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revision 1.2213 by mlosch, Thu Dec 17 11:39:20 2015 UTC revision 1.2269 by mlosch, Fri Sep 23 07:16:11 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 pkg/seaice: fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects  o pkg/seaice: make seaice_fgmres.F fit for multithreading; this first
8    the JFNK solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice    attempt appears to be a bit of a hack and my need some repair down the road
9    -> updated  o pkg/exf:
10  o pkg/seaice:    - interpolation near South Pole: fix criteria on input field latitude.
11    - fix a bug in computing areaS in (J-J -> J-1) that affects runs  o pkg/icefront & pkg/exf:
12      - move setting of icefront Sub-Glacial RunOff forcing (currently unused)
13        from pkg/exf (read from data.exf) to pkg/icefront (read from data.icefront)
14    o pkg/exf:
15      - replace CPP option ALLOW_EXF_OUTPUT_INTERP with run-time parameter
16        "exf_output_interp" (in namelist: EXF_NML_04); change output file name
17        (add suffix "_out" instead of a prefix); keep same record number as in
18        input file but always write record 1 first (to avoid a STOP in I/O S/R).
19        Change output file content by writing interpolated field before applying
20        land-sea mask (helpful for debug).
21      - 2 compon. vector interpolation with rotation: apply scaling factor on
22        each compon. (Eastward and Northward) just before rotation.
23    o pkg/bling:
24      - Cleaned package. Removed not needed code and comments.
25      - adjoint example now works
26        (MITgcm_contrib/verification_other/global_oce_biogeo_bling/code_ad)
27    o pkg/ptracers:
28      - add Bruno Deremble's code to complete the linear surface correction
29        for tracer conservation;
30      - enabled for individual ptracers by PTRACERS_linFSConserve(iTr)=.TRUE.
31    
32    checkpoint65y (2016/07/29)
33    o pkg/debug (stats):
34      - change GLOBAL_SUM to GLOBAL_SUM_TILE (result independent of tile to
35        proc/thread mapping);
36      - fix Min & Max for case where 1 thread has only empty tiles;
37      - use RL variable to count number of wet grid points (with big domain,
38        can be too large to fit into integer*4).
39    o pkg/monitor:
40      - use RL variable to count number of wet grid points (but used only for del2)
41      - add new routine to compute Advective CFL within tracer time-stepping with
42        writing delayed until next monitor output.
43    o pkg/obcs:
44      - fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW)
45    o pkg/cal:
46      - calandar-dump: treat case myTime < timePhase in the same way as in
47        eesupp/src/diff_phase_multiple.F (when not using calandar-dump).
48    o pkg/dic & seaice:
49      - fix compilation of ocean component for coupled atm+ocn model with
50        seaice dynamics & dic.
51    
52    checkpoint65x (2016/06/11)
53    o add a license text file in main MITgcm tree.
54    o added pkg/bling:
55      - intermediate complexity biogeochemical model
56      - see bling_description.txt for details
57      - verification experiment is global_oce_biogeo_bling (for now, in
58        Contrib/verification_other/); tested daily on baudelaire with gfortran.
59      - add entry point in pkg/gchem for new pkg "bling".
60    o pkg/seaice: fix tensile stength computation
61      - replace global field tensileStrength by tensileStrFac
62      - tensileStrFac can be computed once in S/R seaice_init_varia
63      - fortunately that does not affect any verification results
64    
65    checkpoint65w (2016/05/12)
66    o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles
67         with ECCO_CTRL_DEPRECATED defined
68    o verification/global_ocean.cs32x15:
69      - change secondary test "viscA4" to also test "selectP_inEOS_Zc=3"
70        with "selectNHfreeSurf=1".
71    o model/src (non-hydrostatic free-surface):
72      - More "natural" expression of NH free-surface term (case selectNHfreeSurf=1):
73        was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf.
74      - Calculate surface vertical velocity after 2-D solver adjustment (accounts
75        for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv
76        and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1.
77        This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux.
78      - Update output (changes at machine truncation level) of verification exp:
79        exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d),
80        short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d).
81    o pkg/seaice: ITD code
82      - fix picking up from a single category model by initialising
83        heff/area/hsnowITD = 0. in seaice_itd_pickup.F
84      - split a long warning message in seaice_check_pickup.F into two lines,
85        because NEC SX-ACE cannot deal with the long line.
86    o model/src:
87      - fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3)
88    o pkg/seaice:
89      - add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG
90    o pkg/seaice:
91      - add basal stress as parameterisation for grounding ice
92        following Lemieux et al. (2015)
93      - turn on by setting new parameter SEAICEbasalDragK2 to a value
94        larger than 0. Lemieux et al. (2015) recommend 15.
95      - The adjoint complains with extra recomputations so there is also a
96        new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in
97        order to postpone the problem
98      - compile the new code in lab_sea
99    o verification/halfpipe_streamice:
100      - update both TAF and OpenAD adm output (machine truncation differences)
101    
102    checkpoint65v (2016/04/08)
103    o verification/advect_xz:
104      - increase overlap size from 3 to 4 and add new secondary test for PQM
105        advection scheme (with mono & wino limiter).
106      - change main exp. to test PPM (with weno limiter) adv.scheme on Temp.
107    o model/src:
108      - new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently
109        added phi0Ref) to set vertical axis origin and phiRef origin;
110        keep Ro_SeaLevel for backward compatibility (with a warning).
111       According to coordinate and fluid type:
112        OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top)
113        ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom)
114        OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top)
115        ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom)
116      - remove Ro_SeaLevel from ATM experiment parameter files;
117      - in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the
118        complement; update output.txt (changes at machine truncation level).
119    o pkg/seaice/seaice_evp.F
120      - simplify computation of deltaZ and zetaZ to simple averaging following
121        Bouillon et al. (2013). This removes a lot of code, but also changes
122        verification experiment lab_sea.hb87 -> updated
123    
124    checkpoint65u (2016/03/14)
125    o pkg/generic_advdiff:
126      - from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52)
127        with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP);
128        Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for
129        testing and not for actual use.
130    o model/src:
131      - add parameter "phi0Ref" to specify reference [pressure/geo] potential at
132        origin r = rF(1);
133      - add options (parameter selectP_inEOS_Zc) to select which pressure to use
134        in EOS for height coordinate: enable to include NH Pressure or to use
135        more accurate pressure vertical profile; options not linked to EOS type
136        (as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type;
137      - start to implement variable gravity (along vertical): for now, only with
138        z-coords (not even z*).
139      - add Ideal Gas equation of state for height coordinate.
140      - update OpenAD output (affected at machine truncation level) of exp:
141        global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo.
142    o pkg/exf:
143      - add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result
144        of exf interpolation (before any rescaling, rotation or interpolation
145        to velocity point) for each field that gets loaded from file. This option
146        identically mimics the input file organization (e.g. record numbers in year
147        by year input files) besides the change in horizontal grid.
148      - add rotateStressOnAgrid run-time switch so that wind stress fields
149        can be provided on the A-grid in zonal/meridional direction and
150        rotated on the fly. This only applies to the case when the exf
151        interpolation is off and rotateStressOnAgrid is false by default.
152    o model/src:
153      - rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since
154        it's also used with pkg/atm_phys) and add few more parameters (but still
155        inactive, src code yet to come)
156    
157    checkpoint65t (2016/02/10)
158    o pkg/atm_phys:
159      - from Ruth Geen: add optical depth dependence on CO2 concentration.
160    o model/src:
161      - fix vertical inter/extra-polation of density factor rhoFacF (for anelastic)
162        for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F.
163        Update output of exp. deep_anelastic (changes at truncation level).
164    o tools:
165      - add a hack in "remove_comments_sed" (used only with TAF) for recent
166        version of OpenMPI (shipped with FC.23): comment out the new header
167        file "mpif-sizeof.h" which causes problems to TAF.
168    o pkg/seaice:
169      - change the termination criterion so that maxits (SEAICElinearIterMax)
170        has an effect
171      - unify iteration parameters for implicit solvers (JFNK and Picard)
172        SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS
173        SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER
174        SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner
175        SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner
176        SEAICEnonLinTol     replaces JFNKgamma_nonlin
177      - remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN
178      - add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and
179        use with SEAICEuseKrylov
180    o pkg/seaice/seaice_lsr.F
181        fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only
182        relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have
183        an effect.
184    o pkg/seaice: add two new parameters
185      - SEAICEuseLSR to simplify the logic in seaice_dynsolver (this
186        parameter is not in any namelist)
187      - SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as
188        a preconditioner for the non-linear Newton iteration of the JFNK
189        solver
190    o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT,
191      affects some experiments at truncation level:
192      - global_ocean.cs32x15.icedyn (11 digits),
193      - global_ocean.cs32x15.seaice (11 digits),
194      - seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update
195      - also update global_ocean.cs32x15 adjoint and tangent-linear results
196    o pkg/salt_plume & pkg/thsice:
197      - for coupled  set-up with pkg/thsice in ATM and pkg/salt_plume in OCN,
198        connect salt_plume flux to ATM-OCN coupling pkgs interface:
199       a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for
200         export to coupler interface) even without compiling pkg/salt_plume ;
201       b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field
202         (saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH.
203    o pkg/dic:
204      - use the updated seaice fraction (from seaice pkgs) for DIC forcing
205        instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE
206        called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD);
207      - move also update with values from ATM-OCN Coupler in the same new S/R
208        (previously done in ocn_apply_import.F).
209    o tools/adjoint_options:
210      - specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default)
211        has been changed on Jan 14, 2016.
212    o pkg/ggl90:
213      - add alternative discretisation of vertical shear (off by default), to
214        compute the mean (@ grid-cell center) of vertical shear compon instead of
215        vertical shear of mean flow (@ grid-cell center).
216      - add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated
217        results on adjacent faces of cubed-sphere grids; this fix the restart.
218    o pkg/atm_compon_interf:
219      - skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just
220        pass last value, stored directly before export to CPL ;
221        Note: this affects results of Coupled set-up where OCN uses useImportSLP=T
222      - remove atmSLPr from pickup files (no longer needed for restart)
223    
224    checkpoint65s (2016/01/13)
225    o eesupp & genmake2:
226       - first check for Function ETIME and, if it fails, then check for subroutine
227         ETIME and consistent output; use the appropriate version in timers.F
228    o model/src:
229      - to check restart test, add option to apply EXCH to U,V earlier, just before
230        integr_continuity; turned off by default.
231    o pkg/dic:
232      - remove CPP option USE_ATMOSCO2 (not needed)
233    o tools/tst_2+2:
234      - try to ignore difference between +0 and -0 in binary file, causing test
235        to fail for no good reason.
236    o eesupp & genmake2:
237      - put back modif from Jinxuan Zhu - change etime fct call to S/R call -
238        but also check (in genmake2) that test runs and returns meaningful results.
239    o coupler pkgs:
240      Finish implementation of optionally-exchanged variable switches (started on
241       Nov 12) with addition of few more exchanged fields, including 2-way exchange
242       of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
243       advection in OCN component; this requires sequential coupling.
244      coupler (pkg/atm_ocn_coupler):
245      - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
246        routines (useful for debug).
247      - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
248         flux, DIC fields) if corresponding switch is ON.
249      - add option to export RunOff to OCN (to use for DIC river input)
250      - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
251      components (pkg/atm_ & ocn_compon_interf):
252      - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
253        optionally exchanged fields; add a check & stop in cpl_readparms.F.
254        ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
255        OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice.
256      - rename:   fracIce     -> sIceFrac_cpl (<- match coupler var name)
257        + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
258      - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
259      - hold in common block coupler optionally-exchanged variable switch
260        and set default "useImportXXX" accordingly; + check & stop if inconsistent.
261      - add diagnostics for all imported fields from coupler (in both OCN & ATM);
262        this is intended to replace the OCN cplFldtave.* output files (not updated
263        to contain new additional exchanged fields).
264    o pkg/dic:
265      - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
266    o pkg/thsice:
267      - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
268        and writing of thsice pickup files.
269    o pkg/atm_compon_interf:
270      - move all field individual export-call out of cpl_export_import_data.F
271        into new S/R ATM_EXPORT_FIELDS
272    o pkg/atm_compon_interf:
273      - store state variables (for now, only thSIce fields) just before beeing
274        exported (in cpl_export_import_data.F, like on ocean side) instead of from
275        atm_store_my_data.F like all exported fluxes.
276      - new version of pickup_cpl: write field names into meta file and read meta
277        file to find field postion in pickup. Also only write/read fields meeded for
278        restart (same logic as main pickup file ; also using pickupStrictlyMatch)
279    o pkg/dic:
280      - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
281    o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
282        pressure replacement method (=1., default) or original Hibler (1979) (=0.)
283        value can be from domain [0,1] to average between the two methods
284    o pkg/atm_phys:
285      - allow to provide 2-d map of albedo and mixed-layer depth from files (but
286        hold fixed in time).
287    
288    checkpoint65r (2015/12/21)
289    o pkg/seaice:
290        fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
291        solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
292    o pkg/seaice:
293      - fix a bug in computing areaS in (J-J -> J-1) that affects runs
294      when SEAICEscaleSurfStress=.TRUE.,      when SEAICEscaleSurfStress=.TRUE.,
295    - apply areaW and areaS in S/R seaice_calc_lhs    - apply areaW and areaS in S/R seaice_calc_lhs
296  o pkg/atm_phys:  o pkg/atm_phys:
297    - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes    - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
298      (shortwave & longwave, net & downward) and diagnostics of temp. tendency      (shortwave & longwave, net & downward) and diagnostics of temp. tendency
299      for individual contribution (convection, LSC cond, radiation)      for individual contribution (convection, LSC cond, radiation)
300    - add Ruth Geen etal, GRL 2016, radiation optionis (see paper supp.    - add Ruth Geen etal, GRL 2016, radiation options (see paper supp.
301      information); activated with: solar_exponent=0. and wv_exponent=-1.      information); activated with: solar_exponent=0. and wv_exponent=-1.
302  o pkg/ggl90:  o pkg/ggl90:
303    - within IDEMIX add upper limit for horizontal group velocity to    - within IDEMIX add upper limit for horizontal group velocity to
# Line 538  o model/src & mom pkgs: Line 820  o model/src & mom pkgs:
820      just copy level Nr value to level Nr+1.      just copy level Nr value to level Nr+1.
821  o doc:  o doc:
822    - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.    - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
823  o pkg/streamice:  o pkg/shelfice:
824    - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,    - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
825      SHELFICE.h: move array shelficemass to init_varia, initialise      SHELFICE.h: move array shelficemass to init_varia, initialise
826      from array shelficemassinit, which is set in init_fixed and      from array shelficemassinit, which is set in init_fixed and

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