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revision 1.1881 by m_bates, Tue Jun 18 21:30:33 2013 UTC revision 1.1908 by jmc, Fri Aug 9 14:14:05 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 switch to TAF version-2:
8      - add flow directives to "freeze" naming convention for ad-routines that
9        are used in I/O routines of adjoint state and associated common blocks
10        that are used in adcommon.h (backward compatible with version-1)
11      - update all ad-optfiles (in tools/adjoint_options + few local to some
12        verification exp) to switch to latest TAF version (currently 2.5.5);
13        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
14        out except for diva).
15      - the major change with TAF version-2 is that both the differentiated
16        routines and the forward routines (new) are returned as part of the TAF
17        output source code. Update genmake2 accordingly.
18      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
19        with version-2 when compared to TLM or FWD gradient); other experiments
20        output show minor changes (machine truncation level); update the few AD &
21        TLM output with 12 matching digits only (some prior to version-2 switch).
22    
23    checkpoint64l (2013/08/05)
24    o model/src:
25      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
26      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
27        when using TAF but only if using OpenAD.
28    o pkg/mom_common+fluxform+vecinv:
29      - always set horiz. viscosity arrays to background value before calling
30        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
31        only when using variable horiz. viscosity (useVariableVisc=T);
32      - simplify mom_vecinv.F (only 1 block for momViscosity).
33    o pkg/mom_common: variable horiz. viscosity in NH code
34      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
35        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
36      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
37        useBiharmonicVisc & useVariableVisc.
38      - fix old bug (already in 1rst implementation of variable horizontal viscosity
39        in calc_gw.F, version 1.27, 2006/06/20):
40        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
41        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
42      - change background horiz viscosity in vertical momentum (gW) to always be
43        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
44        any type of variable viscosity, e.g., viscAh/4Grid)
45      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
46        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
47        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
48        default viscAh,viscA4 is zero).
49    o model/src:
50      - extend length of drC & recip_drC from Nr to Nr+1.
51    o Divided Adjoint (DIVA) with MPI:
52      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
53      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
54        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
55    
56    checkpoint64k (2013/07/23)
57    o tools/OAD_support:
58      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
59        and remove it from genmake2.
60    o tools/build_options:
61      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
62        MPI_HEADER_FILES list (let genmake2 find the missing headers)
63    o verification/halfpipe_streamice:
64      - change to driving stress formulation; update both Fwd & AD output.
65    o tools/genmake2 and Divided Adjoint with MPI:
66      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
67      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
68      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
69        Makefile, which is set by genmake2, and check which mpi-headers are needed.
70        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
71      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
72    o testreport:
73      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
74        perform additional runs (number of additional runs is "add_DIVA_runs" taken
75        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
76    o verification/lab_sea (AD test):
77      - change to test Divided Adjoint Run in this set-up (both standard AD test
78        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
79    o pkg atm_ & ocn_compon_interf:
80      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
81        staggerTimeStep implementation) and disable (retired) corresponding
82        parameter.
83    o pkg/offline:
84      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
85      - add S/R OFFLINE_CHECK to print offline parameter summary
86        and stop if loading a file that is not used;
87      - enable to calculate GMRedi tensor, KPP mixing and convective index
88        when the corresponding file(s) is/are not specified (but pkg is used).
89      - comment out resetting of monitorFreq (to endTime) since it still useful
90        for monitoring CFL numbers and checking offline fields.
91    o OpenAD:
92      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
93        smaller standard output) and generate new (smaller) output (on baudelaire
94        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
95    o model/src:
96      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
97        (where external_forcing_adjust was called) and change list of arguments;
98      - merge external_forcing_adjust.F into external_forcing_surf.F
99      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
100        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
101        previously in file "balance_relax.F", now removed); remove corresponding
102        arrays in FFIELDS.h.
103      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
104        a hack for getting back surfaceForcingS (loaded from file) when using
105        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
106      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
107        (was getting only 11 digits for AD-grad, due to different truncation
108         error in AD code).
109    
110    checkpoint64j (2013/07/04)
111    o pkg/offline:
112      - to enable the use of other features with pkg offline (e.g., obcs),
113        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
114      - comment out "allowFreezing" (now active) in 2 offline testing exp.
115    o pkg/exf ALLOW_RUNOFTEMP
116      - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
117      - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
118      - changes verification/global_ocean.cs32x15/results/output.seaice.txt
119    o pkg/atm_phys:
120      - allows to add some damping on uVel,vVel (strength only function of k).
121    o verification, ad-tests:
122      - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
123        global_ocean_ebm and offline_exf_seaice.thsice.
124    o verification/halfpipe_streamice:
125      - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
126        flux input boundary conditions to be ignored; a fix for this bug changed
127        verification results for forward test.
128      - add adjoint test.
129    o pkg/ptracers:
130      - allow to restart without SOM pickup (resetting SOM to zero).
131    o pkg/gmredi:
132      - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
133      - It uses mixing length theory and suppression by steering level effects to
134        calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
135        to JPO, for more details).
136      - It also uses the diffusivity to calculate an eddy induced streamfunction
137        based on a PV closure (rather than a buoyancy closure as in GM).
138      - New files added to pkg/gmredi:
139        gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
140          induced overturning streamfunction (called from gmredi_calc_tensor)
141        gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
142          for use in gmredi_k3d
143        gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
144          the eddy diffusivity
145    
146  checkpoint64i (2013/06/18)  checkpoint64i (2013/06/18)
147  o pkg/cheapaml:  o pkg/cheapaml:
# Line 40  o pkg/cfc: Line 178  o pkg/cfc:
178      atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.      atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
179    - 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
180    - new routine to print summary of CFC params and check for consistency.    - new routine to print summary of CFC params and check for consistency.
181    o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
182      similar to thsice_advdiff.
183      Note that for the B-grid case the routine parameters uc/vc are overwritten.
184  o pkg/cfc:  o pkg/cfc:
185    - 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);
186      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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