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revision 1.2225 by jmc, Sat Jan 16 22:05:05 2016 UTC revision 1.2262 by mlosch, Mon Aug 22 14:38:37 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/ptracers: add Bruno Deremble's code to complete the linear surface
8      correction for tracer conservation
9    
10    checkpoint65y (2016/07/29)
11    o pkg/debug (stats):
12      - change GLOBAL_SUM to GLOBAL_SUM_TILE (result independent of tile to
13        proc/thread mapping);
14      - fix Min & Max for case where 1 thread has only empty tiles;
15      - use RL variable to count number of wet grid points (with big domain,
16        can be too large to fit into integer*4).
17    o pkg/monitor:
18      - use RL variable to count number of wet grid points (but used only for del2)
19      - add new routine to compute Advective CFL within tracer time-stepping with
20        writing delayed until next monitor output.
21    o pkg/obcs:
22      - fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW)
23    o pkg/dic & seaice:
24      - fix compilation of ocean component for coupled atm+ocn model with
25        seaice dynamics & dic.
26    
27    checkpoint65x (2016/06/11)
28    o add a license text file in main MITgcm tree.
29    o added pkg/bling:
30      - intermediate complexity biogeochemical model
31      - see bling_description.txt for details
32      - verification experiment is global_oce_biogeo_bling (for now, in
33        Contrib/verification_other/); tested daily on baudelaire with gfortran.
34      - add entry point in pkg/gchem for new pkg "bling".
35    o pkg/seaice: fix tensile stength computation
36      - replace global field tensileStrength by tensileStrFac
37      - tensileStrFac can be computed once in S/R seaice_init_varia
38      - fortunately that does not affect any verification results
39    
40    checkpoint65w (2016/05/12)
41    o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles
42         with ECCO_CTRL_DEPRECATED defined
43    o verification/global_ocean.cs32x15:
44      - change secondary test "viscA4" to also test "selectP_inEOS_Zc=3"
45        with "selectNHfreeSurf=1".
46    o model/src (non-hydrostatic free-surface):
47      - More "natural" expression of NH free-surface term (case selectNHfreeSurf=1):
48        was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf.
49      - Calculate surface vertical velocity after 2-D solver adjustment (accounts
50        for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv
51        and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1.
52        This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux.
53      - Update output (changes at machine truncation level) of verification exp:
54        exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d),
55        short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d).
56    o pkg/seaice: ITD code
57      - fix picking up from a single category model by initialising
58        heff/area/hsnowITD = 0. in seaice_itd_pickup.F
59      - split a long warning message in seaice_check_pickup.F into two lines,
60        because NEC SX-ACE cannot deal with the long line.
61    o model/src:
62      - fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3)
63    o pkg/seaice:
64      - add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG
65    o pkg/seaice:
66      - add basal stress as parameterisation for grounding ice
67        following Lemieux et al. (2015)
68      - turn on by setting new parameter SEAICEbasalDragK2 to a value
69        larger than 0. Lemieux et al. (2015) recommend 15.
70      - The adjoint complains with extra recomputations so there is also a
71        new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in
72        order to postpone the problem
73      - compile the new code in lab_sea
74    o verification/halfpipe_streamice:
75      - update both TAF and OpenAD adm output (machine truncation differences)
76    
77    checkpoint65v (2016/04/08)
78    o verification/advect_xz:
79      - increase overlap size from 3 to 4 and add new secondary test for PQM
80        advection scheme (with mono & wino limiter).
81      - change main exp. to test PPM (with weno limiter) adv.scheme on Temp.
82    o model/src:
83      - new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently
84        added phi0Ref) to set vertical axis origin and phiRef origin;
85        keep Ro_SeaLevel for backward compatibility (with a warning).
86       According to coordinate and fluid type:
87        OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top)
88        ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom)
89        OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top)
90        ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom)
91      - remove Ro_SeaLevel from ATM experiment parameter files;
92      - in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the
93        complement; update output.txt (changes at machine truncation level).
94    o pkg/seaice/seaice_evp.F
95      - simplify computation of deltaZ and zetaZ to simple averaging following
96        Bouillon et al. (2013). This removes a lot of code, but also changes
97        verification experiment lab_sea.hb87 -> updated
98    
99    checkpoint65u (2016/03/14)
100    o pkg/generic_advdiff:
101      - from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52)
102        with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP);
103        Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for
104        testing and not for actual use.
105    o model/src:
106      - add parameter "phi0Ref" to specify reference [pressure/geo] potential at
107        origin r = rF(1);
108      - add options (parameter selectP_inEOS_Zc) to select which pressure to use
109        in EOS for height coordinate: enable to include NH Pressure or to use
110        more accurate pressure vertical profile; options not linked to EOS type
111        (as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type;
112      - start to implement variable gravity (along vertical): for now, only with
113        z-coords (not even z*).
114      - add Ideal Gas equation of state for height coordinate.
115      - update OpenAD output (affected at machine truncation level) of exp:
116        global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo.
117    o pkg/exf:
118      - add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result
119        of exf interpolation (before any rescaling, rotation or interpolation
120        to velocity point) for each field that gets loaded from file. This option
121        identically mimics the input file organization (e.g. record numbers in year
122        by year input files) besides the change in horizontal grid.
123      - add rotateStressOnAgrid run-time switch so that wind stress fields
124        can be provided on the A-grid in zonal/meridional direction and
125        rotated on the fly. This only applies to the case when the exf
126        interpolation is off and rotateStressOnAgrid is false by default.
127    o model/src:
128      - rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since
129        it's also used with pkg/atm_phys) and add few more parameters (but still
130        inactive, src code yet to come)
131    
132    checkpoint65t (2016/02/10)
133    o pkg/atm_phys:
134      - from Ruth Geen: add optical depth dependence on CO2 concentration.
135    o model/src:
136      - fix vertical inter/extra-polation of density factor rhoFacF (for anelastic)
137        for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F.
138        Update output of exp. deep_anelastic (changes at truncation level).
139    o tools:
140      - add a hack in "remove_comments_sed" (used only with TAF) for recent
141        version of OpenMPI (shipped with FC.23): comment out the new header
142        file "mpif-sizeof.h" which causes problems to TAF.
143    o pkg/seaice:
144      - change the termination criterion so that maxits (SEAICElinearIterMax)
145        has an effect
146      - unify iteration parameters for implicit solvers (JFNK and Picard)
147        SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS
148        SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER
149        SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner
150        SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner
151        SEAICEnonLinTol     replaces JFNKgamma_nonlin
152      - remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN
153      - add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and
154        use with SEAICEuseKrylov
155    o pkg/seaice/seaice_lsr.F
156        fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only
157        relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have
158        an effect.
159    o pkg/seaice: add two new parameters
160      - SEAICEuseLSR to simplify the logic in seaice_dynsolver (this
161        parameter is not in any namelist)
162      - SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as
163        a preconditioner for the non-linear Newton iteration of the JFNK
164        solver
165    o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT,
166      affects some experiments at truncation level:
167      - global_ocean.cs32x15.icedyn (11 digits),
168      - global_ocean.cs32x15.seaice (11 digits),
169      - seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update
170      - also update global_ocean.cs32x15 adjoint and tangent-linear results
171    o pkg/salt_plume & pkg/thsice:
172      - for coupled  set-up with pkg/thsice in ATM and pkg/salt_plume in OCN,
173        connect salt_plume flux to ATM-OCN coupling pkgs interface:
174       a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for
175         export to coupler interface) even without compiling pkg/salt_plume ;
176       b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field
177         (saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH.
178  o pkg/dic:  o pkg/dic:
179    - use the updated seaice fraction (from seaice pkgs) for DIC forcing    - use the updated seaice fraction (from seaice pkgs) for DIC forcing
180      instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE      instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE
# Line 101  o pkg/atm_phys: Line 272  o pkg/atm_phys:
272    - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes    - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
273      (shortwave & longwave, net & downward) and diagnostics of temp. tendency      (shortwave & longwave, net & downward) and diagnostics of temp. tendency
274      for individual contribution (convection, LSC cond, radiation)      for individual contribution (convection, LSC cond, radiation)
275    - add Ruth Geen etal, GRL 2016, radiation optionis (see paper supp.    - add Ruth Geen etal, GRL 2016, radiation options (see paper supp.
276      information); activated with: solar_exponent=0. and wv_exponent=-1.      information); activated with: solar_exponent=0. and wv_exponent=-1.
277  o pkg/ggl90:  o pkg/ggl90:
278    - within IDEMIX add upper limit for horizontal group velocity to    - within IDEMIX add upper limit for horizontal group velocity to
# Line 624  o model/src & mom pkgs: Line 795  o model/src & mom pkgs:
795      just copy level Nr value to level Nr+1.      just copy level Nr value to level Nr+1.
796  o doc:  o doc:
797    - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.    - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
798  o pkg/streamice:  o pkg/shelfice:
799    - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,    - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
800      SHELFICE.h: move array shelficemass to init_varia, initialise      SHELFICE.h: move array shelficemass to init_varia, initialise
801      from array shelficemassinit, which is set in init_fixed and      from array shelficemassinit, which is set in init_fixed and
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