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revision 1.1880 by jmc, Tue Jun 18 13:33:34 2013 UTC revision 1.1912 by jmc, Wed Aug 14 21:16:35 2013 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/diagnostics:
8      - add a parameter to track the status of pkg/diagnostics activation;
9        this replace/extend the use of logical param "settingDiags" (to check
10        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
11        New S/R to print error message and stop when pkgStatus is not right.
12      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
13    
14    checkpoint64m (2013/08/13)
15    o model/inc:
16      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
17        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
18    o pkg/kpp & aim_v23:
19      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
20    o pkg/seaice:
21      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
22        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
23      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
24    o eesupp/src:
25      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
26        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
27    o switch to TAF version-2:
28      - add flow directives to "freeze" naming convention for ad-routines that
29        are used in I/O routines of adjoint state and associated common blocks
30        that are used in adcommon.h (backward compatible with version-1)
31      - update all ad-optfiles (in tools/adjoint_options + few local to some
32        verification exp) to switch to latest TAF version (currently 2.5.5);
33        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
34        out except for diva).
35      - the major change with TAF version-2 is that both the differentiated
36        routines and the forward routines (new) are returned as part of the TAF
37        output source code. Update genmake2 accordingly.
38      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
39        with version-2 when compared to TLM or FWD gradient); other experiments
40        output show minor changes (machine truncation level); update the few AD &
41        TLM output with 12 matching digits only (some prior to version-2 switch).
42    
43    checkpoint64l (2013/08/05)
44    o model/src:
45      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
46      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
47        when using TAF but only if using OpenAD.
48    o pkg/mom_common+fluxform+vecinv:
49      - always set horiz. viscosity arrays to background value before calling
50        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
51        only when using variable horiz. viscosity (useVariableVisc=T);
52      - simplify mom_vecinv.F (only 1 block for momViscosity).
53    o pkg/mom_common: variable horiz. viscosity in NH code
54      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
55        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
56      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
57        useBiharmonicVisc & useVariableVisc.
58      - fix old bug (already in 1rst implementation of variable horizontal viscosity
59        in calc_gw.F, version 1.27, 2006/06/20):
60        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
61        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
62      - change background horiz viscosity in vertical momentum (gW) to always be
63        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
64        any type of variable viscosity, e.g., viscAh/4Grid)
65      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
66        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
67        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
68        default viscAh,viscA4 is zero).
69    o model/src:
70      - extend length of drC & recip_drC from Nr to Nr+1.
71    o Divided Adjoint (DIVA) with MPI:
72      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
73      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
74        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
75    
76    checkpoint64k (2013/07/23)
77    o tools/OAD_support:
78      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
79        and remove it from genmake2.
80    o tools/build_options:
81      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
82        MPI_HEADER_FILES list (let genmake2 find the missing headers)
83    o verification/halfpipe_streamice:
84      - change to driving stress formulation; update both Fwd & AD output.
85    o tools/genmake2 and Divided Adjoint with MPI:
86      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
87      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
88      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
89        Makefile, which is set by genmake2, and check which mpi-headers are needed.
90        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
91      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
92    o testreport:
93      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
94        perform additional runs (number of additional runs is "add_DIVA_runs" taken
95        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
96    o verification/lab_sea (AD test):
97      - change to test Divided Adjoint Run in this set-up (both standard AD test
98        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
99    o pkg atm_ & ocn_compon_interf:
100      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
101        staggerTimeStep implementation) and disable (retired) corresponding
102        parameter.
103    o pkg/offline:
104      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
105      - add S/R OFFLINE_CHECK to print offline parameter summary
106        and stop if loading a file that is not used;
107      - enable to calculate GMRedi tensor, KPP mixing and convective index
108        when the corresponding file(s) is/are not specified (but pkg is used).
109      - comment out resetting of monitorFreq (to endTime) since it still useful
110        for monitoring CFL numbers and checking offline fields.
111    o OpenAD:
112      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
113        smaller standard output) and generate new (smaller) output (on baudelaire
114        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
115    o model/src:
116      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
117        (where external_forcing_adjust was called) and change list of arguments;
118      - merge external_forcing_adjust.F into external_forcing_surf.F
119      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
120        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
121        previously in file "balance_relax.F", now removed); remove corresponding
122        arrays in FFIELDS.h.
123      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
124        a hack for getting back surfaceForcingS (loaded from file) when using
125        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
126      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
127        (was getting only 11 digits for AD-grad, due to different truncation
128         error in AD code).
129    
130    checkpoint64j (2013/07/04)
131    o pkg/offline:
132      - to enable the use of other features with pkg offline (e.g., obcs),
133        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
134      - comment out "allowFreezing" (now active) in 2 offline testing exp.
135    o pkg/exf ALLOW_RUNOFTEMP
136      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
137      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
138      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
139    o pkg/atm_phys:
140      - allows to add some damping on uVel,vVel (strength only function of k).
141    o verification, ad-tests:
142      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
143        global_ocean_ebm and offline_exf_seaice.thsice.
144    o verification/halfpipe_streamice:
145      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
146        flux input boundary conditions to be ignored; a fix for this bug changed
147        verification results for forward test.
148      - add adjoint test.
149    o pkg/ptracers:
150      - allow to restart without SOM pickup (resetting SOM to zero).
151    o pkg/gmredi:
152      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
153      - It uses mixing length theory and suppression by steering level effects to
154        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
155        to JPO, for more details).
156      - It also uses the diffusivity to calculate an eddy induced streamfunction
157        based on a PV closure (rather than a buoyancy closure as in GM).
158      - New files added to pkg/gmredi:
159        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
160          induced overturning streamfunction (called from gmredi_calc_tensor)
161        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
162          for use in gmredi_k3d
163        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
164          the eddy diffusivity
165    
166  checkpoint64i (2013/06/18)  checkpoint64i (2013/06/18)
167  o pkg/cheapaml:  o pkg/cheapaml:
168    - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code    - take src files from MITgcm_contrib/verification_other/offline_cheapaml/code
# Line 39  o pkg/cfc: Line 198  o pkg/cfc:
198      atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.      atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
199    - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf    - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
200    - new routine to print summary of CFC params and check for consistency.    - new routine to print summary of CFC params and check for consistency.
201    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
202      similar to thsice_advdiff.
203      Note that for the B-grid case the routine parameters uc/vc are overwritten.
204  o pkg/cfc:  o pkg/cfc:
205    - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);    - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
206      update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.      update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.
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