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revision 1.2195 by dimitri, Mon Nov 2 21:27:41 2015 UTC revision 1.2261 by jmc, Fri Jul 29 19:49:59 2016 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint65y (2016/07/29)
8    o pkg/debug (stats):
9      - change GLOBAL_SUM to GLOBAL_SUM_TILE (result independent of tile to
10        proc/thread mapping);
11      - fix Min & Max for case where 1 thread has only empty tiles;
12      - use RL variable to count number of wet grid points (with big domain,
13        can be too large to fit into integer*4).
14    o pkg/monitor:
15      - use RL variable to count number of wet grid points (but used only for del2)
16      - add new routine to compute Advective CFL within tracer time-stepping with
17        writing delayed until next monitor output.
18    o pkg/obcs:
19      - fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW)
20    o pkg/dic & seaice:
21      - fix compilation of ocean component for coupled atm+ocn model with
22        seaice dynamics & dic.
23    
24    checkpoint65x (2016/06/11)
25    o add a license text file in main MITgcm tree.
26    o added pkg/bling:
27      - intermediate complexity biogeochemical model
28      - see bling_description.txt for details
29      - verification experiment is global_oce_biogeo_bling (for now, in
30        Contrib/verification_other/); tested daily on baudelaire with gfortran.
31      - add entry point in pkg/gchem for new pkg "bling".
32    o pkg/seaice: fix tensile stength computation
33      - replace global field tensileStrength by tensileStrFac
34      - tensileStrFac can be computed once in S/R seaice_init_varia
35      - fortunately that does not affect any verification results
36    
37    checkpoint65w (2016/05/12)
38    o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles
39         with ECCO_CTRL_DEPRECATED defined
40    o verification/global_ocean.cs32x15:
41      - change secondary test "viscA4" to also test "selectP_inEOS_Zc=3"
42        with "selectNHfreeSurf=1".
43    o model/src (non-hydrostatic free-surface):
44      - More "natural" expression of NH free-surface term (case selectNHfreeSurf=1):
45        was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf.
46      - Calculate surface vertical velocity after 2-D solver adjustment (accounts
47        for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv
48        and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1.
49        This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux.
50      - Update output (changes at machine truncation level) of verification exp:
51        exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d),
52        short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d).
53    o pkg/seaice: ITD code
54      - fix picking up from a single category model by initialising
55        heff/area/hsnowITD = 0. in seaice_itd_pickup.F
56      - split a long warning message in seaice_check_pickup.F into two lines,
57        because NEC SX-ACE cannot deal with the long line.
58    o model/src:
59      - fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3)
60    o pkg/seaice:
61      - add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG
62    o pkg/seaice:
63      - add basal stress as parameterisation for grounding ice
64        following Lemieux et al. (2015)
65      - turn on by setting new parameter SEAICEbasalDragK2 to a value
66        larger than 0. Lemieux et al. (2015) recommend 15.
67      - The adjoint complains with extra recomputations so there is also a
68        new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in
69        order to postpone the problem
70      - compile the new code in lab_sea
71    o verification/halfpipe_streamice:
72      - update both TAF and OpenAD adm output (machine truncation differences)
73    
74    checkpoint65v (2016/04/08)
75    o verification/advect_xz:
76      - increase overlap size from 3 to 4 and add new secondary test for PQM
77        advection scheme (with mono & wino limiter).
78      - change main exp. to test PPM (with weno limiter) adv.scheme on Temp.
79    o model/src:
80      - new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently
81        added phi0Ref) to set vertical axis origin and phiRef origin;
82        keep Ro_SeaLevel for backward compatibility (with a warning).
83       According to coordinate and fluid type:
84        OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top)
85        ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom)
86        OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top)
87        ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom)
88      - remove Ro_SeaLevel from ATM experiment parameter files;
89      - in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the
90        complement; update output.txt (changes at machine truncation level).
91    o pkg/seaice/seaice_evp.F
92      - simplify computation of deltaZ and zetaZ to simple averaging following
93        Bouillon et al. (2013). This removes a lot of code, but also changes
94        verification experiment lab_sea.hb87 -> updated
95    
96    checkpoint65u (2016/03/14)
97    o pkg/generic_advdiff:
98      - from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52)
99        with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP);
100        Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for
101        testing and not for actual use.
102    o model/src:
103      - add parameter "phi0Ref" to specify reference [pressure/geo] potential at
104        origin r = rF(1);
105      - add options (parameter selectP_inEOS_Zc) to select which pressure to use
106        in EOS for height coordinate: enable to include NH Pressure or to use
107        more accurate pressure vertical profile; options not linked to EOS type
108        (as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type;
109      - start to implement variable gravity (along vertical): for now, only with
110        z-coords (not even z*).
111      - add Ideal Gas equation of state for height coordinate.
112      - update OpenAD output (affected at machine truncation level) of exp:
113        global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo.
114    o pkg/exf:
115      - add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result
116        of exf interpolation (before any rescaling, rotation or interpolation
117        to velocity point) for each field that gets loaded from file. This option
118        identically mimics the input file organization (e.g. record numbers in year
119        by year input files) besides the change in horizontal grid.
120      - add rotateStressOnAgrid run-time switch so that wind stress fields
121        can be provided on the A-grid in zonal/meridional direction and
122        rotated on the fly. This only applies to the case when the exf
123        interpolation is off and rotateStressOnAgrid is false by default.
124    o model/src:
125      - rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since
126        it's also used with pkg/atm_phys) and add few more parameters (but still
127        inactive, src code yet to come)
128    
129    checkpoint65t (2016/02/10)
130    o pkg/atm_phys:
131      - from Ruth Geen: add optical depth dependence on CO2 concentration.
132    o model/src:
133      - fix vertical inter/extra-polation of density factor rhoFacF (for anelastic)
134        for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F.
135        Update output of exp. deep_anelastic (changes at truncation level).
136    o tools:
137      - add a hack in "remove_comments_sed" (used only with TAF) for recent
138        version of OpenMPI (shipped with FC.23): comment out the new header
139        file "mpif-sizeof.h" which causes problems to TAF.
140    o pkg/seaice:
141      - change the termination criterion so that maxits (SEAICElinearIterMax)
142        has an effect
143      - unify iteration parameters for implicit solvers (JFNK and Picard)
144        SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS
145        SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER
146        SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner
147        SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner
148        SEAICEnonLinTol     replaces JFNKgamma_nonlin
149      - remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN
150      - add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and
151        use with SEAICEuseKrylov
152    o pkg/seaice/seaice_lsr.F
153        fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only
154        relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have
155        an effect.
156    o pkg/seaice: add two new parameters
157      - SEAICEuseLSR to simplify the logic in seaice_dynsolver (this
158        parameter is not in any namelist)
159      - SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as
160        a preconditioner for the non-linear Newton iteration of the JFNK
161        solver
162    o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT,
163      affects some experiments at truncation level:
164      - global_ocean.cs32x15.icedyn (11 digits),
165      - global_ocean.cs32x15.seaice (11 digits),
166      - seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update
167      - also update global_ocean.cs32x15 adjoint and tangent-linear results
168    o pkg/salt_plume & pkg/thsice:
169      - for coupled  set-up with pkg/thsice in ATM and pkg/salt_plume in OCN,
170        connect salt_plume flux to ATM-OCN coupling pkgs interface:
171       a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for
172         export to coupler interface) even without compiling pkg/salt_plume ;
173       b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field
174         (saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH.
175    o pkg/dic:
176      - use the updated seaice fraction (from seaice pkgs) for DIC forcing
177        instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE
178        called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD);
179      - move also update with values from ATM-OCN Coupler in the same new S/R
180        (previously done in ocn_apply_import.F).
181    o tools/adjoint_options:
182      - specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default)
183        has been changed on Jan 14, 2016.
184    o pkg/ggl90:
185      - add alternative discretisation of vertical shear (off by default), to
186        compute the mean (@ grid-cell center) of vertical shear compon instead of
187        vertical shear of mean flow (@ grid-cell center).
188      - add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated
189        results on adjacent faces of cubed-sphere grids; this fix the restart.
190    o pkg/atm_compon_interf:
191      - skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just
192        pass last value, stored directly before export to CPL ;
193        Note: this affects results of Coupled set-up where OCN uses useImportSLP=T
194      - remove atmSLPr from pickup files (no longer needed for restart)
195    
196    checkpoint65s (2016/01/13)
197    o eesupp & genmake2:
198       - first check for Function ETIME and, if it fails, then check for subroutine
199         ETIME and consistent output; use the appropriate version in timers.F
200    o model/src:
201      - to check restart test, add option to apply EXCH to U,V earlier, just before
202        integr_continuity; turned off by default.
203    o pkg/dic:
204      - remove CPP option USE_ATMOSCO2 (not needed)
205    o tools/tst_2+2:
206      - try to ignore difference between +0 and -0 in binary file, causing test
207        to fail for no good reason.
208    o eesupp & genmake2:
209      - put back modif from Jinxuan Zhu - change etime fct call to S/R call -
210        but also check (in genmake2) that test runs and returns meaningful results.
211    o coupler pkgs:
212      Finish implementation of optionally-exchanged variable switches (started on
213       Nov 12) with addition of few more exchanged fields, including 2-way exchange
214       of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
215       advection in OCN component; this requires sequential coupling.
216      coupler (pkg/atm_ocn_coupler):
217      - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
218        routines (useful for debug).
219      - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
220         flux, DIC fields) if corresponding switch is ON.
221      - add option to export RunOff to OCN (to use for DIC river input)
222      - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
223      components (pkg/atm_ & ocn_compon_interf):
224      - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
225        optionally exchanged fields; add a check & stop in cpl_readparms.F.
226        ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
227        OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice.
228      - rename:   fracIce     -> sIceFrac_cpl (<- match coupler var name)
229        + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
230      - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
231      - hold in common block coupler optionally-exchanged variable switch
232        and set default "useImportXXX" accordingly; + check & stop if inconsistent.
233      - add diagnostics for all imported fields from coupler (in both OCN & ATM);
234        this is intended to replace the OCN cplFldtave.* output files (not updated
235        to contain new additional exchanged fields).
236    o pkg/dic:
237      - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
238    o pkg/thsice:
239      - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
240        and writing of thsice pickup files.
241    o pkg/atm_compon_interf:
242      - move all field individual export-call out of cpl_export_import_data.F
243        into new S/R ATM_EXPORT_FIELDS
244    o pkg/atm_compon_interf:
245      - store state variables (for now, only thSIce fields) just before beeing
246        exported (in cpl_export_import_data.F, like on ocean side) instead of from
247        atm_store_my_data.F like all exported fluxes.
248      - new version of pickup_cpl: write field names into meta file and read meta
249        file to find field postion in pickup. Also only write/read fields meeded for
250        restart (same logic as main pickup file ; also using pickupStrictlyMatch)
251    o pkg/dic:
252      - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
253    o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
254        pressure replacement method (=1., default) or original Hibler (1979) (=0.)
255        value can be from domain [0,1] to average between the two methods
256    o pkg/atm_phys:
257      - allow to provide 2-d map of albedo and mixed-layer depth from files (but
258        hold fixed in time).
259    
260    checkpoint65r (2015/12/21)
261    o pkg/seaice:
262        fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
263        solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
264    o pkg/seaice:
265      - fix a bug in computing areaS in (J-J -> J-1) that affects runs
266        when SEAICEscaleSurfStress=.TRUE.,
267      - apply areaW and areaS in S/R seaice_calc_lhs
268    o pkg/atm_phys:
269      - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
270        (shortwave & longwave, net & downward) and diagnostics of temp. tendency
271        for individual contribution (convection, LSC cond, radiation)
272      - add Ruth Geen etal, GRL 2016, radiation options (see paper supp.
273        information); activated with: solar_exponent=0. and wv_exponent=-1.
274    o pkg/ggl90:
275      - within IDEMIX add upper limit for horizontal group velocity to
276        avoid instability problems in the explicit horizontal diffusion term for
277        long time steps or high resolution
278    o pkg/diagnostics:
279      - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
280        (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
281    o testreport:
282      - remove "-v" (verbose option) in default mpirun command.
283    o pkg/seaice/seaice_growth:
284      - catch potential division by zero in ITD code, does not change
285        verification results
286    o pkg/ecco:
287      - retire old codes to the Attic. The calls to retired functions are
288        left in a commented form in case they ever need to be re-activated.
289      - ecco_check.F: issue warning if any old CPP option is
290        defined that corresponds to retired codes -- then stop.
291    o pkg/atm_compon_interf:
292      - change seaice fraction (use for OCN dic surf.flux) stored and sent to
293        coupler: use last time-step value instead of average over cplSendFrq_iter
294        time-step, similar to what is done for seaIceMass.
295        This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
296    o eesupp & genmake2:
297      - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
298        <= remove until a fix is found for some ifort version on ia32 machine.
299    o pkg/seaice/seaice_evp:
300      - refine residual computation
301    
302    checkpoint65q (2015/11/18)
303    o pkg/seaice/seaice_evp:
304      - fix residual computations so that they no longer affect the actual
305        simulation code
306      - fix seaice_readparams to be able to actually set new parameters
307        SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
308    o model/src:
309      - fix wrong truncation (single prec) from "FLOAT" function in expressions
310        like: deltaT*FLOAT(myIter) when myIter is large:
311         a) replaced by DFLOAT (if not seen by TAF);
312         b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
313    o pkg/aim_v23:
314      - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
315        when pickupSuff is set ; do write rolling pickups + at the end of the run.
316    o pkg/atm_ocn_coupler + ocn_compon_interf:
317      - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
318        coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
319        add corresponding call in DO_OCEANIC_PHYS.
320    o coupler pkgs:
321      Start a new way to set-up optionally-exchanged variables (previously, only
322       there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
323       data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
324       send switch to ATM & OCN compon before reading their own "data.cpl" (so that
325       compononent param default can be set accordingly).
326      Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
327       but rather applies to a group a fields (going both ways like for DIC)
328       and corresponds to an option of coupling config.
329      coupler (pkg/atm_ocn_coupler):
330      - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
331        and read namelist directly (without eessup S/R calls) instead of
332        in the very un-flexible old way, 1 param per line, in fixed order;
333      - add error-counter to track errors (e.g., missing "data.cpl") and to stop
334        cleanly in CPL_CHECK_CPLCONFIG
335      - add new coupling-exchange selectors (some not yet active) including
336        cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
337                                             and ocnCpl_exchange_DIC=T in OCNIDS.h);
338      - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
339        component ; called directly from coupler.F, after comp. registrations;
340      - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
341         atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
342          -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
343      components (pkg/atm_ & ocn_compon_interf):
344      - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
345        CPP header file in all pkg source files.
346      - move checking of comp. configs out of cpl_exch_configs.F into new S/R
347        ATM/OCN_CHECK_CPLCONFIG;
348      - add error-counter to track errors (e.g., in "data.cpl") and to stop
349        cleanly in ATM/OCN_CHECK_CPLCONFIG;
350      - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
351        from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
352        before PACKAGES_READPARMS;
353      verification/cpl_aim+ocn/:
354      - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
355        "data.cpl" for coupler (in input_cpl).
356    o eesupp/inc:
357      - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
358        #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
359        to always cumulate tile local-sum in the same order (still uses
360        MPI_Allreduce like standard code).
361      - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
362        that are now identical to standard version (in eesupp/inc).
363  o pkg/shelfice:  o pkg/shelfice:
364    - add SHELFICETransCoeffTFile for initializing spatially varying    - add SHELFICETransCoeffTFile for initializing spatially varying
365      heat and salt transfer coefficients      heat and salt transfer coefficients
# Line 436  o model/src & mom pkgs: Line 792  o model/src & mom pkgs:
792      just copy level Nr value to level Nr+1.      just copy level Nr value to level Nr+1.
793  o doc:  o doc:
794    - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.    - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
795  o pkg/streamice:  o pkg/shelfice:
796    - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,    - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
797      SHELFICE.h: move array shelficemass to init_varia, initialise      SHELFICE.h: move array shelficemass to init_varia, initialise
798      from array shelficemassinit, which is set in init_fixed and      from array shelficemassinit, which is set in init_fixed and

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