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revision 1.2179 by mlosch, Thu Sep 10 15:58:25 2015 UTC revision 1.2293 by jmc, Thu Jan 12 00:08:24 2017 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:
8      - add new option "-src" to testreport to only produce source code (*.f),
9        including taf output src code (if using '-adm'/'-tlm' option).
10    o pkg/exf:
11      - add saltflx :: Net upward salt flux in psu.kg/m^2/s
12    o pkg/diagnostics:
13      - add run-time variable diagMdsDir to specify a subdirectory for
14        diagnostic output when mds is being used and mdsioLocalDir is not.
15    o pkg/mnc:
16      - mnc_utils.F: edit stop message
17    o pkg/autodiff:
18      - autodiff_ini_model_io.F: PRINT_MESSAGE, clean-up comments, add _*_MASTER,
19        add HAVE_SYSTEM bracket around system call to mkdir
20    o pkg/profiles:
21      - profiles_findunit.F, profiles_init_fixed.F, profiles_interp.F,
22        profiles_readparms.F: call ALL_PROC_DIE before 'stop'
23      - profiles_ini_io.F: use PRINT_MESSAGE, clean-up comments, add _*_MASTER,
24        add HAVE_SYSTEM bracket around system call to mkdir
25    o pkg/smooth:
26      - smooth_filtervar2d.F, smooth_filtervar3d.F: call ALL_PROC_DIE before 'stop'
27      - smooth_init2d.F, smooth_init3d.F: move print statements to readparms
28      - smooth_readparms.F: add cleaner print statements from smooth_init?d.F
29    o pkg/exf:
30      - check: count errors and stop cleanly at the end (call to ALL_PROC_DIE);
31        issue error message when climsst_interpMethod.GT.0 and climsst_lon_inc > 500
32        generalize tests on interpMethod, nlat, and lon_inc to all exf variables.
33      - summary: skip detailed field report if not used (empty file-name).
34    o tools/xmakedepend:
35      - In case line editor "ed" is missing, switch to "sed" command to clean-up
36        Makefile from previous dependencies (anything after "# DO NOT DELETE" line).
37    o pkg/exf:
38      - change definition of "hflux" input file to always include Short-Wave;
39        this is now consistent with hflux computation (if using bulk-formulae)
40        and hflux diagnostic & documentation (in EXF_FIELDS.h).
41    
42    checkpoint66b (2016/12/01)
43    o model & momentum pkgs:
44      - implement fully implicit bottom friction combined with implicit surf.
45        pressure, for now, only in hydrostic formulation:
46        + to use: compile with #define ALLOW_SOLVE4_PS_AND_DRAG in CPP_OPTIONS.h
47          and run with selectImplicitDrag=2 ;
48        + currently missing diagnostics of bottom drag and vert. viscosity tendency;
49      - partial implicit time-stepping (bot. friction + vert. visc first, then
50        surf. press) corresponding to selectImplicitDrag=1 should be applicable
51        to NH formulation but not available until we solve for surf. pressure
52        increment (instead of full etaN).
53      - change exp. global_ocean.cs32x15.thsice to test implicit bottom drag
54        with implicit vertical viscosity.
55    o pkg/seaice: add linear remapping scheme (Lipscomb 2001) to ITD model
56      - this is a first version that includes many regularisations that may
57        not all be necessary, to be sorted out,
58      - turned on by runtime parameter SEAICEuseLinRemapITD (true by default)
59      - change one verification experiment in seaice_itd to use and test new code
60      - seaice_growth: catch a case where the argument of log can be zero
61        or smaller (important for code stability)
62    o model/src:
63      - modify SOLVE_DIAGONAL_LOWMEMORY version of solve_tridiagonal.F
64        & solve_pentadiagonal.F to enable to re-used inverse matrix for solving
65        similar A.X'=Y' system (with same matrix A) in subsequent calls;
66        switch based on errCode (In/Out) argument value; in calling routines,
67        initialise errCode before first call.
68    
69    checkpoint66a (2016/10/18)
70    o pkg/bling:
71      - BLING package now loads in atmospheric pCO2 file using exf package routines
72        Enable with #define USE_EXFCO2 in BLING_OPTIONS.h
73    o model/src & pkg/ptracers:
74      - with INCLUDE_IMPLVERTADV_CODE defined, also call MOM_U,V_IMPLICIT_R &
75        GAD_IMPLICIT_R (instead of IMPLDIFF) when just implicitViscosity and
76        implicitDiffusion (respectively) are used (even without momImplVertAdv
77        or temp,salt,PTRACERS_ImplVertAdv).
78    o model/src & generic_advdiff:
79      - add parenthesis in main diagonal calculation of implicit vertical
80        diffusion matrix (impldiff.F & gad_implicit_r.F).
81        This affects results at machine truncation level; update output of many
82        verification experiments (31 fwd ; 10 adm ; 8 tlm ; 3 oad).
83    o pkg/mom_commom & generic_advdiff:
84      - add deep atmosphere and anelastic scaling factor in implicit vertical
85        advection routines (mom_u,v_implicit_r.F & gad*_impl*_r.F).
86    o model/src:
87      - remove few unnecessary temp array copies in solve_tridiagonal.F
88        & solve_pentadiagonal.F
89    
90    checkpoint65z (2016/09/28)
91    o pkg/seaice: fix multithreading for seaice_fgmres.F
92      - remove unecessary variables from common blocks
93      - use extra dimension MAX_NO_THREADS for all variables of the Krylov space
94        basis, that are stored in commom blocks (including integer variable i1)
95      - clean up code a little by removing commented lines that refer to
96        original code
97      - turn on multi-threaded test for experiment offline_exf_seaice.dyn_jfnk.
98    o MITgcm manual:
99      - add uptodate pkg/ecco documentation to the manual (section 8.1; ecco.tex),
100        preliminary documentation for generic controls (8.3; ctrl.tex),
101        a placeholder for smooth (8.4; smooth.tex), and comment out the deprecated
102        ecco_costfunction.tex
103    o pkg/ecco:
104      - update and cleanup list of CCP options
105      - re-assign gencost_mask to specify masks rather than gencost_errfile; 'c'
106        is now always passed to cost_generic; gencost_mask is now MAX_LEN_FNAM
107      - add checks that retired run-time options are not used, and in relation
108        to gencost_mask and gencost_errfile
109      - finish deprecating gencost_scalefile, gencost_smooth2Ddiffnbt, and
110        gencost_nrecperiod
111      - fix m_eta computation for virtual salt flux case
112      - add m_horflux_vol case (selected via gencost_barfile) that computes
113        transports via cost_gencost_boxmean (gencost_flag=-3)
114      - use gencost_flag more systematically (i.e., avoid using gencost_name)
115        for code switches (aside from physical variable selection)
116    o pkg/seaice: make seaice_fgmres.F fit for multithreading; this first
117      attempt appears to be a bit of a hack and my need some repair down the road
118    o pkg/exf:
119      - interpolation near South Pole: fix criteria on input field latitude.
120    o pkg/icefront & pkg/exf:
121      - move setting of icefront Sub-Glacial RunOff forcing (currently unused)
122        from pkg/exf (read from data.exf) to pkg/icefront (read from data.icefront)
123    o pkg/exf:
124      - replace CPP option ALLOW_EXF_OUTPUT_INTERP with run-time parameter
125        "exf_output_interp" (in namelist: EXF_NML_04); change output file name
126        (add suffix "_out" instead of a prefix); keep same record number as in
127        input file but always write record 1 first (to avoid a STOP in I/O S/R).
128        Change output file content by writing interpolated field before applying
129        land-sea mask (helpful for debug).
130      - 2 compon. vector interpolation with rotation: apply scaling factor on
131        each compon. (Eastward and Northward) just before rotation.
132    o pkg/bling:
133      - Cleaned package. Removed not needed code and comments.
134      - adjoint example now works
135        (MITgcm_contrib/verification_other/global_oce_biogeo_bling/code_ad)
136    o pkg/ptracers:
137      - add Bruno Deremble's code to complete the linear surface correction
138        for tracer conservation;
139      - enabled for individual ptracers by PTRACERS_linFSConserve(iTr)=.TRUE.
140    
141    checkpoint65y (2016/07/29)
142    o pkg/debug (stats):
143      - change GLOBAL_SUM to GLOBAL_SUM_TILE (result independent of tile to
144        proc/thread mapping);
145      - fix Min & Max for case where 1 thread has only empty tiles;
146      - use RL variable to count number of wet grid points (with big domain,
147        can be too large to fit into integer*4).
148    o pkg/monitor:
149      - use RL variable to count number of wet grid points (but used only for del2)
150      - add new routine to compute Advective CFL within tracer time-stepping with
151        writing delayed until next monitor output.
152    o pkg/obcs:
153      - fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW)
154    o pkg/cal:
155      - calandar-dump: treat case myTime < timePhase in the same way as in
156        eesupp/src/diff_phase_multiple.F (when not using calandar-dump).
157    o pkg/dic & seaice:
158      - fix compilation of ocean component for coupled atm+ocn model with
159        seaice dynamics & dic.
160    
161    checkpoint65x (2016/06/11)
162    o add a license text file in main MITgcm tree.
163    o added pkg/bling:
164      - intermediate complexity biogeochemical model
165      - see bling_description.txt for details
166      - verification experiment is global_oce_biogeo_bling (for now, in
167        Contrib/verification_other/); tested daily on baudelaire with gfortran.
168      - add entry point in pkg/gchem for new pkg "bling".
169    o pkg/seaice: fix tensile stength computation
170      - replace global field tensileStrength by tensileStrFac
171      - tensileStrFac can be computed once in S/R seaice_init_varia
172      - fortunately that does not affect any verification results
173    
174    checkpoint65w (2016/05/12)
175    o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles
176         with ECCO_CTRL_DEPRECATED defined
177    o verification/global_ocean.cs32x15:
178      - change secondary test "viscA4" to also test "selectP_inEOS_Zc=3"
179        with "selectNHfreeSurf=1".
180    o model/src (non-hydrostatic free-surface):
181      - More "natural" expression of NH free-surface term (case selectNHfreeSurf=1):
182        was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf.
183      - Calculate surface vertical velocity after 2-D solver adjustment (accounts
184        for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv
185        and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1.
186        This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux.
187      - Update output (changes at machine truncation level) of verification exp:
188        exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d),
189        short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d).
190    o pkg/seaice: ITD code
191      - fix picking up from a single category model by initialising
192        heff/area/hsnowITD = 0. in seaice_itd_pickup.F
193      - split a long warning message in seaice_check_pickup.F into two lines,
194        because NEC SX-ACE cannot deal with the long line.
195    o model/src:
196      - fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3)
197    o pkg/seaice:
198      - add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG
199    o pkg/seaice:
200      - add basal stress as parameterisation for grounding ice
201        following Lemieux et al. (2015)
202      - turn on by setting new parameter SEAICEbasalDragK2 to a value
203        larger than 0. Lemieux et al. (2015) recommend 15.
204      - The adjoint complains with extra recomputations so there is also a
205        new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in
206        order to postpone the problem
207      - compile the new code in lab_sea
208    o verification/halfpipe_streamice:
209      - update both TAF and OpenAD adm output (machine truncation differences)
210    
211    checkpoint65v (2016/04/08)
212    o verification/advect_xz:
213      - increase overlap size from 3 to 4 and add new secondary test for PQM
214        advection scheme (with mono & wino limiter).
215      - change main exp. to test PPM (with weno limiter) adv.scheme on Temp.
216    o model/src:
217      - new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently
218        added phi0Ref) to set vertical axis origin and phiRef origin;
219        keep Ro_SeaLevel for backward compatibility (with a warning).
220       According to coordinate and fluid type:
221        OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top)
222        ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom)
223        OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top)
224        ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom)
225      - remove Ro_SeaLevel from ATM experiment parameter files;
226      - in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the
227        complement; update output.txt (changes at machine truncation level).
228    o pkg/seaice/seaice_evp.F
229      - simplify computation of deltaZ and zetaZ to simple averaging following
230        Bouillon et al. (2013). This removes a lot of code, but also changes
231        verification experiment lab_sea.hb87 -> updated
232    
233    checkpoint65u (2016/03/14)
234    o pkg/generic_advdiff:
235      - from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52)
236        with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP);
237        Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for
238        testing and not for actual use.
239    o model/src:
240      - add parameter "phi0Ref" to specify reference [pressure/geo] potential at
241        origin r = rF(1);
242      - add options (parameter selectP_inEOS_Zc) to select which pressure to use
243        in EOS for height coordinate: enable to include NH Pressure or to use
244        more accurate pressure vertical profile; options not linked to EOS type
245        (as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type;
246      - start to implement variable gravity (along vertical): for now, only with
247        z-coords (not even z*).
248      - add Ideal Gas equation of state for height coordinate.
249      - update OpenAD output (affected at machine truncation level) of exp:
250        global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo.
251    o pkg/exf:
252      - add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result
253        of exf interpolation (before any rescaling, rotation or interpolation
254        to velocity point) for each field that gets loaded from file. This option
255        identically mimics the input file organization (e.g. record numbers in year
256        by year input files) besides the change in horizontal grid.
257      - add rotateStressOnAgrid run-time switch so that wind stress fields
258        can be provided on the A-grid in zonal/meridional direction and
259        rotated on the fly. This only applies to the case when the exf
260        interpolation is off and rotateStressOnAgrid is false by default.
261    o model/src:
262      - rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since
263        it's also used with pkg/atm_phys) and add few more parameters (but still
264        inactive, src code yet to come)
265    
266    checkpoint65t (2016/02/10)
267    o pkg/atm_phys:
268      - from Ruth Geen: add optical depth dependence on CO2 concentration.
269    o model/src:
270      - fix vertical inter/extra-polation of density factor rhoFacF (for anelastic)
271        for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F.
272        Update output of exp. deep_anelastic (changes at truncation level).
273    o tools:
274      - add a hack in "remove_comments_sed" (used only with TAF) for recent
275        version of OpenMPI (shipped with FC.23): comment out the new header
276        file "mpif-sizeof.h" which causes problems to TAF.
277    o pkg/seaice:
278      - change the termination criterion so that maxits (SEAICElinearIterMax)
279        has an effect
280      - unify iteration parameters for implicit solvers (JFNK and Picard)
281        SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS
282        SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER
283        SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner
284        SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner
285        SEAICEnonLinTol     replaces JFNKgamma_nonlin
286      - remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN
287      - add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and
288        use with SEAICEuseKrylov
289    o pkg/seaice/seaice_lsr.F
290        fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only
291        relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have
292        an effect.
293    o pkg/seaice: add two new parameters
294      - SEAICEuseLSR to simplify the logic in seaice_dynsolver (this
295        parameter is not in any namelist)
296      - SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as
297        a preconditioner for the non-linear Newton iteration of the JFNK
298        solver
299    o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT,
300      affects some experiments at truncation level:
301      - global_ocean.cs32x15.icedyn (11 digits),
302      - global_ocean.cs32x15.seaice (11 digits),
303      - seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update
304      - also update global_ocean.cs32x15 adjoint and tangent-linear results
305    o pkg/salt_plume & pkg/thsice:
306      - for coupled  set-up with pkg/thsice in ATM and pkg/salt_plume in OCN,
307        connect salt_plume flux to ATM-OCN coupling pkgs interface:
308       a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for
309         export to coupler interface) even without compiling pkg/salt_plume ;
310       b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field
311         (saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH.
312    o pkg/dic:
313      - use the updated seaice fraction (from seaice pkgs) for DIC forcing
314        instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE
315        called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD);
316      - move also update with values from ATM-OCN Coupler in the same new S/R
317        (previously done in ocn_apply_import.F).
318    o tools/adjoint_options:
319      - specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default)
320        has been changed on Jan 14, 2016.
321    o pkg/ggl90:
322      - add alternative discretisation of vertical shear (off by default), to
323        compute the mean (@ grid-cell center) of vertical shear compon instead of
324        vertical shear of mean flow (@ grid-cell center).
325      - add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated
326        results on adjacent faces of cubed-sphere grids; this fix the restart.
327    o pkg/atm_compon_interf:
328      - skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just
329        pass last value, stored directly before export to CPL ;
330        Note: this affects results of Coupled set-up where OCN uses useImportSLP=T
331      - remove atmSLPr from pickup files (no longer needed for restart)
332    
333    checkpoint65s (2016/01/13)
334    o eesupp & genmake2:
335       - first check for Function ETIME and, if it fails, then check for subroutine
336         ETIME and consistent output; use the appropriate version in timers.F
337    o model/src:
338      - to check restart test, add option to apply EXCH to U,V earlier, just before
339        integr_continuity; turned off by default.
340    o pkg/dic:
341      - remove CPP option USE_ATMOSCO2 (not needed)
342    o tools/tst_2+2:
343      - try to ignore difference between +0 and -0 in binary file, causing test
344        to fail for no good reason.
345    o eesupp & genmake2:
346      - put back modif from Jinxuan Zhu - change etime fct call to S/R call -
347        but also check (in genmake2) that test runs and returns meaningful results.
348    o coupler pkgs:
349      Finish implementation of optionally-exchanged variable switches (started on
350       Nov 12) with addition of few more exchanged fields, including 2-way exchange
351       of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
352       advection in OCN component; this requires sequential coupling.
353      coupler (pkg/atm_ocn_coupler):
354      - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
355        routines (useful for debug).
356      - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
357         flux, DIC fields) if corresponding switch is ON.
358      - add option to export RunOff to OCN (to use for DIC river input)
359      - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
360      components (pkg/atm_ & ocn_compon_interf):
361      - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
362        optionally exchanged fields; add a check & stop in cpl_readparms.F.
363        ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
364        OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice.
365      - rename:   fracIce     -> sIceFrac_cpl (<- match coupler var name)
366        + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
367      - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
368      - hold in common block coupler optionally-exchanged variable switch
369        and set default "useImportXXX" accordingly; + check & stop if inconsistent.
370      - add diagnostics for all imported fields from coupler (in both OCN & ATM);
371        this is intended to replace the OCN cplFldtave.* output files (not updated
372        to contain new additional exchanged fields).
373    o pkg/dic:
374      - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
375    o pkg/thsice:
376      - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
377        and writing of thsice pickup files.
378    o pkg/atm_compon_interf:
379      - move all field individual export-call out of cpl_export_import_data.F
380        into new S/R ATM_EXPORT_FIELDS
381    o pkg/atm_compon_interf:
382      - store state variables (for now, only thSIce fields) just before beeing
383        exported (in cpl_export_import_data.F, like on ocean side) instead of from
384        atm_store_my_data.F like all exported fluxes.
385      - new version of pickup_cpl: write field names into meta file and read meta
386        file to find field postion in pickup. Also only write/read fields meeded for
387        restart (same logic as main pickup file ; also using pickupStrictlyMatch)
388    o pkg/dic:
389      - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
390    o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
391        pressure replacement method (=1., default) or original Hibler (1979) (=0.)
392        value can be from domain [0,1] to average between the two methods
393    o pkg/atm_phys:
394      - allow to provide 2-d map of albedo and mixed-layer depth from files (but
395        hold fixed in time).
396    
397    checkpoint65r (2015/12/21)
398    o pkg/seaice:
399        fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
400        solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
401    o pkg/seaice:
402      - fix a bug in computing areaS in (J-J -> J-1) that affects runs
403        when SEAICEscaleSurfStress=.TRUE.,
404      - apply areaW and areaS in S/R seaice_calc_lhs
405    o pkg/atm_phys:
406      - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
407        (shortwave & longwave, net & downward) and diagnostics of temp. tendency
408        for individual contribution (convection, LSC cond, radiation)
409      - add Ruth Geen etal, GRL 2016, radiation options (see paper supp.
410        information); activated with: solar_exponent=0. and wv_exponent=-1.
411    o pkg/ggl90:
412      - within IDEMIX add upper limit for horizontal group velocity to
413        avoid instability problems in the explicit horizontal diffusion term for
414        long time steps or high resolution
415    o pkg/diagnostics:
416      - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
417        (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
418    o testreport:
419      - remove "-v" (verbose option) in default mpirun command.
420    o pkg/seaice/seaice_growth:
421      - catch potential division by zero in ITD code, does not change
422        verification results
423    o pkg/ecco:
424      - retire old codes to the Attic. The calls to retired functions are
425        left in a commented form in case they ever need to be re-activated.
426      - ecco_check.F: issue warning if any old CPP option is
427        defined that corresponds to retired codes -- then stop.
428    o pkg/atm_compon_interf:
429      - change seaice fraction (use for OCN dic surf.flux) stored and sent to
430        coupler: use last time-step value instead of average over cplSendFrq_iter
431        time-step, similar to what is done for seaIceMass.
432        This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
433    o eesupp & genmake2:
434      - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
435        <= remove until a fix is found for some ifort version on ia32 machine.
436    o pkg/seaice/seaice_evp:
437      - refine residual computation
438    
439    checkpoint65q (2015/11/18)
440    o pkg/seaice/seaice_evp:
441      - fix residual computations so that they no longer affect the actual
442        simulation code
443      - fix seaice_readparams to be able to actually set new parameters
444        SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
445    o model/src:
446      - fix wrong truncation (single prec) from "FLOAT" function in expressions
447        like: deltaT*FLOAT(myIter) when myIter is large:
448         a) replaced by DFLOAT (if not seen by TAF);
449         b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
450    o pkg/aim_v23:
451      - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
452        when pickupSuff is set ; do write rolling pickups + at the end of the run.
453    o pkg/atm_ocn_coupler + ocn_compon_interf:
454      - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
455        coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
456        add corresponding call in DO_OCEANIC_PHYS.
457    o coupler pkgs:
458      Start a new way to set-up optionally-exchanged variables (previously, only
459       there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
460       data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
461       send switch to ATM & OCN compon before reading their own "data.cpl" (so that
462       compononent param default can be set accordingly).
463      Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
464       but rather applies to a group a fields (going both ways like for DIC)
465       and corresponds to an option of coupling config.
466      coupler (pkg/atm_ocn_coupler):
467      - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
468        and read namelist directly (without eessup S/R calls) instead of
469        in the very un-flexible old way, 1 param per line, in fixed order;
470      - add error-counter to track errors (e.g., missing "data.cpl") and to stop
471        cleanly in CPL_CHECK_CPLCONFIG
472      - add new coupling-exchange selectors (some not yet active) including
473        cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
474                                             and ocnCpl_exchange_DIC=T in OCNIDS.h);
475      - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
476        component ; called directly from coupler.F, after comp. registrations;
477      - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
478         atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
479          -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
480      components (pkg/atm_ & ocn_compon_interf):
481      - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
482        CPP header file in all pkg source files.
483      - move checking of comp. configs out of cpl_exch_configs.F into new S/R
484        ATM/OCN_CHECK_CPLCONFIG;
485      - add error-counter to track errors (e.g., in "data.cpl") and to stop
486        cleanly in ATM/OCN_CHECK_CPLCONFIG;
487      - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
488        from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
489        before PACKAGES_READPARMS;
490      verification/cpl_aim+ocn/:
491      - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
492        "data.cpl" for coupler (in input_cpl).
493    o eesupp/inc:
494      - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
495        #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
496        to always cumulate tile local-sum in the same order (still uses
497        MPI_Allreduce like standard code).
498      - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
499        that are now identical to standard version (in eesupp/inc).
500    o pkg/shelfice:
501      - add SHELFICETransCoeffTFile for initializing spatially varying
502        heat and salt transfer coefficients
503    o pkg/atm_compon_interf & ocn_compon_interf:
504      - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
505        S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
506      - move bi,bj loops inside S/R OCN_STORE_MY_DATA
507    o pkg/atm_ocn_coupler:
508      - initialise to zero ATMVARS.h & OCNVARS.h arrays.
509    o pkg/rbcs:
510      - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
511        to compile with maskLEN=1 when all tracers use the same RBCS-mask.
512      - add a short report (to STDOUT) about RBCS-mask settings.
513    
514    checkpoint65p (2015/10/23)
515    o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
516        there is no adjoint test for EVP, we don't know what it does to the adjoint
517        solution, but at least there are no more recomputation warnings left
518    o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
519        a chance of giving the same results as a fully converged VP (JFNK) solver
520    o tools/adjoint_options/adjoint_diva:
521      - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
522    o pkg/streamice:
523      - spotted bug in streamice_driving_stress using dyG where should have been dxG
524    o pkg/exf:
525      - remove STOP statement that prevented to use wind or (wind-)stress
526        interpolation for constant-in-time forcing fields (wind/stress period = 0).
527    o pkg/seaice:
528      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
529        5 additionals 2D fields and 6 new store directives
530      - change logic in seaice_readparms.F: EVP code can now be turned on in
531        various ways, setting SEAICE_deltaTev is no longer required,
532        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
533        or SEAICEaEVPcoeff
534    o pkg/shelfice/shelfice_thermodynamics.F
535      - redefining uLoc/vLoc to u/v, instead of 2u/v
536    o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
537      - this is an intermediate state of a truely converging EVP that has
538        the potential of outperforming implicit VP methods, I do not recommend
539        using it yet.
540      - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
541        and all parameters are hardwired
542      - for convergence it still requires very smooth regularisations, that means,
543        if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
544        different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
545        specific averaging appears to be required, still subject to tuning
546      - still needs cleaning and I need to turn parameter into runtime parameters
547      - add code to compute and print residuals of iteration, compile with
548        defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
549    o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
550      that entered with r1.54 on Sep04, 2015, -> update results
551    
552    checkpoint65o (2015/09/14)
553    o pkg/mom_vecinv & mom_common:
554      - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
555        called from there.
556      - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
557        allows to use Vector-Invariant form in deep atmos and anelastic formulation
558  o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)  o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
559    and Koenig-Beatty+Holland (2012)    and Koenig-Beatty+Holland (2012)
560    - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth    - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
# Line 15  o pkg/seaice: introduce new parameter SE Line 566  o pkg/seaice: introduce new parameter SE
566    - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice    - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
567      by AREA according to Connelly et al. (2004), JPO.      by AREA according to Connelly et al. (2004), JPO.
568    - For EVP and the LSR solver, the implicit part of the drag term is    - For EVP and the LSR solver, the implicit part of the drag term is
569      the only non-zero term in the denominator when there is no ice (which      the only non-zero term in the denominator when there is no ice (which
570      prevented running the model with zero ice-ocean drag). If      prevented running the model with zero ice-ocean drag). If
571      SEAICEscaleSurfStress = .TRUE., this results in a division by zero      SEAICEscaleSurfStress = .TRUE., this results in a division by zero
572      (or zero main diagonals BU/BV) which need to be caught. A practical      (or zero main diagonals BU/BV) which need to be caught. A practical
573      consequence is that for open water, the momentum equation reduce      consequence is that for open water, the momentum equation reduce
574      to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if      to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
575      they happen to be zero, often leading to a non-zero solution over      they happen to be zero, often leading to a non-zero solution over
576      open water.      open water.
577  o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more  o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
578      efficient EVP method.      efficient EVP method.
579    - introduce area-weighted averages for e12 (analogously to    - introduce area-weighted averages for e12 (analogously to
580      seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits      seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
581      remain, but also changing the order of terms in the previous average      remain, but also changing the order of terms in the previous average
582      changed the results as much) -> update experiment      changed the results as much) -> update experiment
583    - add SEAICE_DELTA_SMOOTHREG code    - add SEAICE_DELTA_SMOOTHREG code
584    - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for    - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
585      TEM-code      TEM-code
586    - adjust loop bounds so that only required fields are computed    - adjust loop bounds so that only required fields are computed
587    - add new averaging code for zetaZ/deltaZ (again similar to    - add new averaging code for zetaZ/deltaZ (again similar to
588      seaice_calc_viscosities.F), inactive by default for now (will change      seaice_calc_viscosities.F), inactive by default for now (will change
589      results again), but will replace old code eventually      results again), but will replace old code eventually
590  o eesupp/src:  o eesupp/src:
# Line 44  o eesupp/src: Line 595  o eesupp/src:
595      and should be faster than GLOBAL_SUM_SEND_RECV code.      and should be faster than GLOBAL_SUM_SEND_RECV code.
596    - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV    - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
597      (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.      (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
598    - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 13 more exp.:    - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
599       aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,       aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
600       fizhi-cs-aqualev20, global_ocean_ebm, matrix_example, natl_box,       fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
601       solid-body.cs-32x32x1, tutorial_advection_in_gyre, tutorial_baroclinic_gyre       natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
602       and tutorial_held_suarez_cs.       tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
603    
604  checkpoint65n (2015/07/29)  checkpoint65n (2015/07/29)
605  o pkg/thsice:  o pkg/thsice:
# Line 378  o model/src & mom pkgs: Line 929  o model/src & mom pkgs:
929      just copy level Nr value to level Nr+1.      just copy level Nr value to level Nr+1.
930  o doc:  o doc:
931    - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.    - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
932  o pkg/streamice:  o pkg/shelfice:
933    - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,    - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
934      SHELFICE.h: move array shelficemass to init_varia, initialise      SHELFICE.h: move array shelficemass to init_varia, initialise
935      from array shelficemassinit, which is set in init_fixed and      from array shelficemassinit, which is set in init_fixed and
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