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revision 1.2151 by jmc, Wed May 13 21:39:51 2015 UTC revision 1.2215 by jmc, Mon Dec 21 20:07:11 2015 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/atm_phys:
8      - allow to provide 2-d map of albedo and mixed-layer depth from files (but
9        hold fixed in time).
10    
11    checkpoint65r (2015/12/21)
12    o pkg/seaice:
13        fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
14        solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
15    o pkg/seaice:
16      - fix a bug in computing areaS in (J-J -> J-1) that affects runs
17        when SEAICEscaleSurfStress=.TRUE.,
18      - apply areaW and areaS in S/R seaice_calc_lhs
19    o pkg/atm_phys:
20      - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
21        (shortwave & longwave, net & downward) and diagnostics of temp. tendency
22        for individual contribution (convection, LSC cond, radiation)
23      - add Ruth Geen etal, GRL 2016, radiation optionis (see paper supp.
24        information); activated with: solar_exponent=0. and wv_exponent=-1.
25    o pkg/ggl90:
26      - within IDEMIX add upper limit for horizontal group velocity to
27        avoid instability problems in the explicit horizontal diffusion term for
28        long time steps or high resolution
29    o pkg/diagnostics:
30      - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
31        (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
32    o testreport:
33      - remove "-v" (verbose option) in default mpirun command.
34    o pkg/seaice/seaice_growth:
35      - catch potential division by zero in ITD code, does not change
36        verification results
37    o pkg/ecco:
38      - retire old codes to the Attic. The calls to retired functions are
39        left in a commented form in case they ever need to be re-activated.
40      - ecco_check.F: issue warning if any old CPP option is
41        defined that corresponds to retired codes -- then stop.
42    o pkg/atm_compon_interf:
43      - change seaice fraction (use for OCN dic surf.flux) stored and sent to
44        coupler: use last time-step value instead of average over cplSendFrq_iter
45        time-step, similar to what is done for seaIceMass.
46        This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
47    o eesupp & genmake2:
48      - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
49        <= remove until a fix is found for some ifort version on ia32 machine.
50    o pkg/seaice/seaice_evp:
51      - refine residual computation
52    
53    checkpoint65q (2015/11/18)
54    o pkg/seaice/seaice_evp:
55      - fix residual computations so that they no longer affect the actual
56        simulation code
57      - fix seaice_readparams to be able to actually set new parameters
58        SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
59    o model/src:
60      - fix wrong truncation (single prec) from "FLOAT" function in expressions
61        like: deltaT*FLOAT(myIter) when myIter is large:
62         a) replaced by DFLOAT (if not seen by TAF);
63         b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
64    o pkg/aim_v23:
65      - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
66        when pickupSuff is set ; do write rolling pickups + at the end of the run.
67    o pkg/atm_ocn_coupler + ocn_compon_interf:
68      - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
69        coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
70        add corresponding call in DO_OCEANIC_PHYS.
71    o coupler pkgs:
72      Start a new way to set-up optionally-exchanged variables (previously, only
73       there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
74       data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
75       send switch to ATM & OCN compon before reading their own "data.cpl" (so that
76       compononent param default can be set accordingly).
77      Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
78       but rather applies to a group a fields (going both ways like for DIC)
79       and corresponds to an option of coupling config.
80      coupler (pkg/atm_ocn_coupler):
81      - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
82        and read namelist directly (without eessup S/R calls) instead of
83        in the very un-flexible old way, 1 param per line, in fixed order;
84      - add error-counter to track errors (e.g., missing "data.cpl") and to stop
85        cleanly in CPL_CHECK_CPLCONFIG
86      - add new coupling-exchange selectors (some not yet active) including
87        cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
88                                             and ocnCpl_exchange_DIC=T in OCNIDS.h);
89      - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
90        component ; called directly from coupler.F, after comp. registrations;
91      - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
92         atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
93          -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
94      components (pkg/atm_ & ocn_compon_interf):
95      - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
96        CPP header file in all pkg source files.
97      - move checking of comp. configs out of cpl_exch_configs.F into new S/R
98        ATM/OCN_CHECK_CPLCONFIG;
99      - add error-counter to track errors (e.g., in "data.cpl") and to stop
100        cleanly in ATM/OCN_CHECK_CPLCONFIG;
101      - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
102        from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
103        before PACKAGES_READPARMS;
104      verification/cpl_aim+ocn/:
105      - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
106        "data.cpl" for coupler (in input_cpl).
107    o eesupp/inc:
108      - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
109        #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
110        to always cumulate tile local-sum in the same order (still uses
111        MPI_Allreduce like standard code).
112      - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
113        that are now identical to standard version (in eesupp/inc).
114    o pkg/shelfice:
115      - add SHELFICETransCoeffTFile for initializing spatially varying
116        heat and salt transfer coefficients
117    o pkg/atm_compon_interf & ocn_compon_interf:
118      - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
119        S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
120      - move bi,bj loops inside S/R OCN_STORE_MY_DATA
121    o pkg/atm_ocn_coupler:
122      - initialise to zero ATMVARS.h & OCNVARS.h arrays.
123    o pkg/rbcs:
124      - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
125        to compile with maskLEN=1 when all tracers use the same RBCS-mask.
126      - add a short report (to STDOUT) about RBCS-mask settings.
127    
128    checkpoint65p (2015/10/23)
129    o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
130        there is no adjoint test for EVP, we don't know what it does to the adjoint
131        solution, but at least there are no more recomputation warnings left
132    o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
133        a chance of giving the same results as a fully converged VP (JFNK) solver
134    o tools/adjoint_options/adjoint_diva:
135      - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
136    o pkg/streamice:
137      - spotted bug in streamice_driving_stress using dyG where should have been dxG
138    o pkg/exf:
139      - remove STOP statement that prevented to use wind or (wind-)stress
140        interpolation for constant-in-time forcing fields (wind/stress period = 0).
141    o pkg/seaice:
142      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
143        5 additionals 2D fields and 6 new store directives
144      - change logic in seaice_readparms.F: EVP code can now be turned on in
145        various ways, setting SEAICE_deltaTev is no longer required,
146        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
147        or SEAICEaEVPcoeff
148    o pkg/shelfice/shelfice_thermodynamics.F
149      - redefining uLoc/vLoc to u/v, instead of 2u/v
150    o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
151      - this is an intermediate state of a truely converging EVP that has
152        the potential of outperforming implicit VP methods, I do not recommend
153        using it yet.
154      - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
155        and all parameters are hardwired
156      - for convergence it still requires very smooth regularisations, that means,
157        if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
158        different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
159        specific averaging appears to be required, still subject to tuning
160      - still needs cleaning and I need to turn parameter into runtime parameters
161      - add code to compute and print residuals of iteration, compile with
162        defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
163    o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
164      that entered with r1.54 on Sep04, 2015, -> update results
165    
166    checkpoint65o (2015/09/14)
167    o pkg/mom_vecinv & mom_common:
168      - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
169        called from there.
170      - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
171        allows to use Vector-Invariant form in deep atmos and anelastic formulation
172    o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
173      and Koenig-Beatty+Holland (2012)
174      - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
175      - global 2D field tensileStrength, computed in seaice_calc_ice_strength
176      - requires an extra input argument for S/R seaice_calc_viscosities
177      - tensileStrength's depth dependence is different from Itkin et al. (2015)
178        (to be changed and played with, for now exponential)
179    o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
180      - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
181        by AREA according to Connelly et al. (2004), JPO.
182      - For EVP and the LSR solver, the implicit part of the drag term is
183        the only non-zero term in the denominator when there is no ice (which
184        prevented running the model with zero ice-ocean drag). If
185        SEAICEscaleSurfStress = .TRUE., this results in a division by zero
186        (or zero main diagonals BU/BV) which need to be caught. A practical
187        consequence is that for open water, the momentum equation reduce
188        to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
189        they happen to be zero, often leading to a non-zero solution over
190        open water.
191    o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
192        efficient EVP method.
193      - introduce area-weighted averages for e12 (analogously to
194        seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
195        remain, but also changing the order of terms in the previous average
196        changed the results as much) -> update experiment
197      - add SEAICE_DELTA_SMOOTHREG code
198      - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
199        TEM-code
200      - adjust loop bounds so that only required fields are computed
201      - add new averaging code for zetaZ/deltaZ (again similar to
202        seaice_calc_viscosities.F), inactive by default for now (will change
203        results again), but will replace old code eventually
204    o eesupp/src:
205      - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
206        to always cumulate tile local-sum in the same order
207        (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
208        Still uses MPI_Allreduce (like standard code) but on array of tiles
209        and should be faster than GLOBAL_SUM_SEND_RECV code.
210      - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
211        (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
212      - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
213         aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
214         fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
215         natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
216         tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
217    
218    checkpoint65n (2015/07/29)
219    o pkg/thsice:
220      - add a warning when used with pkg/aim but without updating SST
221        (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
222    o pkg/offline:
223      - change where Offline-Fields are loaded, from load_fields_driver.F to
224        directly within FORWARD_STEP, just after updating iter number and time;
225      - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
226        S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
227       These changes allow:
228        a) to recover exactly on-line results using deltaToffline=deltaTClock,
229        tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
230        both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
231        time-step, both with GM & KPP files and with recomputing these fields;
232        b) no needs to switch on staggerTimeStep anymore;
233        c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
234      - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
235    o pkg/offline:
236      - change (rarely used) offset-iteration parameter to an offset time (in s):
237        can easily recover previous offset-iter effect by setting offset-time
238        (offlineTimeOffset) to offset-iter x deltaToffline;
239      - do not turn-off Temp & Salinity surface relaxation when using KPP (used
240        in KPP as part of surface buoyancy forcing) in offline run.
241      - fix ptracers KPP non-local term in the case where KPP is re-computed.
242    o OpenAD
243      - Adding preliminary ggl90 test to OpenAD verification.
244        Config. with ggl90 currently diverges after 64 time steps
245        so will need more work to become more stable
246      - Adding preliminary kpp test to OpenAD verification.
247        required small tweakes in kpp_routines.F
248      - Merge and update from Krishna Narayanan's contrib area:
249        * Add one variable for preliminary OpenAD DIVA
250        * Add replacement time-stepping for OpenAD DIVA
251        * genmake2 flag -diva (but only for OpenAD; preliminary)
252        * required modifs for OAD_support
253        successful preliminary test for tutorial_global_oce_biogeo/
254    o pkg/seaice:
255      - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
256      - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
257        delta with a smooth function in s/r seaice_calc_viscosity
258        (no effect on EVP)
259      - rename local suffix "sqr" into "sq" for more consistent variable names
260    o pkg/seaice:
261        add new parameter SEAICE_deltaMin that is used ***only***
262        for regularizing Delta (and nothing else, like the parameter
263        which is also used for all sorts of things SEAICE_EPS).
264        Defaults to SEAICE_EPS for backward compatibility only.
265    o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
266        the wrong key by inialising it before use -> fixes a recomputation
267        problem but does not fix the gradient
268    o pkg/layers:
269      - move resetting of flux arrays to outside the iLa loop
270        (this caused layers_diapycnal to not work with more than one layer coord.)
271      - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
272    o pkg/layers:
273      - remove from common block 3D layers fields (used to diagnose transport
274        in tracer coords) and declare them as local arrays in layers_calc.F
275    o pkg/seaice:
276      - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
277        in lab_sea forward experiment (changes results -> updated)
278      - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
279    o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
280       computations; for SEAICE_VECTORIZE_LSR
281      - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
282        sweep to the outside,
283      - remove store directives and add "CADJ loop sequential" directives
284        in analogy to model/src/solve_tridiagonal.F
285      - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
286        boundaries to yield more readable code. This has also the charming side
287        effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
288        SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
289        seaice_lsr_tridiagu/v now requires either of these flags, vectorization
290        still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
291        an additional option)
292       The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
293       but the adjoint gradients (which are affected by this change) still explode.
294    o coupler (atm & ocn _compon_interf):
295      - avoid using Exch2 IO mapping if not suitable.
296    
297    checkpoint65m (2015/06/15)
298    o pkg/layers:
299      - clean-up old parameters setting (from Sep 2012):
300        + remove old parameters setting from common block (declared locally);
301        + stop if any old parameter is mixed with new parameters;
302        + check for valid or consistent parameter setting (e.g., layers_name)
303      - check that layers_bounds for Pot.Density are in the right range;
304        this is supposed to catch un-updated setting after recently shifting
305        potential density field "prho" by -1000 (now in "sigma" scale).
306    o pkg/layers:
307      - Added missing call to layers_fill for keeping track of tottend in
308        pkg/diagnostics/diagnostics_fill_state.F
309    o pkg/layers:
310      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
311        of diapycnal fluxes
312    o pkg/layers:
313      - reverted changes to interpolation to previous treatment; there
314        was never actually a problem
315    o pkg/layers:
316      - fix interpolation of layers tracers in the presence of partial cells
317      - add lots of new functionality to compute water mass transformation
318        (enabled by CPP flag LAYERS_THERMODYNAMICS)
319      - add new calls from main code (diags_oceanic_surf_flux.F,
320        thermodynamics.F, impldiff.F) and gad to save the necessary fields
321        for layers_thermodynamics calculations
322    o pkg/ptracers:
323      - add capability of stepping a passive tracer forward without advection
324        by setting PTRACERS_advScheme to 0.
325    o pkg/diagnostics:
326      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
327  o pkg/layers:  o pkg/layers:
328    - shift potential density field "prho" by -1000 for density layer averaging so    - shift potential density field "prho" by -1000 for density layer averaging so
329      that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);      that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);

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