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revision 1.2144 by mlosch, Tue Apr 7 15:43:21 2015 UTC revision 1.2207 by mlosch, Thu Nov 26 15:54:48 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/seaice/seaice_growth:
8      - catch potential division by zero in ITD code, does not change
9        verification results
10    o pkg/ecco:
11      - retire old codes to the Attic. The calls to retired
12        functions are left in a commented form in case they
13        ever need to be re-activated.
14      - ecco_check.F: issue warning if any old CPP option is
15        defined that corresponds to retired codes -- then stop.
16    o pkg/atm_compon_interf:
17      - change seaice fraction (use for OCN dic surf.flux) stored and sent to
18        coupler: use last time-step value instead of average over cplSendFrq_iter
19        time-step, similar to what is done for seaIceMass.
20        This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
21    o eesupp & genmake2:
22      - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
23        <= remove until a fix is found for some ifort version on ia32 machine.
24    o pkg/seaice/seaice_evp:
25      - refine residual computation
26    
27    checkpoint65q (2015/11/18)
28    o pkg/seaice/seaice_evp:
29      - fix residual computations so that they no longer affect the actual
30        simulation code
31      - fix seaice_readparams to be able to actually set new parameters
32        SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
33    o model/src:
34      - fix wrong truncation (single prec) from "FLOAT" function in expressions
35        like: deltaT*FLOAT(myIter) when myIter is large:
36         a) replaced by DFLOAT (if not seen by TAF);
37         b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
38    o pkg/aim_v23:
39      - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
40        when pickupSuff is set ; do write rolling pickups + at the end of the run.
41    o pkg/atm_ocn_coupler + ocn_compon_interf:
42      - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
43        coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
44        add corresponding call in DO_OCEANIC_PHYS.
45    o coupler pkgs:
46      Start a new way to set-up optionally-exchanged variables (previously, only
47       there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
48       data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
49       send switch to ATM & OCN compon before reading their own "data.cpl" (so that
50       compononent param default can be set accordingly).
51      Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
52       but rather applies to a group a fields (going both ways like for DIC)
53       and corresponds to an option of coupling config.
54      coupler (pkg/atm_ocn_coupler):
55      - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
56        and read namelist directly (without eessup S/R calls) instead of
57        in the very un-flexible old way, 1 param per line, in fixed order;
58      - add error-counter to track errors (e.g., missing "data.cpl") and to stop
59        cleanly in CPL_CHECK_CPLCONFIG
60      - add new coupling-exchange selectors (some not yet active) including
61        cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
62                                             and ocnCpl_exchange_DIC=T in OCNIDS.h);
63      - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
64        component ; called directly from coupler.F, after comp. registrations;
65      - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
66         atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
67          -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
68      components (pkg/atm_ & ocn_compon_interf):
69      - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
70        CPP header file in all pkg source files.
71      - move checking of comp. configs out of cpl_exch_configs.F into new S/R
72        ATM/OCN_CHECK_CPLCONFIG;
73      - add error-counter to track errors (e.g., in "data.cpl") and to stop
74        cleanly in ATM/OCN_CHECK_CPLCONFIG;
75      - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
76        from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
77        before PACKAGES_READPARMS;
78      verification/cpl_aim+ocn/:
79      - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
80        "data.cpl" for coupler (in input_cpl).
81    o eesupp/inc:
82      - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
83        #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
84        to always cumulate tile local-sum in the same order (still uses
85        MPI_Allreduce like standard code).
86      - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
87        that are now identical to standard version (in eesupp/inc).
88    o pkg/shelfice:
89      - add SHELFICETransCoeffTFile for initializing spatially varying
90        heat and salt transfer coefficients
91    o pkg/atm_compon_interf & ocn_compon_interf:
92      - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
93        S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
94      - move bi,bj loops inside S/R OCN_STORE_MY_DATA
95    o pkg/atm_ocn_coupler:
96      - initialise to zero ATMVARS.h & OCNVARS.h arrays.
97    o pkg/rbcs:
98      - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
99        to compile with maskLEN=1 when all tracers use the same RBCS-mask.
100      - add a short report (to STDOUT) about RBCS-mask settings.
101    
102    checkpoint65p (2015/10/23)
103    o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
104        there is no adjoint test for EVP, we don't know what it does to the adjoint
105        solution, but at least there are no more recomputation warnings left
106    o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
107        a chance of giving the same results as a fully converged VP (JFNK) solver
108    o tools/adjoint_options/adjoint_diva:
109      - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
110    o pkg/streamice:
111      - spotted bug in streamice_driving_stress using dyG where should have been dxG
112    o pkg/exf:
113      - remove STOP statement that prevented to use wind or (wind-)stress
114        interpolation for constant-in-time forcing fields (wind/stress period = 0).
115    o pkg/seaice:
116      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
117        5 additionals 2D fields and 6 new store directives
118      - change logic in seaice_readparms.F: EVP code can now be turned on in
119        various ways, setting SEAICE_deltaTev is no longer required,
120        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
121        or SEAICEaEVPcoeff
122    o pkg/shelfice/shelfice_thermodynamics.F
123      - redefining uLoc/vLoc to u/v, instead of 2u/v
124    o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
125      - this is an intermediate state of a truely converging EVP that has
126        the potential of outperforming implicit VP methods, I do not recommend
127        using it yet.
128      - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
129        and all parameters are hardwired
130      - for convergence it still requires very smooth regularisations, that means,
131        if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
132        different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
133        specific averaging appears to be required, still subject to tuning
134      - still needs cleaning and I need to turn parameter into runtime parameters
135      - add code to compute and print residuals of iteration, compile with
136        defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
137    o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
138      that entered with r1.54 on Sep04, 2015, -> update results
139    
140    checkpoint65o (2015/09/14)
141    o pkg/mom_vecinv & mom_common:
142      - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
143        called from there.
144      - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
145        allows to use Vector-Invariant form in deep atmos and anelastic formulation
146    o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
147      and Koenig-Beatty+Holland (2012)
148      - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
149      - global 2D field tensileStrength, computed in seaice_calc_ice_strength
150      - requires an extra input argument for S/R seaice_calc_viscosities
151      - tensileStrength's depth dependence is different from Itkin et al. (2015)
152        (to be changed and played with, for now exponential)
153    o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
154      - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
155        by AREA according to Connelly et al. (2004), JPO.
156      - For EVP and the LSR solver, the implicit part of the drag term is
157        the only non-zero term in the denominator when there is no ice (which
158        prevented running the model with zero ice-ocean drag). If
159        SEAICEscaleSurfStress = .TRUE., this results in a division by zero
160        (or zero main diagonals BU/BV) which need to be caught. A practical
161        consequence is that for open water, the momentum equation reduce
162        to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
163        they happen to be zero, often leading to a non-zero solution over
164        open water.
165    o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
166        efficient EVP method.
167      - introduce area-weighted averages for e12 (analogously to
168        seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
169        remain, but also changing the order of terms in the previous average
170        changed the results as much) -> update experiment
171      - add SEAICE_DELTA_SMOOTHREG code
172      - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
173        TEM-code
174      - adjust loop bounds so that only required fields are computed
175      - add new averaging code for zetaZ/deltaZ (again similar to
176        seaice_calc_viscosities.F), inactive by default for now (will change
177        results again), but will replace old code eventually
178    o eesupp/src:
179      - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
180        to always cumulate tile local-sum in the same order
181        (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
182        Still uses MPI_Allreduce (like standard code) but on array of tiles
183        and should be faster than GLOBAL_SUM_SEND_RECV code.
184      - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
185        (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
186      - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
187         aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
188         fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
189         natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
190         tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
191    
192    checkpoint65n (2015/07/29)
193    o pkg/thsice:
194      - add a warning when used with pkg/aim but without updating SST
195        (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
196    o pkg/offline:
197      - change where Offline-Fields are loaded, from load_fields_driver.F to
198        directly within FORWARD_STEP, just after updating iter number and time;
199      - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
200        S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
201       These changes allow:
202        a) to recover exactly on-line results using deltaToffline=deltaTClock,
203        tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
204        both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
205        time-step, both with GM & KPP files and with recomputing these fields;
206        b) no needs to switch on staggerTimeStep anymore;
207        c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
208      - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
209    o pkg/offline:
210      - change (rarely used) offset-iteration parameter to an offset time (in s):
211        can easily recover previous offset-iter effect by setting offset-time
212        (offlineTimeOffset) to offset-iter x deltaToffline;
213      - do not turn-off Temp & Salinity surface relaxation when using KPP (used
214        in KPP as part of surface buoyancy forcing) in offline run.
215      - fix ptracers KPP non-local term in the case where KPP is re-computed.
216    o OpenAD
217      - Adding preliminary ggl90 test to OpenAD verification.
218        Config. with ggl90 currently diverges after 64 time steps
219        so will need more work to become more stable
220      - Adding preliminary kpp test to OpenAD verification.
221        required small tweakes in kpp_routines.F
222      - Merge and update from Krishna Narayanan's contrib area:
223        * Add one variable for preliminary OpenAD DIVA
224        * Add replacement time-stepping for OpenAD DIVA
225        * genmake2 flag -diva (but only for OpenAD; preliminary)
226        * required modifs for OAD_support
227        successful preliminary test for tutorial_global_oce_biogeo/
228    o pkg/seaice:
229      - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
230      - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
231        delta with a smooth function in s/r seaice_calc_viscosity
232        (no effect on EVP)
233      - rename local suffix "sqr" into "sq" for more consistent variable names
234    o pkg/seaice:
235        add new parameter SEAICE_deltaMin that is used ***only***
236        for regularizing Delta (and nothing else, like the parameter
237        which is also used for all sorts of things SEAICE_EPS).
238        Defaults to SEAICE_EPS for backward compatibility only.
239    o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
240        the wrong key by inialising it before use -> fixes a recomputation
241        problem but does not fix the gradient
242    o pkg/layers:
243      - move resetting of flux arrays to outside the iLa loop
244        (this caused layers_diapycnal to not work with more than one layer coord.)
245      - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
246    o pkg/layers:
247      - remove from common block 3D layers fields (used to diagnose transport
248        in tracer coords) and declare them as local arrays in layers_calc.F
249    o pkg/seaice:
250      - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
251        in lab_sea forward experiment (changes results -> updated)
252      - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
253    o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
254       computations; for SEAICE_VECTORIZE_LSR
255      - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
256        sweep to the outside,
257      - remove store directives and add "CADJ loop sequential" directives
258        in analogy to model/src/solve_tridiagonal.F
259      - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
260        boundaries to yield more readable code. This has also the charming side
261        effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
262        SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
263        seaice_lsr_tridiagu/v now requires either of these flags, vectorization
264        still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
265        an additional option)
266       The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
267       but the adjoint gradients (which are affected by this change) still explode.
268    o coupler (atm & ocn _compon_interf):
269      - avoid using Exch2 IO mapping if not suitable.
270    
271    checkpoint65m (2015/06/15)
272    o pkg/layers:
273      - clean-up old parameters setting (from Sep 2012):
274        + remove old parameters setting from common block (declared locally);
275        + stop if any old parameter is mixed with new parameters;
276        + check for valid or consistent parameter setting (e.g., layers_name)
277      - check that layers_bounds for Pot.Density are in the right range;
278        this is supposed to catch un-updated setting after recently shifting
279        potential density field "prho" by -1000 (now in "sigma" scale).
280    o pkg/layers:
281      - Added missing call to layers_fill for keeping track of tottend in
282        pkg/diagnostics/diagnostics_fill_state.F
283    o pkg/layers:
284      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
285        of diapycnal fluxes
286    o pkg/layers:
287      - reverted changes to interpolation to previous treatment; there
288        was never actually a problem
289    o pkg/layers:
290      - fix interpolation of layers tracers in the presence of partial cells
291      - add lots of new functionality to compute water mass transformation
292        (enabled by CPP flag LAYERS_THERMODYNAMICS)
293      - add new calls from main code (diags_oceanic_surf_flux.F,
294        thermodynamics.F, impldiff.F) and gad to save the necessary fields
295        for layers_thermodynamics calculations
296    o pkg/ptracers:
297      - add capability of stepping a passive tracer forward without advection
298        by setting PTRACERS_advScheme to 0.
299    o pkg/diagnostics:
300      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
301    o pkg/layers:
302      - shift potential density field "prho" by -1000 for density layer averaging so
303        that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
304        Note that density bin boundaries (layers_bounds in data.layers) have
305        to be set accordingly (i.e., shifted, in sigma scale).
306    o pkg/layers:
307      - fix snap-shot output of layer thickness @ V.pt and output of pot.density
308      - fix calculation of layer non-weighted velocity and layer probability
309      - add diagnostics for pot.density used for layer averaging
310    o pkg/seaice:
311      - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
312        positiveness, modify a few comments and improve variable names,
313      - the changed computation of deltaC affects most seaice-related
314        experiments at the truncation level.
315        seaice_itd.thermo is affected by far the most, with
316        only 7 digits of agreement remaining; update experiments.
317    
318    checkpoint65l (2015/05/04)
319    o pkg/shelfice:
320      - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
321        factor drKp1 to zero where it is negative (ie. do not use
322        SHELFICEBoundaryLayer if hFacC>1)
323      - the same for factor drLoc in shelfice_forcing.F
324    o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
325        with modules in ptracers, when using testreport option "-small_f"
326    o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
327      - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
328  o verification/testreport  o verification/testreport
329    - add new option -small_f    - add new option -small_f
330      with this option testreport first makes the target small_f (*.f files)      with this option testreport first makes the target small_f (*.f files)
331      before running make (all). This is useful for explicit inlining when      before running make (all). This is useful for explicit inlining when
332      all sources need to be full available.      all sources need to be full available.
333    o pkg/exf/exf_interp.F:
334        remove previous changes related to reverse (decreasing) input grids latitude
335    
336  checkpoint65k (2015/04/01)  checkpoint65k (2015/04/01)
337  o pkg/ecco:  o pkg/ecco:

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