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-revision 1.2281 by mlosch,
Mon Nov 28 15:53:11 2016 UTC
+revision 1.2350 by jmc,
Tue Aug 22 03:02:30 2017 UTC
 Line 4 
 $Name$
      Notes on tags used in MITgcmUV
      ==============================
+ o model/src:
+   - move k loop inside correction_step.F (+ update calling S/R)
+   - collect implicit pressure gradient tendencies in local 2-D array;
+     affect results (at machine truncation level) when using 3-D solver; update
+     output of exp.: exp4 (x1), global_ocean.cs32x15 (x2),hs94.cs-32x32x5.impIGW,
+                     rotating_tank, short_surf_wave,tutorial_deep_convection (x2)
+                     & tutorial_plume_on_slope.
+ checkpoint66j (2017/08/15)
+ o pkg/ptracers:
+   - fix surface forcing under ice-shelf (useShelfIce=T).
+ o pkg/atm_phys:
+   - use hFac weighted average when applying A-grid atm-phys momentum tendency
+     to C-grid dynamics; this ensures wind-stress match mom tendency.
+ o eesupp/src:
+   - change default for opening scratch files to avoid STATUS='SCRATCH'
+   - close scratch files with STATUS='DELETE'
+   - changes affect eeset_parms.F and open_copy_data_file.F and many routines
+     that read namelists (because they close the scratch files)
+   - you can revert to old default by setting USE_FORTRAN_SCRATCH_FILES
+     in CPP_EEOPTIONS.h (tested in ideal_2D_oce/code & lab_sea/code_ad)
+ o pkg/atm_phys:
+   - fix unset arguments in (unused) S/R surface_flux_0d.
+ o eesupp/src:
+   - add argument "procId" to S/R EESET_PARMS to fix  scratchFile1 & 2 setting
+     (case TARGET_BGL or TARGET_CRAYXT) for early call (from eeboot_minimal.F):
+     called with myProcId in eeboot.F and with mpiMyWId in eeboot_minimal.F
+ o pkg/streamice:
+   - remove blank between _EXCH_XY_RL and "()", which my Apple Xcode
+     preprocessor /usr/bin/cpp cannot interpret; 3 instances in total in
+     streamice_driving_stress_fd.F and streamice_advect_2dtracer.F
+ o pkg/diagnostics:
+   - new option to allow to cumulate thickness-factor (hFac) weighted field
+     (if field permitted); implemented by changing sign of "jdiag" pointer
+     (> 0: cumlulate field, < 0: cumulate hFac weighted field).
+     a) restricted to 3-d (Nr levels), level centered diagnostics at U,V or Cell
+        center position (gcode(2)='U','V','M' & gcode(3,5,9:10)='R',' ','MR')
+     b) for now, activated by setting fileFlags 3rd character to 'h'.
+ checkpoint66i (2017/07/18)
+ o pkg/cheapaml:
+   - add parameter "useRelativeWind", default set to False; this change the
+     previous setting which was always using relative wind.
+ o add hooks for the Parallel Data Assimilation Framework PDAF
+     (http://pdaf.awi.de/) in eeboot_minimal.F and the_main_loop.F;
+     to use set CPP-flag USE_PDAF in CPP_EEOPTIONS.h
+ o pkg/exf:
+   - interpolation of vector fields (exf_interp_uv.F): fix bug in calculation
+     of South-Pole mean value.
+   - interpolation near the poles, case where second additional row is at the
+     pole (or beyond the pole and moved to the pole): change first addition row
+     value to a linear interpolation between pole and 1rst (S.pole)/last (N.pole)
+     row (instead of just a copy of it).
+ o pkg/seaice:
+   - prevent JFNK and KRYLOV solvers from trying to reduce a residual of 0
+   - add the option to compute no-slip du/dy, dv/dx (i.e.
+     the offdiagonal strain rate e12) by a second order approximation
+     on the boundary; works only with JFNK, KRYLOV, or EVP solvers, because
+     it is too messy to implement for the implicit LSR matrix.
+     SEAICE_2ndOrderBC = .FALSE. by default
+ checkpoint66h (2017/06/02)
+ o pkg/seaice:
+   - add new routines to compute stress tensor components and stress tensor
+     divergence to be reused in s/r seaice_lsr and s/r seaice_calc_lhs
+   - change names of diagnostics SIsigI/II (commonly used for invariants)
+     to SIsig1/sig2 (more common for principal components) to avoid confusion
+ o pkf/exf:
+   - add a stop if useRelativeWind with un-updated uwind/vwind (e.g., constant);
+     similarly, stop if rotateStressOnAgrid with constant wind-stress.
+ o pkg/seaice:
+   - remove (comment out) diagnostics SIuwind,SIvwind,SIfu,SIfv (duplicate of
+     EXFuwind,EXFvwind,oceTAUX,oceTAUY) and point them to their equivalent.
+   - add diagnostics of wind-stress over seaice (SItaux,SItauy) and seaice
+     fraction weighted wind stress over ocean+seaice (SIatmTx,SIatmTy).
+ o pkg/diagnostics:
+   - small piece of code to rename (old) diagnostics, when namelist is processed.
+ o model/src:
+   - new run-time param (useMin4hFacEdges) to select method for setting hFacW,S:
+     originally, set as minimum of adjacent hFacC factor ; now (new default)
+     computed from rSurfW,S and rLowW,S by applying same rules as for hFacC.
+     Only matters when useShelfIce=T with particular ice-shelf cavity geometry.
+ o pkg/seaice:
+   - add momemtum advection, off by default, still in test phase
+     most of the momentum advection code is adapted and reused from mom_vecinv
+ o pkg/mom_vecinv:
+   - pass these runtime flags:
+     selectVortScheme, highOrderVorticity, upwindVorticity, useJamartMomAdv
+     as formal parameters to s/r mom_vi_u/v_coriolis, mom_vi_u/v_coriolis_c4,
+     so that these routines can also be used in pkg/seaice.
+ checkpoint66g (2017/04/24)
+ o model/src:
+   - more robust ordering of column thickness integral (=Sum_k(drF*hFac) )
+     to get same expression (regarding machine truncation) in different places
+     in ini_masks_etc.F (e.g., rSurfC,W,S is now exactly zero when it should).
+     Update forward output of experiments: global_ocean.cs32x15 (all 5 except
+     viscA4), isomip (x3), tutorial_global_oce_in_p & tutorial_plume_on_slope.
+ o pkg/shelfice:
+   - ALLOW_SHIFWFLX_CONTROL: move setting of maskSHI from shelfice_update_masks.F
+     to shelfice_init_fixed.F
+   - change S/R SHELFICE_UPDATE_MASKS to SHELFICE_INIT_DEPTHS (still called from
+     ini_masks_etc.F for now) to update ocean upper boundary position according
+     to ice-shelf topography (instead of directly updating hFacC).
+ o model/src:
+   - move call to CTRL_INIT & CTRL_ADMTLM from the middle to the bottom of
+     packages_init_fixed.F to allow other pkgs to set mask and weight fields.
+ checkpoint66f (2017/04/06)
+ o model/src:
+   - add specific run-time param to select level of printed plot-field-maps,
+     set by default to debugLevel. Remove internal param "printDomain".
+ o pkg/seaice:
+   - add flag to add snow mass to seaiceMassC/U/V, the default is
+     SEAICEaddSnowMass=.FALSE., not to change previous results
+ o pkg/bling
+   - Bug fix in bling_production regarding unit conversion for diagnostics
+     being put in the wrong place
+ o model/src:
+   - add back recomputation of rSurfW & S to ensure consistent column thickness
+     (needed for rStar) between Sum_k(hFac*drF) and rSurf-rLow, for now only
+     when using pkg/shelfice; was initially added on 2012/06/01 (ini_masks_etc.F
+     revision 1.51) but was removed accidentally on 2014/02/08 (v1.53).
+ o pkg/autodiff:
+   - clean-up "checkpoint.flow"
+ o pkg/rw (Contribution from Jody Klymak):
+     option to set mds file suffix as function of time in simulation:
+     *) new input parameter "rwSuffixType" (read from PARM03 namelist)
+        to select file suffix format; by default (=0), use iteration number;
+     *) add simple routine to return file suffix according to rwSuffixType;
+     *) in model/src and in most pkgs (except: atm2d, fizhi, regrid & streamice),
+        use new S/R to get file suffix, except for debug output file (diagFreq)
+        and pkgs offline & rbcs input files.
+ o pkg/rw:
+   - uniform processing of "I10" suffix across writing fld routines; used to
+     simplify debug writing of cg2/3d_b/x in solve_for_pressure.F & post_cg3d.F
+     (similar to cg3d.F, cg3d_ex0.F)
+ o pkg/mom_vecinv:
+   - highOrderVorticity in selectVortScheme=2 case: fix c4 coeff in splitted
+     vorticity flux (keep same sum in case vBarXm=vBaXp, uBarYm=uBarYp).
+ o pkg/bling:
+   - Many small changes intended to clean the code.
+     Unnecessary ADJOINT_SAFEs removed ;
+     removed BLING_COST.h BLING_CTRL.h bling_cost.F ;
+     diagnostics added.
+ checkpoint66e (2017/03/14)
+ o pkg/exf:
+   - interpolation with #undef EXF_INTERP_USE_DYNALLOC: move buffer size
+     definition outside EXF_PARAM.h in new header file: EXF_INTERP_SIZE.h;
+     use fixed size buffer (passed to S/R EXF_INTERP & EXF_INTERP_UV) to
+     avoid any dynamic allocation ;
+   - S/R EXF_CHECK: add new check & stop when file-name is defined but not
+     read-in ; add warning when file is read-in but not used within pkg/exf ;
+     + check for buffer-size (if #undef EXF_INTERP_USE_DYNALLOC).
+   - update exf_summary.F (print {FLD}RepCycle).
+ o verification/global_with_exf:
+   - switch on exf interpolation in AD test (just like the forward test)
+ o pkg/mom_vecinv:
+   - add storage directives to avoid recomputations within mom_vecinv.F
+     which were generating seg. fault with gfortran -devel
+ o pkg/ctrl, pkg/smooth:
+   - initialize array halos which were generating seg. fault with
+     gfortran -devel in adjoint mode
+ o pkg/exf:
+   - for each input field, enable to specify a field specific repeat-cycle
+     ({FLD}RepCycle) which defaults to pkg/exf main "repeatPeriod".
+ o verification/lab_sea:
+   - update AD results of primary test and noseaicedyn test after switching
+     to new version of TAF (5.3.13 vs 5.3.2 before); agreement with gradient
+     check stays about the same.
+ o pkg/exf:
+   - fix bug in exf_zenithangle.F for cases select_ZenAlbedo > 0 with useCAL=T.
+   - exf_check: MAX_LAT_INC need only be "loc_nlat-1", not equal to loc_nlat
+ o pkg/bling, USE_EXFCO2 code:
+   - add parameter "apco2RepCycle" (set to pkg/exf "repeatPeriod" by default);
+   - update calls to EXF S/R (use new version: EXF_INIT_FLD & EXF_SET_FLD).
+ o pkg/exf:
+   - rename S/R EXF_INIT to EXF_INIT_VARIA ;
+   - add arguments: fldName (for debug msg) and fldRepeatCycle (set to
+     repeatPeriod) to S/R EXF_SET_UV and to S/R EXF_SET_GEN (renamed EXF_SET_FLD)
+     and update calls in pkg/exf calling S/R (exf_getffields.F & exf_getclim.F) ;
+   - add argument: fldName (for debug msg) to S/R EXF_INIT_GEN (renamed
+     EXF_INIT_FLD) and update calls in exf_init_varia.F
+   - For now, for backward compatibility, keep a simplified version of S/Rs
+     EXF_SET_GEN & EXF_INIT_GEN in file exf_set_gen.F
+   - add and pass new arguments: fldName (for debug msg) and fldRepeatCycle
+     to S/R EXF_GetFFieldRec ; update calls in pkg/obcs/obcs_exf_load.F
+ o tools/genmake2:
+   - replace "bc -l" (only used once) by "expr" (already used).
+ o verification/global_ocean.cs32x15:
+   - turn off pkg/cal (useCAL=F) in secondary FWD exp. "icedyn".
+     Note: exf setting (data.exf) can be compared to other exf secondary exp
+     "seaice" (kept with useCAL=T) which has same time dependent forcing.
+ checkpoint66d (2017/02/13)
+ o pkg/exf:
+   - remove setting of useCAL=T when using pkg/exf (useEXF=T); add warning
+     early on (in packages_boot.F) to stress this change in pkg setting.
+   - In (most) verification exp. that use pkg/exf, add useCAL=.TRUE. to data.pkg
+ o model/src:
+   - move call to ecco_phys to end of time step; this may induce minor
+     cost function changes by shifting time averages by one time step
+     for some variables; this revision resulted in changed adjoint results
+     in MITgcm_contrib/verification_other/global_oce_cs32
+ o pkg/exf:
+   - Change EXF_READ_EVAP to only activate code within #ifdef ALLOW_ATM_TEMP ;
+     this prevents to read evap when ALLOW_ATM_TEMP is undef and other fields,
+     e.g. precip, are not available.
+ o pkg/flt:
+   - flt_init_varia.F: use pickupSuff if specified
+   - add code (within #ifdef DEVEL_FLT_EXCH2) and test case as a first,
+     intermediate, step towards completing pkg/exch2 support within pkg/flt;
+     ifdef DEVEL_FLT_EXCH2 then:
+     - flt_init_fixed.F: comment out stop
+     - flt_exch2.F: conserve ipart, jpart (grid coordinates)
+     - exch2_recv_get_vec.F: transform ipart, jpart (grid coordinates)
+     - flt_mapping.F: attempt to fix longitude diagnostic near date-line
+     - flt_init_varia.F: hack initialization (for testing purposes w. LLC90)
+ o tools/genmake2 & pkg/pkg_depend:
+   - define new type of pkg dependency rule ("=pkg_x"), less strict than
+     the "+" rule, that add the dependent pkg (pkg_x) unless it's disabled
+     (-pkg_x in packages.conf).
+   - change pkg/exf dependency rule from "exf +cal" to "exf =cal";
+   - add "+cal" to dependency list of pkg/ecco (needed to compile).
+   - simplify FWD experiment "offline_exf_seaice" by removing pkg/cal.
+ o utils/matlab:
+   - adding ocean_basin routines for defining basin masks.
+ o pkg/exf:
+   - new S/R EXF_GETFFIELD_START replacing EXF_GETFIELD_START, but with more
+     arguments, allowing to check (and stop) if parameter setting of
+      {FLD}startdate1 & date2 and of {FLD}StartTime are consistent with
+     useCAL= T or F. For now, kept a simplified version of EXF_GETFIELD_START
+     for backward compatibility.
+   - change accordingly calls in exf_init_fixed.F + default {FLD}StartTime in
+     exf_readparms.F ; apply same changes to pkg/icefront (for SGRunOff field).
+ o pkg/bling (USE_EXFCO2 code):
+   - fix missing setting of apco2StartTime according to apco2startdate1 & date2
+     by adding a call to S/R EXF_GETFFIELD_START.
+ o pkg/exf:
+   - allows to compile without pkg/cal (but disabled by current dependency
+     rules, i.e., default "pkg/pkg_depend"). Minimal changes to enable to
+     run with useCAL=F ; this involves setting directly {FLD}StartTime instead
+     of {FLD}startdate1 & date2 ; consistency check not yet coded.
+ o verification/global_ocean.cs32x15:
+   - fix all data.exf for a shift of 1 day in all field startdate1 so that it now
+     corresponds to middle of 1rst month; update outputs (2 fwd + 3 adm + 3 tlm).
+ o pkg/exf:
+   - allow to use EXF_ZENITHANGLE without pkg/cal + simplify (saving some
+     calculations); change FWD experiment global_ocean.cs32x15
+     (#define ALLOW_ZENITHANGLE) to test/check that this code compiles.
+ o pkg/exf:
+   - In preparation for addition to NAMELIST, rename internal (_RL) parameter
+      {FIELD}startdate to {FIELD}StartTime
+     Note: new name also fit better the content, i.e, a start time in second.
+ o eesupp/src:
+   - add 1 argument to S/R EEBOOT & EEBOOT_MINIMAL for interface with ESMF
+ o pkg/exf:
+   - add option ALLOW_READ_TURBFLUXES (and corresponding set of parameters)
+     to allow to read-in Sensible & Latent Heat flux ;
+   - simplify pkg/exf main options:
+) move small piece of code (case ALLOW_ATM_TEMP undef) out of
+        exf_bulkformulae.F into exf_wind.F so that exf_bulkformulae.F is
+        compiled only when both ALLOW_ATM_TEMP & ALLOW_BULKFORMULAE are defined;
+) make call to EXF_RADIATION and to EXF_WIND independent of CPP option
+        ALLOW_BULKFORMULAE which now only applies to S/R EXF_BULKFORMULAE ;
+) improve options documentation in EXF_OPTIONS.h.
+ o pkg/ecco:
+   - cost_gencost_customize.F,ecco.h,ecco_phys.F,ecco_readparms.F, and
+     ecco_summary.F: add passive tracer cost functions to gencost;
+     m_ptracer and m_boxmean_ptracer
+ o pkg/ctrl:
+   - ctrl_map_forcing.F: pass myIter and myTime to ctrl_map_forcing as input
+     parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing; add to list
+     of implemented gentim2d contol parameters: xx_qnet, xx_empmr, xx_qsw,
+     xx_sst, xx_sss, xx_pload, xx_saltflux, xx_fu, xx_fv, xx_fe, xx_fn
+ o model/src:
+   - forward_step.F: pass myIter and myTime to ctrl_map_forcing as input
+     parameters; move myIter .EQ. nIter0 inside ctrl_map_forcing
+ o pkg/exf:
+   - exf_getffields.F: add to list of implemented gentim2d contol parameters:
+     xx_lwflux, xx_swflux, xx_evap, xx_apressure, xx_areamask
+ checkpoint66c (2017/01/19)
+ o verification:
+   - add new option "-src" to testreport to only produce source code (*.f),
+     including taf output src code (if using '-adm'/'-tlm' option).
+ o pkg/exf:
+   - add saltflx :: Net upward salt flux in psu.kg/m^2/s
+ o pkg/diagnostics:
+   - add run-time variable diagMdsDir to specify a subdirectory for
+     diagnostic output when mds is being used and mdsioLocalDir is not.
+ o pkg/mnc:
+   - mnc_utils.F: edit stop message
+ o pkg/autodiff:
+   - autodiff_ini_model_io.F: PRINT_MESSAGE, clean-up comments, add _*_MASTER,
+     add HAVE_SYSTEM bracket around system call to mkdir
+ o pkg/profiles:
+   - profiles_findunit.F, profiles_init_fixed.F, profiles_interp.F,
+     profiles_readparms.F: call ALL_PROC_DIE before 'stop'
+   - profiles_ini_io.F: use PRINT_MESSAGE, clean-up comments, add _*_MASTER,
+     add HAVE_SYSTEM bracket around system call to mkdir
+ o pkg/smooth:
+   - smooth_filtervar2d.F, smooth_filtervar3d.F: call ALL_PROC_DIE before 'stop'
+   - smooth_init2d.F, smooth_init3d.F: move print statements to readparms
+   - smooth_readparms.F: add cleaner print statements from smooth_init?d.F
+ o pkg/exf:
+   - check: count errors and stop cleanly at the end (call to ALL_PROC_DIE);
+     issue error message when climsst_interpMethod.GT.0 and climsst_lon_inc > 500
+     generalize tests on interpMethod, nlat, and lon_inc to all exf variables.
+   - summary: skip detailed field report if not used (empty file-name).
+ o tools/xmakedepend:
+   - In case line editor "ed" is missing, switch to "sed" command to clean-up
+     Makefile from previous dependencies (anything after "# DO NOT DELETE" line).
+ o pkg/exf:
+   - change definition of "hflux" input file to always include Short-Wave;
+     this is now consistent with hflux computation (if using bulk-formulae)
+     and hflux diagnostic & documentation (in EXF_FIELDS.h).
+ checkpoint66b (2016/12/01)
+ o model & momentum pkgs:
+   - implement fully implicit bottom friction combined with implicit surf.
+     pressure, for now, only in hydrostic formulation:
+     + to use: compile with #define ALLOW_SOLVE4_PS_AND_DRAG in CPP_OPTIONS.h
+       and run with selectImplicitDrag=2 ;
+     + currently missing diagnostics of bottom drag and vert. viscosity tendency;
+   - partial implicit time-stepping (bot. friction + vert. visc first, then
+     surf. press) corresponding to selectImplicitDrag=1 should be applicable
+     to NH formulation but not available until we solve for surf. pressure
+     increment (instead of full etaN).
+   - change exp. global_ocean.cs32x15.thsice to test implicit bottom drag
+     with implicit vertical viscosity.
  o pkg/seaice: add linear remapping scheme (Lipscomb 2001) to ITD model
    - this is a first version that includes many regularisations that may
      not all be necessary, to be sorted out,
    - turned on by runtime parameter SEAICEuseLinRemapITD (true by default)
    - change one verification experiment in seaice_itd to use and test new code
    - seaice_growth: catch a case where the argument of log can be zero
      or smaller (important for code stability)
  o model/src:
    - modify SOLVE_DIAGONAL_LOWMEMORY version of solve_tridiagonal.F

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