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revision 1.2183 by mlosch, Thu Sep 24 08:17:32 2015 UTC revision 1.2242 by jmc, Tue Apr 5 23:37:25 2016 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/advect_xz:
8      - increase overlap size from 3 to 4 and add new secondary test for PQM
9        advection scheme (with mono & wino limiter).
10      - change main exp. to test PPM (with weno limiter) adv.scheme on Temp.
11    o model/src:
12      - new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently
13        added phi0Ref) to set vertical axis origin and phiRef origin;
14        keep Ro_SeaLevel for backward compatibility (with a warning).
15       According to coordinate and fluid type:
16        OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top)
17        ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom)
18        OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top)
19        ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom)
20      - remove Ro_SeaLevel from ATM experiment parameter files;
21      - in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the
22        complement; update output.txt (changes at machine truncation level).
23    o pkg/seaice/seaice_evp.F
24      - simplify computation of deltaZ and zetaZ to simple averaging following
25        Bouillon et al. (2013). This removes a lot of code, but also changes
26        verification experiment lab_sea.hb87 -> updated
27    
28    checkpoint65u (2016/03/14)
29    o pkg/generic_advdiff:
30      - from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52)
31        with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP);
32        Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for
33        testing and not for actual use.
34    o model/src:
35      - add parameter "phi0Ref" to specify reference [pressure/geo] potential at
36        origin r = rF(1);
37      - add options (parameter selectP_inEOS_Zc) to select which pressure to use
38        in EOS for height coordinate: enable to include NH Pressure or to use
39        more accurate pressure vertical profile; options not linked to EOS type
40        (as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type;
41      - start to implement variable gravity (along vertical): for now, only with
42        z-coords (not even z*).
43      - add Ideal Gas equation of state for height coordinate.
44      - update OpenAD output (affected at machine truncation level) of exp:
45        global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo.
46    o pkg/exf:
47      - add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result
48        of exf interpolation (before any rescaling, rotation or interpolation
49        to velocity point) for each field that gets loaded from file. This option
50        identically mimics the input file organization (e.g. record numbers in year
51        by year input files) besides the change in horizontal grid.
52      - add rotateStressOnAgrid run-time switch so that wind stress fields
53        can be provided on the A-grid in zonal/meridional direction and
54        rotated on the fly. This only applies to the case when the exf
55        interpolation is off and rotateStressOnAgrid is false by default.
56    o model/src:
57      - rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since
58        it's also used with pkg/atm_phys) and add few more parameters (but still
59        inactive, src code yet to come)
60    
61    checkpoint65t (2016/02/10)
62    o pkg/atm_phys:
63      - from Ruth Geen: add optical depth dependence on CO2 concentration.
64    o model/src:
65      - fix vertical inter/extra-polation of density factor rhoFacF (for anelastic)
66        for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F.
67        Update output of exp. deep_anelastic (changes at truncation level).
68    o tools:
69      - add a hack in "remove_comments_sed" (used only with TAF) for recent
70        version of OpenMPI (shipped with FC.23): comment out the new header
71        file "mpif-sizeof.h" which causes problems to TAF.
72    o pkg/seaice:
73      - change the termination criterion so that maxits (SEAICElinearIterMax)
74        has an effect
75      - unify iteration parameters for implicit solvers (JFNK and Picard)
76        SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS
77        SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER
78        SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner
79        SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner
80        SEAICEnonLinTol     replaces JFNKgamma_nonlin
81      - remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN
82      - add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and
83        use with SEAICEuseKrylov
84    o pkg/seaice/seaice_lsr.F
85        fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only
86        relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have
87        an effect.
88    o pkg/seaice: add two new parameters
89      - SEAICEuseLSR to simplify the logic in seaice_dynsolver (this
90        parameter is not in any namelist)
91      - SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as
92        a preconditioner for the non-linear Newton iteration of the JFNK
93        solver
94    o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT,
95      affects some experiments at truncation level:
96      - global_ocean.cs32x15.icedyn (11 digits),
97      - global_ocean.cs32x15.seaice (11 digits),
98      - seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update
99      - also update global_ocean.cs32x15 adjoint and tangent-linear results
100    o pkg/salt_plume & pkg/thsice:
101      - for coupled  set-up with pkg/thsice in ATM and pkg/salt_plume in OCN,
102        connect salt_plume flux to ATM-OCN coupling pkgs interface:
103       a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for
104         export to coupler interface) even without compiling pkg/salt_plume ;
105       b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field
106         (saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH.
107    o pkg/dic:
108      - use the updated seaice fraction (from seaice pkgs) for DIC forcing
109        instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE
110        called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD);
111      - move also update with values from ATM-OCN Coupler in the same new S/R
112        (previously done in ocn_apply_import.F).
113    o tools/adjoint_options:
114      - specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default)
115        has been changed on Jan 14, 2016.
116    o pkg/ggl90:
117      - add alternative discretisation of vertical shear (off by default), to
118        compute the mean (@ grid-cell center) of vertical shear compon instead of
119        vertical shear of mean flow (@ grid-cell center).
120      - add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated
121        results on adjacent faces of cubed-sphere grids; this fix the restart.
122    o pkg/atm_compon_interf:
123      - skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just
124        pass last value, stored directly before export to CPL ;
125        Note: this affects results of Coupled set-up where OCN uses useImportSLP=T
126      - remove atmSLPr from pickup files (no longer needed for restart)
127    
128    checkpoint65s (2016/01/13)
129    o eesupp & genmake2:
130       - first check for Function ETIME and, if it fails, then check for subroutine
131         ETIME and consistent output; use the appropriate version in timers.F
132    o model/src:
133      - to check restart test, add option to apply EXCH to U,V earlier, just before
134        integr_continuity; turned off by default.
135    o pkg/dic:
136      - remove CPP option USE_ATMOSCO2 (not needed)
137    o tools/tst_2+2:
138      - try to ignore difference between +0 and -0 in binary file, causing test
139        to fail for no good reason.
140    o eesupp & genmake2:
141      - put back modif from Jinxuan Zhu - change etime fct call to S/R call -
142        but also check (in genmake2) that test runs and returns meaningful results.
143    o coupler pkgs:
144      Finish implementation of optionally-exchanged variable switches (started on
145       Nov 12) with addition of few more exchanged fields, including 2-way exchange
146       of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
147       advection in OCN component; this requires sequential coupling.
148      coupler (pkg/atm_ocn_coupler):
149      - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
150        routines (useful for debug).
151      - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
152         flux, DIC fields) if corresponding switch is ON.
153      - add option to export RunOff to OCN (to use for DIC river input)
154      - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
155      components (pkg/atm_ & ocn_compon_interf):
156      - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
157        optionally exchanged fields; add a check & stop in cpl_readparms.F.
158        ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
159        OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice.
160      - rename:   fracIce     -> sIceFrac_cpl (<- match coupler var name)
161        + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
162      - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
163      - hold in common block coupler optionally-exchanged variable switch
164        and set default "useImportXXX" accordingly; + check & stop if inconsistent.
165      - add diagnostics for all imported fields from coupler (in both OCN & ATM);
166        this is intended to replace the OCN cplFldtave.* output files (not updated
167        to contain new additional exchanged fields).
168    o pkg/dic:
169      - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
170    o pkg/thsice:
171      - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
172        and writing of thsice pickup files.
173    o pkg/atm_compon_interf:
174      - move all field individual export-call out of cpl_export_import_data.F
175        into new S/R ATM_EXPORT_FIELDS
176    o pkg/atm_compon_interf:
177      - store state variables (for now, only thSIce fields) just before beeing
178        exported (in cpl_export_import_data.F, like on ocean side) instead of from
179        atm_store_my_data.F like all exported fluxes.
180      - new version of pickup_cpl: write field names into meta file and read meta
181        file to find field postion in pickup. Also only write/read fields meeded for
182        restart (same logic as main pickup file ; also using pickupStrictlyMatch)
183    o pkg/dic:
184      - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
185    o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
186        pressure replacement method (=1., default) or original Hibler (1979) (=0.)
187        value can be from domain [0,1] to average between the two methods
188    o pkg/atm_phys:
189      - allow to provide 2-d map of albedo and mixed-layer depth from files (but
190        hold fixed in time).
191    
192    checkpoint65r (2015/12/21)
193    o pkg/seaice:
194        fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
195        solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
196    o pkg/seaice:
197      - fix a bug in computing areaS in (J-J -> J-1) that affects runs
198        when SEAICEscaleSurfStress=.TRUE.,
199      - apply areaW and areaS in S/R seaice_calc_lhs
200    o pkg/atm_phys:
201      - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
202        (shortwave & longwave, net & downward) and diagnostics of temp. tendency
203        for individual contribution (convection, LSC cond, radiation)
204      - add Ruth Geen etal, GRL 2016, radiation optionis (see paper supp.
205        information); activated with: solar_exponent=0. and wv_exponent=-1.
206    o pkg/ggl90:
207      - within IDEMIX add upper limit for horizontal group velocity to
208        avoid instability problems in the explicit horizontal diffusion term for
209        long time steps or high resolution
210    o pkg/diagnostics:
211      - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
212        (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
213    o testreport:
214      - remove "-v" (verbose option) in default mpirun command.
215    o pkg/seaice/seaice_growth:
216      - catch potential division by zero in ITD code, does not change
217        verification results
218    o pkg/ecco:
219      - retire old codes to the Attic. The calls to retired functions are
220        left in a commented form in case they ever need to be re-activated.
221      - ecco_check.F: issue warning if any old CPP option is
222        defined that corresponds to retired codes -- then stop.
223    o pkg/atm_compon_interf:
224      - change seaice fraction (use for OCN dic surf.flux) stored and sent to
225        coupler: use last time-step value instead of average over cplSendFrq_iter
226        time-step, similar to what is done for seaIceMass.
227        This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
228    o eesupp & genmake2:
229      - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
230        <= remove until a fix is found for some ifort version on ia32 machine.
231    o pkg/seaice/seaice_evp:
232      - refine residual computation
233    
234    checkpoint65q (2015/11/18)
235    o pkg/seaice/seaice_evp:
236      - fix residual computations so that they no longer affect the actual
237        simulation code
238      - fix seaice_readparams to be able to actually set new parameters
239        SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
240    o model/src:
241      - fix wrong truncation (single prec) from "FLOAT" function in expressions
242        like: deltaT*FLOAT(myIter) when myIter is large:
243         a) replaced by DFLOAT (if not seen by TAF);
244         b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
245    o pkg/aim_v23:
246      - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
247        when pickupSuff is set ; do write rolling pickups + at the end of the run.
248    o pkg/atm_ocn_coupler + ocn_compon_interf:
249      - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
250        coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
251        add corresponding call in DO_OCEANIC_PHYS.
252    o coupler pkgs:
253      Start a new way to set-up optionally-exchanged variables (previously, only
254       there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
255       data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
256       send switch to ATM & OCN compon before reading their own "data.cpl" (so that
257       compononent param default can be set accordingly).
258      Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
259       but rather applies to a group a fields (going both ways like for DIC)
260       and corresponds to an option of coupling config.
261      coupler (pkg/atm_ocn_coupler):
262      - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
263        and read namelist directly (without eessup S/R calls) instead of
264        in the very un-flexible old way, 1 param per line, in fixed order;
265      - add error-counter to track errors (e.g., missing "data.cpl") and to stop
266        cleanly in CPL_CHECK_CPLCONFIG
267      - add new coupling-exchange selectors (some not yet active) including
268        cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
269                                             and ocnCpl_exchange_DIC=T in OCNIDS.h);
270      - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
271        component ; called directly from coupler.F, after comp. registrations;
272      - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
273         atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
274          -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
275      components (pkg/atm_ & ocn_compon_interf):
276      - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
277        CPP header file in all pkg source files.
278      - move checking of comp. configs out of cpl_exch_configs.F into new S/R
279        ATM/OCN_CHECK_CPLCONFIG;
280      - add error-counter to track errors (e.g., in "data.cpl") and to stop
281        cleanly in ATM/OCN_CHECK_CPLCONFIG;
282      - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
283        from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
284        before PACKAGES_READPARMS;
285      verification/cpl_aim+ocn/:
286      - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
287        "data.cpl" for coupler (in input_cpl).
288    o eesupp/inc:
289      - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
290        #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
291        to always cumulate tile local-sum in the same order (still uses
292        MPI_Allreduce like standard code).
293      - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
294        that are now identical to standard version (in eesupp/inc).
295    o pkg/shelfice:
296      - add SHELFICETransCoeffTFile for initializing spatially varying
297        heat and salt transfer coefficients
298    o pkg/atm_compon_interf & ocn_compon_interf:
299      - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
300        S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
301      - move bi,bj loops inside S/R OCN_STORE_MY_DATA
302    o pkg/atm_ocn_coupler:
303      - initialise to zero ATMVARS.h & OCNVARS.h arrays.
304    o pkg/rbcs:
305      - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
306        to compile with maskLEN=1 when all tracers use the same RBCS-mask.
307      - add a short report (to STDOUT) about RBCS-mask settings.
308    
309    checkpoint65p (2015/10/23)
310    o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
311        there is no adjoint test for EVP, we don't know what it does to the adjoint
312        solution, but at least there are no more recomputation warnings left
313    o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
314        a chance of giving the same results as a fully converged VP (JFNK) solver
315    o tools/adjoint_options/adjoint_diva:
316      - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
317    o pkg/streamice:
318      - spotted bug in streamice_driving_stress using dyG where should have been dxG
319    o pkg/exf:
320      - remove STOP statement that prevented to use wind or (wind-)stress
321        interpolation for constant-in-time forcing fields (wind/stress period = 0).
322    o pkg/seaice:
323      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
324        5 additionals 2D fields and 6 new store directives
325      - change logic in seaice_readparms.F: EVP code can now be turned on in
326        various ways, setting SEAICE_deltaTev is no longer required,
327        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
328        or SEAICEaEVPcoeff
329    o pkg/shelfice/shelfice_thermodynamics.F
330      - redefining uLoc/vLoc to u/v, instead of 2u/v
331  o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz  o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
332    - this is an intermediate state of a truely converging EVP that has    - this is an intermediate state of a truely converging EVP that has
333      the potential of outperforming implicit VP methods, I do not recommend      the potential of outperforming implicit VP methods, I do not recommend

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