPTIONS.h)
68    o verification/offline_exf_seaice:
69      - replace adjoint experiment (now similar to fwd input.thermo/ setup).
70    o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
71      - add OpenAD setup to this exp and make ptracers package work with OpenAD
72    o pkg/seaice/seaice_evp.F:
73       mask the asymmetric contribution of the ice-ocean stress (when
74       the turningAngle is non-zero) over open water to avoid stripes
75       in the EVP-solutions after many EVP-substeps. This does not change
76       the verification experiment (because turningAngle=0 in that experiment),
77       but will affect other EVP solutions with turningAngle.ne.0
78    o verification, AD & TLM output:
79      - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
80        additions and multiplications which affect results at machine truncation
81        level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
82        lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
83        (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
84        digits of matching.
85    o pkg/seaice:
86       modify lsr-algorithm so that it vectorizes AND converges by using a
87       "zebra" method: split vector loop into two with step size 2; this
88       solves a general convergence problem for the JFNK solver on a vector
89       computer. It has the potential to even improve convergence for
90       non-vector machines, but it does change the results so it is turned
91       off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
92       SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
93    
94    checkpoint64e (2013/03/05)
95    o pkg/ecco and several verification experiments:
96       Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
97       from ecco package, and revert to unified routine in model/src/
98       Adjust verification experiments accordingly, especially gloal_oce_llc90
99       Should conclude long-standing work by Gael to reconsile the_main_loop with
100       ECCO and will enable OpenAD's revolve loop in ECCO setup.
101    o pkg/generic_advdiff:
102      - implement compressible flow method for multi-dim advection (similar to
103        gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
104        TAF generates many recomputations) to use it; no yet coded with implicit
105        vertical advection.
106      - change experiment advect_cs (new output) and advect_xy (same output)
107        to test compressible flow multi-dim advection.
108    o pkg/generic_advdiff:
109      - fix SOM advection for unusual cases (linear Free-Surf in r*, other
110        cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
111    o pkg/seaice:
112      - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
113        bug affects two verification experiments (lab_sea and lab_sea.hb87),
114        recover old (wrong) results by setting noSlipFac = 2. in
115        seaice_calc_strainrates.F;
116      - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
117      - add runtime parameter SEAICE_JFNKepsilon for that finite difference
118        gradient in the Jacobian times vector operation (s/r seaice_jacvec)
119      - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
120    o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
121      - new subroutines seaice_lsr_tridiagu/v
122      - introduce loop bounds i/jmin/max to be able to use a restricted
123        additive Schwarz method, but not used for now.
124      - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
125      - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
126    o OpenAD support
127       Reorganize S/R call for overall time-stepping loop to facilitate
128       OpenAD revolve loop replacement
129       (new S/R main_do_loop.F)
130    o model/src:
131      - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
132      - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
133        ADAMS_BASHFORTH2.
134    o pkg/cheapaml:
135      - add new parameter (default=F, same as before) to disable full domain
136        (including land) periodicity in X & Y dir.
137      - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
138        prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
139        into single S/R CHEAPAML_TIMESTEP.
140    
141    checkpoint64d (2013/02/17)
142    o pkg/monitor (angular momentum):
143      - do not add Eta contribution to the total AM if using rigid-lid;
144      - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
145      - horizontal discretisation: compute Zonal wind contribution separately for
146        each component (instead of from cell centered averaged) and use the 4
147        grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
148      - Check that AM is conserved with linear dynamics (momAdvection=F and linear
149        FreeSurf) if using vectorInvariant momentum.
150    o model/src (horizontal grid):
151      - move initialisation of all horizontal grid arrays to null value
152        from specific horizontal grid S/R to main S/R INI_GRID;
153      - add 2 new arrays to project model C-grid velocity on to zonal direction
154        (similar to AngleCosC & -AngleSinC but at U and V point location) and
155        compute them in S/R CALC_GRID_ANGLES.
156    o pkg/seaice: replace a hard coded parameter by a runtime parameter
157        SEAICE_JFNK_tolIter
158    o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
159        preconditioner for JFNK (run LSR into the overlaps as far as possible,
160        i.e OLx/y-2, but overwrite the solution in the overlaps)
161      - extend loop range in seaice_calc_viscosity
162      - add new parameters SEAICE_OLx/y (default = OLx/y-2)
163      - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
164      - slightly modify loops in tridiagonal solver lsr-preconditioner
165      - by default remove the extra exchange in seaice_preconditioner with a
166        replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
167      - modify offline_exf_seaice so that old results without RAS are reproduced
168        for output.dyn_jfnk.txt
169      in seaice_fgmres.F (unrelated to RAS)
170      - add a cpp-flag option for a re-ordered mapping (potentially more
171        efficient), but because this changes the results, turn it off by
172        default
173      - replace the save statement by local common blocks
174    o utils/matlab:
175      - fix tile-offset in rdmnc.m when output was produced using EXCH2.
176      - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
177        instead of local script "load_cs.m".
178    o pkg/seaice:
179      - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
180        to the scalarProductMetric and the unrolling. By chance this does not
181        change the verification experiment, because of the particular domain
182        decomposition
183    o pkg/diagnostics:
184      - change default missing_value from UNSET_RL to -999.
185    o pkg/layers: improve vectorization of layers_fluxcalc.F
186      - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
187        time spent in this routine by more than a factor of 3 on an NEC-SX8
188      - step 2: replace search algorithm by a bisection algorithm found in
189        Press et al. Numerical Recipes in Fortran. This algorithm can be
190        vectorized and finds the correct bin in approx. log2(Nlayers) steps.
191        For now, use this algorithm only for TARGET_NEC_SX defined.
192      - moved the search algorithm into a separate subroutine, that is kept
193        within the same file for automatic inlining.
194      - modified catching potential errors
195    o pkg/ecco:
196      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
197    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
198      - modifications for ALLOW_GENTIM2D_CONTROL
199      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
200      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
201      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
202      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
203    o model/src:
204      - account for moist thermodynamics in (dry) potential temperature equation;
205        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
206        and cpl_aim+ocn.
207      - also switch to standard compiler (gfortran, was using ifort previously)
208        for fizhi-cs experiments reference output.
209    o pkg/ctrl:
210      - 1st step toward generic time-varying control variable (2D) via CPP option
211        ALLOW_GENTIM2D_CONTROL
212      - note new namelist ctrl_nml_genarr in data.ctrl
213    o verification/global_ocean.cs32x15:
214      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
215        thsice calling sequence and update "output.icedyn.txt" output file.
216    o pkg/ptracers:
217      - from Ryan A.: code to allow to restart a tracer at regular time interval
218        specifying a reset frequency and a reset-phase (for each tracers).
219    o pkg/thsice:
220      - implement new sequence of calls for thsice+seaice:
221          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
222          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
223      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
224        in CPP_OPTIONS.h) to recover old sequence;
225      - update diagnostics for Intermediate State thsice diagnostics: now filled
226        just before advection (instead of just after advection in old sequence);
227      - update output of experiment offline_exf_seaice (standard test);
228      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
229        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
230    o pkg/aim_v23:
231      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
232      - use standard pkg/mdsio routines to read & write CO2 pickup file;
233      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
234      - Implement new sequence of calls for seaice advection (with thsice and
235        seaice diffusion): do ice advection after ice-Thermodynamic (previously
236        was done before); change aim_do_physics.F (split the bi,bj loops block);
237      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
238    o pkg/thsice:
239      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
240        where just seaice diffusion is used without seaice-dynamics.
241    
242    checkpoint64c (2013/01/18)
243    o pkg/seaice:
244      - add a parameter JFNKres_tFac that can replace JFNKres_t
245        (= JFNKres_tFac*JFNKresidual before JFNK solver)
246      - add a line search option to the JFNK solver
247      - move update of u/vIce and computation of initial residual into a separate
248        routine (same file); makes the code a little easier to read (?)
249      - the line search requires computation of the residual and for some reason
250        I cannot do the update of u/vIce at the beginning of the Newton loop
251        without changing the results, so we move computation of the new residual
252        also to the end of the Newton loop, even without the line search
253    o pkg/mdsio:
254      - write missing value (corresponding to undefined array value) to meta files;
255        skip this if missing value is one (UNSET_RL would be a better value for the
256        case of undefined missing value but it's current the default missing-value);
257        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
258    o pkg/exf & thsice:
259      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
260        diagnostics) even when SHORTWAVE_HEATING is #undef;
261    o verification/cfc_example:
262      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
263        illustrate how to use it).
264    o verification/offline_exf_seaice:
265      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
266        files to only one time-record.
267      in input.thermo: narrow the 2 bands of low initial ice-concentration near
268        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
269        snapshot output; same mcPheePiston value as in thsice with
270        surf-current=0.2m/s.
271      in input.thsice: similar set-up as in input.thermo (channel with same seaice
272        initial conditions).
273    o verification/cfc_example:
274      - update file "data" with more standard choice (default rotationPeriod,
275        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
276        set deltaTFreeSurf to deltaTtracer) and update the output.
277    o pkg/layers:
278      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
279      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
280    o verification/offline_exf_seaice:
281      - set all {field}period to zero for constant-in-time forcing (not tested
282        anywhere else).
283    o verification/offline_exf_seaice:
284      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
285      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
286    o model/src:
287      - implement Finite-Volume method for (hydrostatic) presure gradient
288        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
289    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
290      - In order to be compatible with the default EVP code, this requires changing
291        the EVP code around a little; and because any small change immediately
292        breaks the lab_sea.hb87 verification experiment, the reference output is
293        updated two times (each time the remaining aggrement was only 2 digits):
294        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
295        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
296        The adjoint test lab_sea.evp also needed to be updated.
297      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
298        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
299        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
300        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
301        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
302        kept obscure, because I need to test it a little more.
303    o pkg/cheapaml:
304      - fix few incorrect type (_RL/_RS) in subroutine calls.
305    o pkg/seaice:
306      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
307        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
308    o model/src:
309      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
310        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
311        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
312    o pkg/cheapaml:
313      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
314        update output of experiment cheapAML_box.
315      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
316        and set them only in one place (cheapaml_readparms.F).
317      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
318      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
319        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
320    o model/src/the_main_loop.F:
321      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
322    o pkg/seaice:
323      - remove legacy branch code.
324      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
325    o verification/*/code*/SEAICE_OPTIONS.h:
326      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
327        SEAICE_CAP_HEFF).
328    o pkg/cheapaml:
329      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
330        to load new forcing fields.
331      - add missing "_d 0" where it's needed; + some editing (improve indentation).
332      - remove switch to "-r8" compiler option (no longer needed) in verification
333        cheapAML_box, keep same output (small trucation error differences).
334    o verification/offline_exf_seaice:
335      - add thermodynamics only test.
336    o verification/cheapAML_box:
337      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
338        keep same output (same 14 digits for cg2d).
339      - switch on "-r8" compiler option (some numerical values are missing
340        the "_d 0") and update output (only 6 digits for cg2d were preserved).
341    
342  checkpoint64b (2012/12/24)  checkpoint64b (2012/12/24)
343  o pkg/cheapaml:  o pkg/cheapaml:
344    - remove un-used variables (Qnet,EmPmR) from pickup files.    - remove un-used variables (Qnet,EmPmR) from pickup files.

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