--- MITgcm/doc/tag-index	2013/06/18 21:30:33	1.1881
+++ MITgcm/doc/tag-index	2013/07/26 14:25:21	1.1902
@@ -1,9 +1,105 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1881 2013/06/18 21:30:33 m_bates Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1902 2013/07/26 14:25:21 jmc Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o model/src:
+  - extend length of drC & recip_drC from Nr to Nr+1.
+o Divided Adjoint (DIVA) with MPI:
+  - genmake2: do not create local ./mpi_headers dir when no file to copy into.
+  - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
+    and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
+
+checkpoint64k (2013/07/23)
+o tools/OAD_support:
+  - avoid the need for file "oadtempflile" in insertTemplateDir.bash
+    and remove it from genmake2.
+o tools/build_options:
+  - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
+    MPI_HEADER_FILES list (let genmake2 find the missing headers)
+o verification/halfpipe_streamice:
+  - change to driving stress formulation; update both Fwd & AD output.
+o tools/genmake2 and Divided Adjoint with MPI:
+  - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
+  - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
+  - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
+    Makefile, which is set by genmake2, and check which mpi-headers are needed.
+    Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
+  - update target "CLEAN" (to also remove ./mpi_headers/ dir).
+o testreport:
+  - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
+    perform additional runs (number of additional runs is "add_DIVA_runs" taken
+    from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
+o verification/lab_sea (AD test):
+  - change to test Divided Adjoint Run in this set-up (both standard AD test
+    and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
+o pkg atm_ & ocn_compon_interf:
+  - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
+    staggerTimeStep implementation) and disable (retired) corresponding
+    parameter.
+o pkg/offline:
+  - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
+  - add S/R OFFLINE_CHECK to print offline parameter summary
+    and stop if loading a file that is not used;
+  - enable to calculate GMRedi tensor, KPP mixing and convective index
+    when the corresponding file(s) is/are not specified (but pkg is used).
+  - comment out resetting of monitorFreq (to endTime) since it still useful
+    for monitoring CFL numbers and checking offline fields.
+o OpenAD:
+  - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
+    smaller standard output) and generate new (smaller) output (on baudelaire
+    using gfortran with -ieee) for exp. tutorial_tracer_adjsens
+o model/src:
+  - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
+    (where external_forcing_adjust was called) and change list of arguments;
+  - merge external_forcing_adjust.F into external_forcing_surf.F
+  - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
+    which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
+    previously in file "balance_relax.F", now removed); remove corresponding
+    arrays in FFIELDS.h.
+  - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
+    a hack for getting back surfaceForcingS (loaded from file) when using
+    ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
+  - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
+    (was getting only 11 digits for AD-grad, due to different truncation
+     error in AD code).
+
+checkpoint64j (2013/07/04)
+o pkg/offline:
+  - to enable the use of other features with pkg offline (e.g., obcs),
+    also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
+  - comment out "allowFreezing" (now active) in 2 offline testing exp.
+o pkg/exf ALLOW_RUNOFTEMP
+  - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
+  - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
+  - changes verification/global_ocean.cs32x15/results/output.seaice.txt
+o pkg/atm_phys:
+  - allows to add some damping on uVel,vVel (strength only function of k).
+o verification, ad-tests:
+  - reduce length of the simulation for AD test: global_ocean.cs32x15.seaice,
+    global_ocean_ebm and offline_exf_seaice.thsice.
+o verification/halfpipe_streamice:
+  - found a bug in s/r pkg/streamice/streamice_advect_thickness which caused
+    flux input boundary conditions to be ignored; a fix for this bug changed
+    verification results for forward test.
+  - add adjoint test.
+o pkg/ptracers:
+  - allow to restart without SOM pickup (resetting SOM to zero).
+o pkg/gmredi:
+  - New parameterisation for the calculation of K and (GM_PsiX,GM_PsiY) added.
+  - It uses mixing length theory and suppression by steering level effects to
+    calculate a diffusivity used in the Redi tensor (see Bates et al., submitted
+    to JPO, for more details).
+  - It also uses the diffusivity to calculate an eddy induced streamfunction
+    based on a PV closure (rather than a buoyancy closure as in GM).
+  - New files added to pkg/gmredi:
+    gmredi_k3d.F calculates the diffusivity for the Redi tensor and the eddy
+      induced overturning streamfunction (called from gmredi_calc_tensor)
+    gmredi_calc_eigs.F calculates the eigenvalues and eigenvectors required
+      for use in gmredi_k3d
+    gmredi_calc_urms.F calculates the the rms eddy velocity used to calculate
+      the eddy diffusivity
 
 checkpoint64i (2013/06/18)
 o pkg/cheapaml:
@@ -40,6 +136,9 @@
     atmospheric CFC ; fix for the case myIter < PTRACERS_iter0.
   - fix calculation of surf tendencys for partial-cell and/or Non-Lin Free-Surf
   - new routine to print summary of CFC params and check for consistency.
+o pkg/seaice: add uice/vice to the parameter list of s/r seaice_advdiff,
+  similar to thsice_advdiff.
+  Note that for the B-grid case the routine parameters uc/vc are overwritten.
 o pkg/cfc:
   - change time interpolation for atmospheric CFC-11 (now same as for CFC-12);
     update output (CFC-11) of experiment cfc_example and tutorial_cfc_offline.