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revision 1.2107 by jmc, Wed Dec 17 17:58:39 2014 UTC revision 1.2296 by jmc, Fri Jan 27 21:20:53 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 pkg/exf:
8      - add option ALLOW_READ_TURBFLUXES (and corresponding set of parameters)
9        to allow to read-in Sensible & Latent Heat flux ;
10      - simplify pkg/exf main options:
11        1) move small piece of code (case ALLOW_ATM_TEMP undef) out of
12           exf_bulkformulae.F into exf_wind.F so that exf_bulkformulae.F is
13           compiled only when both ALLOW_ATM_TEMP & ALLOW_BULKFORMULAE are defined;
14        2) make call to EXF_RADIATION and to EXF_WIND independent of CPP option
15           ALLOW_BULKFORMULAE which now only applies to S/R EXF_BULKFORMULAE ;
16        3) improve options documentation in EXF_OPTIONS.h.
17    o pkg/ecco:
18      - cost_gencost_customize.F,ecco.h,ecco_phys.F,ecco_readparms.F, and
19        ecco_summary.F: add passive tracer cost functions to gencost;
20        m_ptracer and m_boxmean_ptracer
21    o pkg/ctrl:
22      - ctrl_map_forcing.F: pass myIter and myTime to ctrl_map_forcing as input
23        parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing; add to list
24        of implemented gentim2d contol parameters: xx_qnet, xx_empmr, xx_qsw,
25        xx_sst, xx_sss, xx_pload, xx_saltflux, xx_fu, xx_fv, xx_fe, xx_fn
26    o model/src:
27      - forward_step.F: pass myIter and myTime to ctrl_map_forcing as input
28        parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing
29    o pkg/exf:
30      - exf_getffields.F: add to list of implemented gentim2d contol parameters:
31        xx_lwflux, xx_swflux, xx_evap, xx_apressure, xx_areamask
32    
33    checkpoint66c (2017/01/19)
34    o verification:
35      - add new option "-src" to testreport to only produce source code (*.f),
36        including taf output src code (if using '-adm'/'-tlm' option).
37    o pkg/exf:
38      - add saltflx :: Net upward salt flux in psu.kg/m^2/s
39    o pkg/diagnostics:
40      - add run-time variable diagMdsDir to specify a subdirectory for
41        diagnostic output when mds is being used and mdsioLocalDir is not.
42    o pkg/mnc:
43      - mnc_utils.F: edit stop message
44    o pkg/autodiff:
45      - autodiff_ini_model_io.F: PRINT_MESSAGE, clean-up comments, add _*_MASTER,
46        add HAVE_SYSTEM bracket around system call to mkdir
47    o pkg/profiles:
48      - profiles_findunit.F, profiles_init_fixed.F, profiles_interp.F,
49        profiles_readparms.F: call ALL_PROC_DIE before 'stop'
50      - profiles_ini_io.F: use PRINT_MESSAGE, clean-up comments, add _*_MASTER,
51        add HAVE_SYSTEM bracket around system call to mkdir
52    o pkg/smooth:
53      - smooth_filtervar2d.F, smooth_filtervar3d.F: call ALL_PROC_DIE before 'stop'
54      - smooth_init2d.F, smooth_init3d.F: move print statements to readparms
55      - smooth_readparms.F: add cleaner print statements from smooth_init?d.F
56    o pkg/exf:
57      - check: count errors and stop cleanly at the end (call to ALL_PROC_DIE);
58        issue error message when climsst_interpMethod.GT.0 and climsst_lon_inc > 500
59        generalize tests on interpMethod, nlat, and lon_inc to all exf variables.
60      - summary: skip detailed field report if not used (empty file-name).
61    o tools/xmakedepend:
62      - In case line editor "ed" is missing, switch to "sed" command to clean-up
63        Makefile from previous dependencies (anything after "# DO NOT DELETE" line).
64    o pkg/exf:
65      - change definition of "hflux" input file to always include Short-Wave;
66        this is now consistent with hflux computation (if using bulk-formulae)
67        and hflux diagnostic & documentation (in EXF_FIELDS.h).
68    
69    checkpoint66b (2016/12/01)
70    o model & momentum pkgs:
71      - implement fully implicit bottom friction combined with implicit surf.
72        pressure, for now, only in hydrostic formulation:
73        + to use: compile with #define ALLOW_SOLVE4_PS_AND_DRAG in CPP_OPTIONS.h
74          and run with selectImplicitDrag=2 ;
75        + currently missing diagnostics of bottom drag and vert. viscosity tendency;
76      - partial implicit time-stepping (bot. friction + vert. visc first, then
77        surf. press) corresponding to selectImplicitDrag=1 should be applicable
78        to NH formulation but not available until we solve for surf. pressure
79        increment (instead of full etaN).
80      - change exp. global_ocean.cs32x15.thsice to test implicit bottom drag
81        with implicit vertical viscosity.
82    o pkg/seaice: add linear remapping scheme (Lipscomb 2001) to ITD model
83      - this is a first version that includes many regularisations that may
84        not all be necessary, to be sorted out,
85      - turned on by runtime parameter SEAICEuseLinRemapITD (true by default)
86      - change one verification experiment in seaice_itd to use and test new code
87      - seaice_growth: catch a case where the argument of log can be zero
88        or smaller (important for code stability)
89    o model/src:
90      - modify SOLVE_DIAGONAL_LOWMEMORY version of solve_tridiagonal.F
91        & solve_pentadiagonal.F to enable to re-used inverse matrix for solving
92        similar A.X'=Y' system (with same matrix A) in subsequent calls;
93        switch based on errCode (In/Out) argument value; in calling routines,
94        initialise errCode before first call.
95    
96    checkpoint66a (2016/10/18)
97    o pkg/bling:
98      - BLING package now loads in atmospheric pCO2 file using exf package routines
99        Enable with #define USE_EXFCO2 in BLING_OPTIONS.h
100    o model/src & pkg/ptracers:
101      - with INCLUDE_IMPLVERTADV_CODE defined, also call MOM_U,V_IMPLICIT_R &
102        GAD_IMPLICIT_R (instead of IMPLDIFF) when just implicitViscosity and
103        implicitDiffusion (respectively) are used (even without momImplVertAdv
104        or temp,salt,PTRACERS_ImplVertAdv).
105    o model/src & generic_advdiff:
106      - add parenthesis in main diagonal calculation of implicit vertical
107        diffusion matrix (impldiff.F & gad_implicit_r.F).
108        This affects results at machine truncation level; update output of many
109        verification experiments (31 fwd ; 10 adm ; 8 tlm ; 3 oad).
110    o pkg/mom_commom & generic_advdiff:
111      - add deep atmosphere and anelastic scaling factor in implicit vertical
112        advection routines (mom_u,v_implicit_r.F & gad*_impl*_r.F).
113    o model/src:
114      - remove few unnecessary temp array copies in solve_tridiagonal.F
115        & solve_pentadiagonal.F
116    
117    checkpoint65z (2016/09/28)
118    o pkg/seaice: fix multithreading for seaice_fgmres.F
119      - remove unecessary variables from common blocks
120      - use extra dimension MAX_NO_THREADS for all variables of the Krylov space
121        basis, that are stored in commom blocks (including integer variable i1)
122      - clean up code a little by removing commented lines that refer to
123        original code
124      - turn on multi-threaded test for experiment offline_exf_seaice.dyn_jfnk.
125    o MITgcm manual:
126      - add uptodate pkg/ecco documentation to the manual (section 8.1; ecco.tex),
127        preliminary documentation for generic controls (8.3; ctrl.tex),
128        a placeholder for smooth (8.4; smooth.tex), and comment out the deprecated
129        ecco_costfunction.tex
130    o pkg/ecco:
131      - update and cleanup list of CCP options
132      - re-assign gencost_mask to specify masks rather than gencost_errfile; 'c'
133        is now always passed to cost_generic; gencost_mask is now MAX_LEN_FNAM
134      - add checks that retired run-time options are not used, and in relation
135        to gencost_mask and gencost_errfile
136      - finish deprecating gencost_scalefile, gencost_smooth2Ddiffnbt, and
137        gencost_nrecperiod
138      - fix m_eta computation for virtual salt flux case
139      - add m_horflux_vol case (selected via gencost_barfile) that computes
140        transports via cost_gencost_boxmean (gencost_flag=-3)
141      - use gencost_flag more systematically (i.e., avoid using gencost_name)
142        for code switches (aside from physical variable selection)
143    o pkg/seaice: make seaice_fgmres.F fit for multithreading; this first
144      attempt appears to be a bit of a hack and my need some repair down the road
145    o pkg/exf:
146      - interpolation near South Pole: fix criteria on input field latitude.
147    o pkg/icefront & pkg/exf:
148      - move setting of icefront Sub-Glacial RunOff forcing (currently unused)
149        from pkg/exf (read from data.exf) to pkg/icefront (read from data.icefront)
150    o pkg/exf:
151      - replace CPP option ALLOW_EXF_OUTPUT_INTERP with run-time parameter
152        "exf_output_interp" (in namelist: EXF_NML_04); change output file name
153        (add suffix "_out" instead of a prefix); keep same record number as in
154        input file but always write record 1 first (to avoid a STOP in I/O S/R).
155        Change output file content by writing interpolated field before applying
156        land-sea mask (helpful for debug).
157      - 2 compon. vector interpolation with rotation: apply scaling factor on
158        each compon. (Eastward and Northward) just before rotation.
159    o pkg/bling:
160      - Cleaned package. Removed not needed code and comments.
161      - adjoint example now works
162        (MITgcm_contrib/verification_other/global_oce_biogeo_bling/code_ad)
163    o pkg/ptracers:
164      - add Bruno Deremble's code to complete the linear surface correction
165        for tracer conservation;
166      - enabled for individual ptracers by PTRACERS_linFSConserve(iTr)=.TRUE.
167    
168    checkpoint65y (2016/07/29)
169    o pkg/debug (stats):
170      - change GLOBAL_SUM to GLOBAL_SUM_TILE (result independent of tile to
171        proc/thread mapping);
172      - fix Min & Max for case where 1 thread has only empty tiles;
173      - use RL variable to count number of wet grid points (with big domain,
174        can be too large to fit into integer*4).
175    o pkg/monitor:
176      - use RL variable to count number of wet grid points (but used only for del2)
177      - add new routine to compute Advective CFL within tracer time-stepping with
178        writing delayed until next monitor output.
179    o pkg/obcs:
180      - fix bug in OBCS_BALANCE_FLOW (OBCS_balanceFacN misspelled OBCS_balanceFacW)
181    o pkg/cal:
182      - calandar-dump: treat case myTime < timePhase in the same way as in
183        eesupp/src/diff_phase_multiple.F (when not using calandar-dump).
184    o pkg/dic & seaice:
185      - fix compilation of ocean component for coupled atm+ocn model with
186        seaice dynamics & dic.
187    
188    checkpoint65x (2016/06/11)
189    o add a license text file in main MITgcm tree.
190    o added pkg/bling:
191      - intermediate complexity biogeochemical model
192      - see bling_description.txt for details
193      - verification experiment is global_oce_biogeo_bling (for now, in
194        Contrib/verification_other/); tested daily on baudelaire with gfortran.
195      - add entry point in pkg/gchem for new pkg "bling".
196    o pkg/seaice: fix tensile stength computation
197      - replace global field tensileStrength by tensileStrFac
198      - tensileStrFac can be computed once in S/R seaice_init_varia
199      - fortunately that does not affect any verification results
200    
201    checkpoint65w (2016/05/12)
202    o pkg/ctrl/ctrl.h: fix a comma in common block list, so that code compiles
203         with ECCO_CTRL_DEPRECATED defined
204    o verification/global_ocean.cs32x15:
205      - change secondary test "viscA4" to also test "selectP_inEOS_Zc=3"
206        with "selectNHfreeSurf=1".
207    o model/src (non-hydrostatic free-surface):
208      - More "natural" expression of NH free-surface term (case selectNHfreeSurf=1):
209        was: tmpSurf/(1+tmpSurf); changed to: 1/(1+Gamma) with Gamma=1/tmpSurf.
210      - Calculate surface vertical velocity after 2-D solver adjustment (accounts
211        for EmPmR if RealFreshWaterFlux); used in RHS (cg3d_b) if exactConserv
212        and used to compute dPhiNH (in post_cg3d.F) if selectNHfreeSurf=1.
213        This fixes EmPmR contribution when selectNHfreeSurf=1 & RealFreshWaterFlux.
214      - Update output (changes at machine truncation level) of verification exp:
215        exp4 (11 digits for cg2d), global_ocean.cs32x15.viscA4 (11.d),
216        short_surf_wave (13.d) and tutorial_deep_convection.smag3d (12.d).
217    o pkg/seaice: ITD code
218      - fix picking up from a single category model by initialising
219        heff/area/hsnowITD = 0. in seaice_itd_pickup.F
220      - split a long warning message in seaice_check_pickup.F into two lines,
221        because NEC SX-ACE cannot deal with the long line.
222    o model/src:
223      - fix missing dPhiNH in pressure_for_eos.F (case: selectP_inEOS_Zc=3)
224    o pkg/seaice:
225      - add missing checks for SEAICE_ALLOW_KRYLOV and SEAICE_ALLOW_BOTTOMDRAG
226    o pkg/seaice:
227      - add basal stress as parameterisation for grounding ice
228        following Lemieux et al. (2015)
229      - turn on by setting new parameter SEAICEbasalDragK2 to a value
230        larger than 0. Lemieux et al. (2015) recommend 15.
231      - The adjoint complains with extra recomputations so there is also a
232        new cpp-flag SEAICE_ALLOW_BOTTOMDRAG that is undefined by default in
233        order to postpone the problem
234      - compile the new code in lab_sea
235    o verification/halfpipe_streamice:
236      - update both TAF and OpenAD adm output (machine truncation differences)
237    
238    checkpoint65v (2016/04/08)
239    o verification/advect_xz:
240      - increase overlap size from 3 to 4 and add new secondary test for PQM
241        advection scheme (with mono & wino limiter).
242      - change main exp. to test PPM (with weno limiter) adv.scheme on Temp.
243    o model/src:
244      - new parameters "top_Pres" & "seaLev_Z" (replacing Ro_SeaLevel and recently
245        added phi0Ref) to set vertical axis origin and phiRef origin;
246        keep Ro_SeaLevel for backward compatibility (with a warning).
247       According to coordinate and fluid type:
248        OCN in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(1), @ the top)
249        ATM in Z: top_Pres(Ref) (=rhoConst*PhiRef(1)), seaLev_Z (=rF(Nr+1) @ bottom)
250        OCN in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(Nr+1)/g, @ the top)
251        ATM in P: top_Pres (=rF(Nr+1)), seaLev_Z (= PhiRef(1)/g, @ the bottom)
252      - remove Ro_SeaLevel from ATM experiment parameter files;
253      - in tutorial_global_oce_in_p, remove Ro_SeaLevel and set top_Pres to the
254        complement; update output.txt (changes at machine truncation level).
255    o pkg/seaice/seaice_evp.F
256      - simplify computation of deltaZ and zetaZ to simple averaging following
257        Bouillon et al. (2013). This removes a lot of code, but also changes
258        verification experiment lab_sea.hb87 -> updated
259    
260    checkpoint65u (2016/03/14)
261    o pkg/generic_advdiff:
262      - from Darren: add PPM and PQM advection schemes (number 40-42 and 50-52)
263        with 2 types of limiter (see: Engwirda & Kelley, submit. to JCP);
264        Note (from Darren): unlimited PPM/PQM scheme (40 & 50) are just for
265        testing and not for actual use.
266    o model/src:
267      - add parameter "phi0Ref" to specify reference [pressure/geo] potential at
268        origin r = rF(1);
269      - add options (parameter selectP_inEOS_Zc) to select which pressure to use
270        in EOS for height coordinate: enable to include NH Pressure or to use
271        more accurate pressure vertical profile; options not linked to EOS type
272        (as previously, e.g., JMD95P/JMD95Z) but set default according to EOS type;
273      - start to implement variable gravity (along vertical): for now, only with
274        z-coords (not even z*).
275      - add Ideal Gas equation of state for height coordinate.
276      - update OpenAD output (affected at machine truncation level) of exp:
277        global_ocean.90x40x15, OpenAD (std) and tutorial_global_oce_biogeo.
278    o pkg/exf:
279      - add ALLOW_EXF_OUTPUT_INTERP cpp switch to output the result
280        of exf interpolation (before any rescaling, rotation or interpolation
281        to velocity point) for each field that gets loaded from file. This option
282        identically mimics the input file organization (e.g. record numbers in year
283        by year input files) besides the change in horizontal grid.
284      - add rotateStressOnAgrid run-time switch so that wind stress fields
285        can be provided on the A-grid in zonal/meridional direction and
286        rotated on the fly. This only applies to the case when the exf
287        interpolation is off and rotateStressOnAgrid is false by default.
288    o model/src:
289      - rename internal parameter "useDynP_inEos_Zc" to "storePhiHyd4Phys" (since
290        it's also used with pkg/atm_phys) and add few more parameters (but still
291        inactive, src code yet to come)
292    
293    checkpoint65t (2016/02/10)
294    o pkg/atm_phys:
295      - from Ruth Geen: add optical depth dependence on CO2 concentration.
296    o model/src:
297      - fix vertical inter/extra-polation of density factor rhoFacF (for anelastic)
298        for the case setCenterDr=T (delRc set from "data"); add output of rhoFacC&F.
299        Update output of exp. deep_anelastic (changes at truncation level).
300    o tools:
301      - add a hack in "remove_comments_sed" (used only with TAF) for recent
302        version of OpenMPI (shipped with FC.23): comment out the new header
303        file "mpif-sizeof.h" which causes problems to TAF.
304    o pkg/seaice:
305      - change the termination criterion so that maxits (SEAICElinearIterMax)
306        has an effect
307      - unify iteration parameters for implicit solvers (JFNK and Picard)
308        SEAICEnonLinIterMax replaces SEAICEnewtonIterMax/NPSEUDOTIMESTEPS
309        SEAICElinearIterMax replaces SEAICEkrylovIterMax/SOLV_MAX_ITER
310        SEAICEpreLinIterMax replaces SOLV_MAX_ITER in preconditioner
311        SEAICEpreNL_IterMax replaces NPSEUDOTIMESTEPS in preconditioner
312        SEAICEnonLinTol     replaces JFNKgamma_nonlin
313      - remove S/R SEAICE_FGMRES_DRIVER and put content into S/R SEAICE_JFKN
314      - add new Picard-Krylov solver, compile with SEAICE_ALLOW_KRYLOV and
315        use with SEAICEuseKrylov
316    o pkg/seaice/seaice_lsr.F
317        fix small bug: replace zetaZ by zetaZloc in S/R seaice_lsr_rhsu/v; only
318        relevant if SEAICEuseStrImpCpl=T, and even then it does not seem to have
319        an effect.
320    o pkg/seaice: add two new parameters
321      - SEAICEuseLSR to simplify the logic in seaice_dynsolver (this
322        parameter is not in any namelist)
323      - SEAICEusrPicardAsPrecon to allow s/r seaice_lsr to be used as
324        a preconditioner for the non-linear Newton iteration of the JFNK
325        solver
326    o pkg/seaice/seaice_lsr.F: replace 1./SEAICE_deltaTdyn with recip_deltaT,
327      affects some experiments at truncation level:
328      - global_ocean.cs32x15.icedyn (11 digits),
329      - global_ocean.cs32x15.seaice (11 digits),
330      - seaice_itd (12 digits), seaice_itd.lipscomb07 (12 digits) -> update
331      - also update global_ocean.cs32x15 adjoint and tangent-linear results
332    o pkg/salt_plume & pkg/thsice:
333      - for coupled  set-up with pkg/thsice in ATM and pkg/salt_plume in OCN,
334        connect salt_plume flux to ATM-OCN coupling pkgs interface:
335       a) in ATM: also cumulate salt-plume flux in S/R THSICE_SALT_PLUME (for
336         export to coupler interface) even without compiling pkg/salt_plume ;
337       b) in OCN: apply coupler salt-plume flux to pkg/salt_plume field
338         (saltPlumeFlux) just before exch call, in S/R SALT_PLUME_DO_EXCH.
339    o pkg/dic:
340      - use the updated seaice fraction (from seaice pkgs) for DIC forcing
341        instead of the previous time-step value ; done in new S/R DIC_FIELDS_UPDATE
342        called from the top of dic_biotic_forcing.F (instead of in DIC_FIELDS_LOAD);
343      - move also update with values from ATM-OCN Coupler in the same new S/R
344        (previously done in ocn_apply_import.F).
345    o tools/adjoint_options:
346      - specify explicitly "-f77" or "-f90" in default ad-optfile since TAF (default)
347        has been changed on Jan 14, 2016.
348    o pkg/ggl90:
349      - add alternative discretisation of vertical shear (off by default), to
350        compute the mean (@ grid-cell center) of vertical shear compon instead of
351        vertical shear of mean flow (@ grid-cell center).
352      - add correct parenthesis in ALLOW_GGL90_SMOOTH code to get the same truncated
353        results on adjacent faces of cubed-sphere grids; this fix the restart.
354    o pkg/atm_compon_interf:
355      - skip time-ave over cpl_atmSendFrq of Sea-Level Pressure (atmSLPr) and just
356        pass last value, stored directly before export to CPL ;
357        Note: this affects results of Coupled set-up where OCN uses useImportSLP=T
358      - remove atmSLPr from pickup files (no longer needed for restart)
359    
360    checkpoint65s (2016/01/13)
361    o eesupp & genmake2:
362       - first check for Function ETIME and, if it fails, then check for subroutine
363         ETIME and consistent output; use the appropriate version in timers.F
364    o model/src:
365      - to check restart test, add option to apply EXCH to U,V earlier, just before
366        integr_continuity; turned off by default.
367    o pkg/dic:
368      - remove CPP option USE_ATMOSCO2 (not needed)
369    o tools/tst_2+2:
370      - try to ignore difference between +0 and -0 in binary file, causing test
371        to fail for no good reason.
372    o eesupp & genmake2:
373      - put back modif from Jinxuan Zhu - change etime fct call to S/R call -
374        but also check (in genmake2) that test runs and returns meaningful results.
375    o coupler pkgs:
376      Finish implementation of optionally-exchanged variable switches (started on
377       Nov 12) with addition of few more exchanged fields, including 2-way exchange
378       of pkg/thsice vars to allow to use seaice dynamics (from pkg/seaice) & seaice
379       advection in OCN component; this requires sequential coupling.
380      coupler (pkg/atm_ocn_coupler):
381      - add argument msgUnit and iter number to CPL_SEND/RECV_ATM/OCN_FIELDS
382        routines (useful for debug).
383      - only export/import optionally exchanged fields (RunOff, seaice, Salt-Plume
384         flux, DIC fields) if corresponding switch is ON.
385      - add option to export RunOff to OCN (to use for DIC river input)
386      - add 2-way thSIce vars exchange; check for consistent cpl_sequential setting.
387      components (pkg/atm_ & ocn_compon_interf):
388      - to save memory space in ATM & OCN comp: add some #ifdef ALLOW_${PKG} around
389        optionally exchanged fields; add a check & stop in cpl_readparms.F.
390        ATMCPL.h: ALLOW_LAND for RunOff, ALLOW_THSICE for seaice, ALLOW_AIM for CO2;
391        OCNCPL.h: ALLOW_SALT_PLUME, ALLOW_DIC for DIC, ALLOW_THSICE for 2-W thsice.
392      - rename:   fracIce     -> sIceFrac_cpl (<- match coupler var name)
393        + in ATM: fracIceTime -> sIceFracTime ; seaIceTime -> sIceMassTime.
394      - add 2-way thSIce vars exchange ; add Salt-Plume flux ; add RunOff in OCN.
395      - hold in common block coupler optionally-exchanged variable switch
396        and set default "useImportXXX" accordingly; + check & stop if inconsistent.
397      - add diagnostics for all imported fields from coupler (in both OCN & ATM);
398        this is intended to replace the OCN cplFldtave.* output files (not updated
399        to contain new additional exchanged fields).
400    o pkg/dic:
401      - fix an other bug (also from 2014/08/30) in dic_atmos.F, in dic_int1=3 code.
402    o pkg/thsice:
403      - when coupled to ATM (useCoupler) with thSIce_skipThermo=T, skip reading
404        and writing of thsice pickup files.
405    o pkg/atm_compon_interf:
406      - move all field individual export-call out of cpl_export_import_data.F
407        into new S/R ATM_EXPORT_FIELDS
408    o pkg/atm_compon_interf:
409      - store state variables (for now, only thSIce fields) just before beeing
410        exported (in cpl_export_import_data.F, like on ocean side) instead of from
411        atm_store_my_data.F like all exported fluxes.
412      - new version of pickup_cpl: write field names into meta file and read meta
413        file to find field postion in pickup. Also only write/read fields meeded for
414        restart (same logic as main pickup file ; also using pickupStrictlyMatch)
415    o pkg/dic:
416      - fix bug (added on 2014/08/30) in dic_atmos.F for the case dic_int1= 2 or 3.
417    o pkg/seaice: add new parameter SEAICEpressReplFac to choose between
418        pressure replacement method (=1., default) or original Hibler (1979) (=0.)
419        value can be from domain [0,1] to average between the two methods
420    o pkg/atm_phys:
421      - allow to provide 2-d map of albedo and mixed-layer depth from files (but
422        hold fixed in time).
423    
424    checkpoint65r (2015/12/21)
425    o pkg/seaice:
426        fix bug in tridiagonal solvers for SEAICE_OLx/y>0, this affects the JFNK
427        solver (offline.dyn_jfnk) and global_ocean.cs32x15.seaice -> updated
428    o pkg/seaice:
429      - fix a bug in computing areaS in (J-J -> J-1) that affects runs
430        when SEAICEscaleSurfStress=.TRUE.,
431      - apply areaW and areaS in S/R seaice_calc_lhs
432    o pkg/atm_phys:
433      - add diagnostics for 3-D, Nr+1 levels diagnostics of radiative fluxes
434        (shortwave & longwave, net & downward) and diagnostics of temp. tendency
435        for individual contribution (convection, LSC cond, radiation)
436      - add Ruth Geen etal, GRL 2016, radiation options (see paper supp.
437        information); activated with: solar_exponent=0. and wv_exponent=-1.
438    o pkg/ggl90:
439      - within IDEMIX add upper limit for horizontal group velocity to
440        avoid instability problems in the explicit horizontal diffusion term for
441        long time steps or high resolution
442    o pkg/diagnostics:
443      - simplify setting of local-array size in diagstats_output.F: uses "numLevels"
444        (from DIAGNOSTICS_SIZE.h) to allow to write out more than Nr levels.
445    o testreport:
446      - remove "-v" (verbose option) in default mpirun command.
447    o pkg/seaice/seaice_growth:
448      - catch potential division by zero in ITD code, does not change
449        verification results
450    o pkg/ecco:
451      - retire old codes to the Attic. The calls to retired functions are
452        left in a commented form in case they ever need to be re-activated.
453      - ecco_check.F: issue warning if any old CPP option is
454        defined that corresponds to retired codes -- then stop.
455    o pkg/atm_compon_interf:
456      - change seaice fraction (use for OCN dic surf.flux) stored and sent to
457        coupler: use last time-step value instead of average over cplSendFrq_iter
458        time-step, similar to what is done for seaIceMass.
459        This will affect results (pkg/dic) of coupled ATM-OCN+dic set-up.
460    o eesupp & genmake2:
461      - from Jinxuan Zhu: change etime fct call to S/R call (fix gfortran ETIME);
462        <= remove until a fix is found for some ifort version on ia32 machine.
463    o pkg/seaice/seaice_evp:
464      - refine residual computation
465    
466    checkpoint65q (2015/11/18)
467    o pkg/seaice/seaice_evp:
468      - fix residual computations so that they no longer affect the actual
469        simulation code
470      - fix seaice_readparams to be able to actually set new parameters
471        SEAICEaEVPcStar and SEAICEaEVPalphaMin, also fix logic a little
472    o model/src:
473      - fix wrong truncation (single prec) from "FLOAT" function in expressions
474        like: deltaT*FLOAT(myIter) when myIter is large:
475         a) replaced by DFLOAT (if not seen by TAF);
476         b) remove "FLOAT" and use implicit type conversion (if seen by TAF).
477    o pkg/aim_v23:
478      - write/read the expected CO2 pickups (from S/R AIM_DO_CO2): fix reading
479        when pickupSuff is set ; do write rolling pickups + at the end of the run.
480    o pkg/atm_ocn_coupler + ocn_compon_interf:
481      - in prep for using pkg/seaice Dyn in coupled set-up, implement sequential
482        coupling option-1: ATM -(cpl)-> OCN and then OCN -(cpl)-> ATM ;
483        add corresponding call in DO_OCEANIC_PHYS.
484    o coupler pkgs:
485      Start a new way to set-up optionally-exchanged variables (previously, only
486       there for exchange_DIC): switch on/off from 1 place, at run-time, in coupler
487       data.cpl (new) instead of at compile time in ATMIDS.h & OCNIDS.h ;
488       send switch to ATM & OCN compon before reading their own "data.cpl" (so that
489       compononent param default can be set accordingly).
490      Note: this new switch (cpl_exchange_[xxx]) is not a per variable switch
491       but rather applies to a group a fields (going both ways like for DIC)
492       and corresponds to an option of coupling config.
493      coupler (pkg/atm_ocn_coupler):
494      - change parameter file from "data" to "data.cpl" (in cpl_read_params.F),
495        and read namelist directly (without eessup S/R calls) instead of
496        in the very un-flexible old way, 1 param per line, in fixed order;
497      - add error-counter to track errors (e.g., missing "data.cpl") and to stop
498        cleanly in CPL_CHECK_CPLCONFIG
499      - add new coupling-exchange selectors (some not yet active) including
500        cpl_exchange_DIC (to set to 3 to replace atmCpl_exchange_DIC=T in ATMIDS.h
501                                             and ocnCpl_exchange_DIC=T in OCNIDS.h);
502      - add 2 new S/R (CPL_SEND_ATM/OCN_CPLPARMS) to send coupler-params to each
503        component ; called directly from coupler.F, after comp. registrations;
504      - rename few variable-ID names (in ATMIDS.h & OCNIDS.h):
505         atm/ocnSeaIceName --> atm/ocnSIceMassName ; atm/ocnFCO2Name ->
506          -> atm/ocnCO2FluxName ; atm/ocnWSpdName --> atm/ocnWindSpdName
507      components (pkg/atm_ & ocn_compon_interf):
508      - add ATM/OCN_CPL_OPTIONS.h in component pkgs and include the corresponding
509        CPP header file in all pkg source files.
510      - move checking of comp. configs out of cpl_exch_configs.F into new S/R
511        ATM/OCN_CHECK_CPLCONFIG;
512      - add error-counter to track errors (e.g., in "data.cpl") and to stop
513        cleanly in ATM/OCN_CHECK_CPLCONFIG;
514      - add new S/R CPL_IMPORT_CPLPARMS to import coupling-exchange selectors
515        from coupler ; called from initialise_fixed.F, after PACKAGES_BOOT and
516        before PACKAGES_READPARMS;
517      verification/cpl_aim+ocn/:
518      - update ATMIDS.h & OCNIDS.h (in shared_code) and use new parameter file
519        "data.cpl" for coupler (in input_cpl).
520    o eesupp/inc:
521      - change the MPI-global-sum default (in CPP_EEOPTIONS.h) to:
522        #define GLOBAL_SUM_ORDER_TILES (only affects MPI built of global_sum_tile.F)
523        to always cumulate tile local-sum in the same order (still uses
524        MPI_Allreduce like standard code).
525      - in verification experiment code, remove local CPP_EEOPTIONS.h_mpi files
526        that are now identical to standard version (in eesupp/inc).
527    o pkg/shelfice:
528      - add SHELFICETransCoeffTFile for initializing spatially varying
529        heat and salt transfer coefficients
530    o pkg/atm_compon_interf & ocn_compon_interf:
531      - combine into 1 (new) S/R CPL_EXPORT_IMPORT_DATA the two previous
532        S/R CPL_EXPORT_MY_DATA & CPL_IMPORT_EXTERNAL_DATA
533      - move bi,bj loops inside S/R OCN_STORE_MY_DATA
534    o pkg/atm_ocn_coupler:
535      - initialise to zero ATMVARS.h & OCNVARS.h arrays.
536    o pkg/rbcs:
537      - select RBCS-mask for Temp & Salt the same way as for pTracer ; this allows
538        to compile with maskLEN=1 when all tracers use the same RBCS-mask.
539      - add a short report (to STDOUT) about RBCS-mask settings.
540    
541    checkpoint65p (2015/10/23)
542    o pkg/seaice/seaice_evp.F: fix store directives and key computations, since
543        there is no adjoint test for EVP, we don't know what it does to the adjoint
544        solution, but at least there are no more recomputation warnings left
545    o pkg/seaice/seaice_evp.F: slight modification of averaging so that EVP stands
546        a chance of giving the same results as a fully converged VP (JFNK) solver
547    o tools/adjoint_options/adjoint_diva:
548      - fix bug (typo) in Tang-Linear FLAGS setting for MPI + DIVA
549    o pkg/streamice:
550      - spotted bug in streamice_driving_stress using dyG where should have been dxG
551    o pkg/exf:
552      - remove STOP statement that prevented to use wind or (wind-)stress
553        interpolation for constant-in-time forcing fields (wind/stress period = 0).
554    o pkg/seaice:
555      - replace SEAICE_EVP_USE_ADAPTATION by run time parameters, requires
556        5 additionals 2D fields and 6 new store directives
557      - change logic in seaice_readparms.F: EVP code can now be turned on in
558        various ways, setting SEAICE_deltaTev is no longer required,
559        alternatively set SEAICE_evpAlpha/Beta, SEAICEuseEVPstar, SEAICEuseEVPrev,
560        or SEAICEaEVPcoeff
561    o pkg/shelfice/shelfice_thermodynamics.F
562      - redefining uLoc/vLoc to u/v, instead of 2u/v
563    o pkg/seaice/seaice_evp.F: introduce "adaptive EVP" by Madlen Kimmritz
564      - this is an intermediate state of a truely converging EVP that has
565        the potential of outperforming implicit VP methods, I do not recommend
566        using it yet.
567      - for now, "adaptive EVP" is turned on by setting SEAICE_EVP_USE_ADAPTATION
568        and all parameters are hardwired
569      - for convergence it still requires very smooth regularisations, that means,
570        if SEAICE_DELTA_SMOOTHREG is defined, deltaCreg=deltaC+deltaMin, which is
571        different from the VP case with deltaCreg=sqrt(deltaC**2+deltaMin**2); also
572        specific averaging appears to be required, still subject to tuning
573      - still needs cleaning and I need to turn parameter into runtime parameters
574      - add code to compute and print residuals of iteration, compile with
575        defining ALLOW_SEAICE_EVP_RESIDUAL to enable it
576    o pkg/seaice/seaice_evp.F: fix a bug (factor of four in front of e12Csq)
577      that entered with r1.54 on Sep04, 2015, -> update results
578    
579    checkpoint65o (2015/09/14)
580    o pkg/mom_vecinv & mom_common:
581      - add deep-atmosphere geometry factor in mom_calc_visc.F + in routines
582        called from there.
583      - add anelastic and deep-atmosphere geometry factor in pkg/mom_vecinv ; this
584        allows to use Vector-Invariant form in deep atmos and anelastic formulation
585    o pkg/seaice: introduce fast ice parameterisation following Itkin et al. (2015)
586      and Koenig-Beatty+Holland (2012)
587      - two new parameters SEAICE_tensilFac and SEAICE_tensilDepth
588      - global 2D field tensileStrength, computed in seaice_calc_ice_strength
589      - requires an extra input argument for S/R seaice_calc_viscosities
590      - tensileStrength's depth dependence is different from Itkin et al. (2015)
591        (to be changed and played with, for now exponential)
592    o pkg/seaice: introduce new parameter SEAICEscaleSurfStress (default = .FALSE.)
593      - if TRUE scale ice-ocean and ice-atmosphere stress acting on sea ice
594        by AREA according to Connelly et al. (2004), JPO.
595      - For EVP and the LSR solver, the implicit part of the drag term is
596        the only non-zero term in the denominator when there is no ice (which
597        prevented running the model with zero ice-ocean drag). If
598        SEAICEscaleSurfStress = .TRUE., this results in a division by zero
599        (or zero main diagonals BU/BV) which need to be caught. A practical
600        consequence is that for open water, the momentum equation reduce
601        to trivially 0 = 0 + 0 (for EVP). For LSR, BU/BV are reset to 1, if
602        they happen to be zero, often leading to a non-zero solution over
603        open water.
604    o pkg/seaice: revise EVP code (seaice_evp.F) in preparation for a more
605        efficient EVP method.
606      - introduce area-weighted averages for e12 (analogously to
607        seaice_calc_viscosities.F); this totally changes lab_sea.hb87 (2 digits
608        remain, but also changing the order of terms in the previous average
609        changed the results as much) -> update experiment
610      - add SEAICE_DELTA_SMOOTHREG code
611      - disentangle computation of zetaC/deltaC and zetaZ/deltaZ, also for
612        TEM-code
613      - adjust loop bounds so that only required fields are computed
614      - add new averaging code for zetaZ/deltaZ (again similar to
615        seaice_calc_viscosities.F), inactive by default for now (will change
616        results again), but will replace old code eventually
617    o eesupp/src:
618      - add an other alternative for multi-proc GLOBAL_SUM (in global_sum_tile.F)
619        to always cumulate tile local-sum in the same order
620        (option #define GLOBAL_SUM_ORDER_TILES in CPP_EEOPTIONS.h).
621        Still uses MPI_Allreduce (like standard code) but on array of tiles
622        and should be faster than GLOBAL_SUM_SEND_RECV code.
623      - switch almost all verification experiments that use GLOBAL_SUM_SEND_RECV
624        (defined in CPP_EEOPTIONS.h_mpi) to GLOBAL_SUM_ORDER_TILES instead.
625      - add CPP_EEOPTIONS.h_mpi with GLOBAL_SUM_ORDER_TILES defined in 14 more exp.:
626         aim.5l_cs, cheapAML_box, deep_anelastic, dome, fizhi-cs-32x32x40,
627         fizhi-cs-aqualev20, fizhi-gridalt-hs, global_ocean_ebm, matrix_example,
628         natl_box, solid-body.cs-32x32x1, tutorial_advection_in_gyre,
629         tutorial_baroclinic_gyre and tutorial_held_suarez_cs.
630    
631    checkpoint65n (2015/07/29)
632    o pkg/thsice:
633      - add a warning when used with pkg/aim but without updating SST
634        (stepFwd_oceMxL=F & useCoupler=F & tauRelax_MxL<>-1 ).
635    o pkg/offline:
636      - change where Offline-Fields are loaded, from load_fields_driver.F to
637        directly within FORWARD_STEP, just after updating iter number and time;
638      - move setting of GM and KPP diffusivity out of OFFLINE_FIELDS_LOAD into new
639        S/R OFFLINE_GET_DIFFUS that is called towards the end of DO_OCEANIC_PHYS;
640       These changes allow:
641        a) to recover exactly on-line results using deltaToffline=deltaTClock,
642        tested (using offlineIter0= nIter0 -1 and offlineTimeOffset= -deltaT/2)
643        both with Lin & Non-Lin Free-Surf, both with staggerTimeStep & synchronous
644        time-step, both with GM & KPP files and with recomputing these fields;
645        b) no needs to switch on staggerTimeStep anymore;
646        c) simplify rescaling of offline horiz. velocity with Non-Lin Free-Surf.
647      - update output of experiment tutorial_dic_adjoffline (only 3 digits left).
648    o pkg/offline:
649      - change (rarely used) offset-iteration parameter to an offset time (in s):
650        can easily recover previous offset-iter effect by setting offset-time
651        (offlineTimeOffset) to offset-iter x deltaToffline;
652      - do not turn-off Temp & Salinity surface relaxation when using KPP (used
653        in KPP as part of surface buoyancy forcing) in offline run.
654      - fix ptracers KPP non-local term in the case where KPP is re-computed.
655    o OpenAD
656      - Adding preliminary ggl90 test to OpenAD verification.
657        Config. with ggl90 currently diverges after 64 time steps
658        so will need more work to become more stable
659      - Adding preliminary kpp test to OpenAD verification.
660        required small tweakes in kpp_routines.F
661      - Merge and update from Krishna Narayanan's contrib area:
662        * Add one variable for preliminary OpenAD DIVA
663        * Add replacement time-stepping for OpenAD DIVA
664        * genmake2 flag -diva (but only for OpenAD; preliminary)
665        * required modifs for OAD_support
666        successful preliminary test for tutorial_global_oce_biogeo/
667    o pkg/seaice:
668      - initialise deltaC in seaice_lsr, cosmetic changes in seaice_lsr
669      - add cpp-flag SEAICE_DELTA_SMOOTHREG for option of regularising
670        delta with a smooth function in s/r seaice_calc_viscosity
671        (no effect on EVP)
672      - rename local suffix "sqr" into "sq" for more consistent variable names
673    o pkg/seaice:
674        add new parameter SEAICE_deltaMin that is used ***only***
675        for regularizing Delta (and nothing else, like the parameter
676        which is also used for all sorts of things SEAICE_EPS).
677        Defaults to SEAICE_EPS for backward compatibility only.
678    o pkg/seaice: replace erroneously storing e12Csqr on the wrong tape with
679        the wrong key by inialising it before use -> fixes a recomputation
680        problem but does not fix the gradient
681    o pkg/layers:
682      - move resetting of flux arrays to outside the iLa loop
683        (this caused layers_diapycnal to not work with more than one layer coord.)
684      - fix bug in calculation of layers_recip_delta in layers_init_fixed.F
685    o pkg/layers:
686      - remove from common block 3D layers fields (used to diagnose transport
687        in tracer coords) and declare them as local arrays in layers_calc.F
688    o pkg/seaice:
689      - Rename SEAICE_VECTORIZE_LSR_ZEBRA to SEAICE_LSR_ZEBRA and define it
690        in lab_sea forward experiment (changes results -> updated)
691      - update adjoint experiment lab_sea after cleaning up seaice_lsr_tridiagu/v
692    o pkg/seaice: modify seaice_lsr.F in order to improve the gradient
693       computations; for SEAICE_VECTORIZE_LSR
694      - move the loops over which the tridiagonal solvers (seaice_lsr_tridiagu/v)
695        sweep to the outside,
696      - remove store directives and add "CADJ loop sequential" directives
697        in analogy to model/src/solve_tridiagonal.F
698      - replace many "#ifdef SEAICE_VECTORIZE_LSR_ZEBRA" by variable loop
699        boundaries to yield more readable code. This has also the charming side
700        effect that your can use SEAICE_VECTORIZE_LSR_ZEBRA without
701        SEAICE_VECTORIZE_LSR (i.e. adjoint without recomputations in
702        seaice_lsr_tridiagu/v now requires either of these flags, vectorization
703        still requires SEAICE_VECTORIZE_LSR with SEAICE_VECTORIZE_LSR_ZEBRA as
704        an additional option)
705       The tridiagonal solvers are now completely analoguous to solve_tridiagonal.F
706       but the adjoint gradients (which are affected by this change) still explode.
707    o coupler (atm & ocn _compon_interf):
708      - avoid using Exch2 IO mapping if not suitable.
709    
710    checkpoint65m (2015/06/15)
711    o pkg/layers:
712      - clean-up old parameters setting (from Sep 2012):
713        + remove old parameters setting from common block (declared locally);
714        + stop if any old parameter is mixed with new parameters;
715        + check for valid or consistent parameter setting (e.g., layers_name)
716      - check that layers_bounds for Pot.Density are in the right range;
717        this is supposed to catch un-updated setting after recently shifting
718        potential density field "prho" by -1000 (now in "sigma" scale).
719    o pkg/layers:
720      - Added missing call to layers_fill for keeping track of tottend in
721        pkg/diagnostics/diagnostics_fill_state.F
722    o pkg/layers:
723      - added CPP flux LAYERS_FINEGRID_DIAPYCNAL to disable fine-grid binning
724        of diapycnal fluxes
725    o pkg/layers:
726      - reverted changes to interpolation to previous treatment; there
727        was never actually a problem
728    o pkg/layers:
729      - fix interpolation of layers tracers in the presence of partial cells
730      - add lots of new functionality to compute water mass transformation
731        (enabled by CPP flag LAYERS_THERMODYNAMICS)
732      - add new calls from main code (diags_oceanic_surf_flux.F,
733        thermodynamics.F, impldiff.F) and gad to save the necessary fields
734        for layers_thermodynamics calculations
735    o pkg/ptracers:
736      - add capability of stepping a passive tracer forward without advection
737        by setting PTRACERS_advScheme to 0.
738    o pkg/diagnostics:
739      - add few (threads) _BARRIER around any update of "diag_pkgStatus".
740    o pkg/layers:
741      - shift potential density field "prho" by -1000 for density layer averaging so
742        that it corresponds to usual "sigma" definition (i.e., rho(p=const)-1000);
743        Note that density bin boundaries (layers_bounds in data.layers) have
744        to be set accordingly (i.e., shifted, in sigma scale).
745    o pkg/layers:
746      - fix snap-shot output of layer thickness @ V.pt and output of pot.density
747      - fix calculation of layer non-weighted velocity and layer probability
748      - add diagnostics for pot.density used for layer averaging
749    o pkg/seaice:
750      - seaice_calc_viscosity.F: change computation of deltaC**2 to ensure
751        positiveness, modify a few comments and improve variable names,
752      - the changed computation of deltaC affects most seaice-related
753        experiments at the truncation level.
754        seaice_itd.thermo is affected by far the most, with
755        only 7 digits of agreement remaining; update experiments.
756    
757    checkpoint65l (2015/05/04)
758    o pkg/shelfice:
759      - in shelfice_thermodynamics.F, if SHELFICEBoundaryLayer=.true., then set
760        factor drKp1 to zero where it is negative (ie. do not use
761        SHELFICEBoundaryLayer if hFacC>1)
762      - the same for factor drLoc in shelfice_forcing.F
763    o tools/genmake2: move FEXTRAFLAGS from FFLAGS to FOPTIM to avoid a problem
764        with modules in ptracers, when using testreport option "-small_f"
765    o pkg/seaice/seaice_growth.F (in case of SEAICE_ITD)
766      - replace tmpscal1**1.36 by faster exp(1.36*log(tmpscal1))
767    o verification/testreport
768      - add new option -small_f
769        with this option testreport first makes the target small_f (*.f files)
770        before running make (all). This is useful for explicit inlining when
771        all sources need to be full available.
772    o pkg/exf/exf_interp.F:
773        remove previous changes related to reverse (decreasing) input grids latitude
774    
775    checkpoint65k (2015/04/01)
776    o pkg/ecco:
777        fix missing cosphi initialization; use eccoiter in place of optimcycle;
778        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
779        instead of active read/write
780    o pkg/ctrl:
781        if autodiff is not compiled then use READ_REC_XY_RL/READ_REC_XYZ_RL
782        instead of active read/write.
783    o pkg/autodiff: make autodiff_readparms.F and autodiff_whtapeio_sync.F
784        return if .NOT.useAUTODIFF
785    o pkg/seaice: add CPP brackets (cost function related).
786    o model/src:
787        add useAUTODIFF run time switch.
788    o pkg/exf/exf_interp.F:
789        add code to allow input grids with latitude starting in the north (i.e. when
790        j=1 corresponds to northern edge of field); modify global_with_exf to test
791        this feature.
792    o verification/testreport:
793      - replace "grep -A3" with POSIX conformal sed command, because there are
794        implementations of grep that cannot do contextual searches
795      - replace "cat -n" by "nl" (two occurrences), because not all implementations
796        of "cat" have the option "-n"
797    o model/src:
798        add new file gsw_teos10.F that contains 3 functions, more or less a copy
799        of the gsw_toolbox.f90 of the TEOS-10 fortran interface, that are used to
800        convert from conservative to potential temperature. For now they are not
801        called anywhere.
802    o pkg/ggl90: make "useIDEMIX" useful
803      - re-organize code in s/r ggl90_calc a little to move computations that
804        are different for idemix into separate loops (changes verification
805        experiment idemix at truncation level, 12 digits remain -> updated)
806      - requires 2 new 2D fields KappaM, verticalShear
807      - make hFacI and recip_hFacI local 3D variables that are passed to
808        s/r ggl90_idemix
809      - fix and improve some comments
810    
811    checkpoint65j (2015/02/25)
812    o pkg/openad
813      - synchronize seawater.F with version in model/src: replace routine
814        body of sw_temp by calling sw_ptmp and fix/add a few comments.
815    o pkg/mnc:
816      - change default value of pickup_read/write_mnc params to FALSE
817        (since few features are missing in reading MNC pickup files).
818    o model/src:
819      - change default (background) vertical diffusivity for salt to be the
820        temperature (background) vertical diffusivity.
821      - change background vertical diffusivity in vertical mixing pkgs ggl90,
822        kl10, my82 and pp81 from temperature diffusivity to salinity diffusivity.
823        This makes ptracers default diffusivity (that uses salt diffKr) more
824        consistent with vertical mixing schemes.
825    o verification/testreport:
826      - fix typo in "-pcls" option ;
827      - put temp files in /tmp (instead of in local dir)
828      - add option "-ncad" to use genmake2 new option "-nocat4ad"
829      - allow to use "-j" option (for multi-procs make) for AD, OAD and TLM.
830    o pkg/ggl90 (idemix code):
831      - apply few fixes ; add some missing "_d 0" ; update output of exp.
832        global_ocean.90x40x15.idemix
833    o OpenAD
834      - enable active file I/O and begin removal of work-around code
835        for OpenAD for handling control variables (memory vs. active files)
836      - new CPP options file OPENAD_OPTIONS.h
837      - revert to genarr2d gradient check for hs94.1x64x5
838      - (genarr3d tested by tutorial_global_oce_biogeo, tutorial_tracer_adjsens)
839      - gentim2d works for halfpipe_streamice but not yet hs94.1x64x5
840    o tools/genmake2:
841      - add option for an alternative Makefile (from Martin) where multiple
842        source files are sent to TAF (instead of all in one file).
843    o pkg/ggl90: add IDEMIX (Olbers and Eden, 2013)
844      - code provided by Carsten Eden as an extension of ggl90
845      - so far the code is turned on within ggl90 by setting a CPP-flag at
846        compile time; a runtime flag implementation is not yet complete
847      - tested in new verification experiment global_ocean.90x40x15.idemix
848    o verification:
849      - reduce length of the AD test run by half for experiments
850        global_ocean.cs32x15 (std + thsice) and isomip
851      - enable active file I/O for OpenAD, adjust verifications accordingly
852      - halfpipe_streamice: change gradient check from genarr2d to gentim2d
853    o verification/testreport:
854      - fix two non-POSIX sed statements so that there are no error messages
855        on Mac OS X
856      - replace hostname -s with hostname | sed 's/\..*$//'
857    o model/src/seawater.F:
858      - simplify SW_TEMP to just calling SW_PTMP with P and PR exchanged
859        (following the matlab code), which would have avoided the bug caught
860        by Matt (see below) in the first place
861    o pkg/shelfice:
862      - implement alternative discretisation of quadratic drag (selectBotDragQuadr)
863        and true distance in no-slip BC (bottomVisc_pCell) similar to bottom-drag.
864      - fix sign of friction tendency (no-slip BC) and fix u,v drag for thin
865        ice-shelf case (i.e., within surface level).
866      - add config summary in shelfice_check.F
867      - remove global variable recip_SHELFICElatentHeat and replace by a local
868        variable recip_latentHeat
869      - introduce diagnostics for friction velocity uStar (in case of
870        SHELFICEuseGammaFrict)
871      - change verification experiment isomip.htd:
872        + start from pickup (as input_ad at nIter0=8640)
873        + start from SHELFICEmassFile instead of SHELFICEloadAnomaly file
874        + test SHELFICEuseGammaFrict = .TRUE.
875        + test SHELFICEadvDiffHeatFlux = .TRUE.
876    o model/src:
877      - fix bug (Thanks to Matt) in function SW_TEMP (to convert Pot.Temp to
878        in-situ Temp) and in routine SW_TEMP (in pkg/openad);
879        update output of experiments global_with_exf.yearly and isomip (all 6).
880    o pkg/shelfice:
881      - change setting of kTopC to also be zero where there is no ice-shelf.
882      - zero out surface forcing arrays (for now, for T & S + EmPmR) where
883        ice-shelf is.
884      - first attempt to get RealFreshWaterFlux effects: for now, only without
885        SHELFICEboundaryLayer ; not consistent if using synchronous time-stepping.
886    o pkg/seaice: add the option to prescribe a fixed thickness PDF
887      for thermodynamic calculations
888      - because of divisions of the type 7/7 not exactly equal to 1, this change
889        affects results of some verification experiments by up to 4 digits:
890        global_ocean.cs32x15.seaice, lab_sea, lab_sea.fd, lab_sea.salt_plume,
891        seaice_obcs, seaice_obcs.seaiceSponge, seaice_obcs.tides
892        adjoint: lab_sea, lab_sea.noseaicedyn
893        -> updated
894    
895    checkpoint65i (2015/01/23)
896    o model/src:
897      - change units of frictionHeating field from W to W/m^2
898      - fix bug in frictional heating from stratospheric drag in
899        S/R ATM_PHYS_TENDENCY_APPLY_V
900      - with synchronous time-stepping: move resetting to zero of frictionHeating
901        field from load_fields_driver.F to thermodynamics.F ;
902      - add diagnostics for frictional heating.
903    o model/src & gmredi K3D:
904      - add frictionHeating field to pickup-files (for synchronous time-stepping)
905      - move ALLOW_EDDYPSI block out of DYNVARS.h and merge it into FFIELDS.h
906      - rename uMean,vMean --> uEulerMean,vEulerMean (+ change diagnostics name
907        and name in pickup file).
908      - fix arguments of few DIAGNOSTICS_FILL calls in gmredi_k3d.F
909    o model/src:
910      - move (from ini_forcing.F) initialisation of all arrays in header file
911        FFIELDS.h into new S/R ini_ffields.F ; this fix broken restart
912        (since Nov 2012) with option selectAddFluid=1.
913    o pkg/shelfice:
914      - change units (+ document) of newly added field "shelfIceMassDynTendency"
915      - upgrade from _RS to _RL shelficeMass & shelficeLoadAnomaly arrays.
916    o pkg/obcs: re-organize obcs_calc_stevens.F to prepare for passive tracers
917    o pkg/seaice: two new runtime parameters:
918      - SEAICE_cStar replaces the hard wired "20" in the strength formulation,
919        long overdue
920      - SEAICE_tensilFac: preparation for Koenig-Beatty+Holland (2012)
921        parameterization of tensil stress for fast ice (does not do anything yet)
922    o pkg/seaice/seaice_check.F: left over from restricted addtive Schwarz method
923        for LSR: move checking overlaps out of JFNK-if-block
924    o pkg/atm_phys:
925      - move copy of grid and dynamical fields out of atm_phys_driver.F into
926        new S/R ATM_PHYS_DYN2PHYS.
927      - fix level height for Linear Free-Surf case (to be consistent with
928        fixed-in-time pressure levels).
929    o pkg/mom_common (bottomdrag):
930      - average bottomDragFld (ALLOW_BOTTOMDRAG_CONTROL) from grid-cell center
931        to correct location (U & V point) in S/R MOM_U/V_BOTTOMDRAG;
932        update output (adm & tlm) of experiment global_ocean.90x40x15.bottomdrag.
933    o pkg/shelfice (u/v_drag):
934      - add one argument (the other velocity component) to S/R SHELFICE_U/V_DRAG;
935      - use SHELFICEDragLinear & SHELFICEDragQuadratic in shelfice_v_drag.F
936        (now similar to shelfice_u_drag.F)
937      - remove condition on bottomDragTerms when calling SHELFICE_U/V_DRAG
938        from mom_vecinv.F (similar to mom_fluxform calls).
939    o pkg/mom_common (bottomdrag):
940      - add one argument (the other velocity component) to S/R MOM_U/V_BOTTOMDRAG;
941      - add options for alternative discretisation of velocity norm in quadratic
942        bottom drag: averaging of grid-cell-center KE to U.point and V.point
943        (selectBotDragQuadr=0, original code) can produce noisy patterns; this
944        improves when averaging only the other component (e.g. vVel for U bottom
945        drag) using wet-point method (selectBotDragQuadr=2) or not (=1).
946      - add options (bottomVisc_pCell) to account for partial-cell in bottom
947        friction (no-slip BC) thus getting the true distance from the bottom;
948        off by default since this also reduces model stability (explicit bottom
949        friction). Changes produce different machine truncation with linear-drag
950        + no-slip BC: update output of experiments exp4.stevens (10 digits) and
951        front_relax (bvp & mxl, 10 & 11 digits).
952    o model/src & mom pkgs:
953      - add one more level to vertical viscosity local arrays (Nr+1, previously Nr)
954        since no-slip bottom BC uses viscosity @ k+1 to update velocity @ level k
955      - for now and until vertical mixing scheme are updated to fill up level Nr+1,
956        just copy level Nr value to level Nr+1.
957    o doc:
958      - add notes form Abhisek Chakraborty on how to close Heat & Salt budgets.
959    o pkg/shelfice:
960      - shelfice_init_varia.F, shelfice_init_fixed.F, shelfice_readparms.F,
961        SHELFICE.h: move array shelficemass to init_varia, initialise
962        from array shelficemassinit, which is set in init_fixed and
963        has option to be set from file; introduce array
964        shelficeMassDynTend array, set thru file in init_fixed
965      - NEW FILE: shelfice_step_icemass.F: update shelficemass from either
966        shelfIceFreshWaterFlux and shelficeMassDynTend or H_streamice in
967        pkg/streamice
968      - shelfice_thermodynamics.F: call shelfice_step_icemass if
969        SHELFICEMassStepping = .true.
970      - shelfice_ad_diff.list: add new subroutine shelfice_step_icemass.f
971    
972  checkpoint65h (2014/12/17)  checkpoint65h (2014/12/17)
973  o verification/global_ocean.90x40x15, global_ocean_ebm:  o verification/global_ocean.90x40x15, global_ocean_ebm:
974    - update to generic controls.    - update to generic controls.

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