[Dart-dev] [6256] DART/trunk: The development branch has been reintegrated onto the TRUNK in preparation for testing

[nancy at ucar.edu]

Revision: 6256
Author:   thoar
Date:     2013-06-12 10:19:10 -0600 (Wed, 12 Jun 2013)
Log Message:
-----------
The development branch has been reintegrated onto the TRUNK in preparation for testing
and eventual tagging as the 'L' release. The development branch is now officially DEAD.
Do not commit anything to it.

Modified Paths:
--------------
    DART/trunk/DART_LAB/matlab/advance_oned.m
    DART/trunk/DART_LAB/matlab/comp_cov_factor.m
    DART/trunk/DART_LAB/matlab/g_prod_plot.m
    DART/trunk/DART_LAB/matlab/gaussian_product.m
    DART/trunk/DART_LAB/matlab/get_ens_rank.m
    DART/trunk/DART_LAB/matlab/get_state_increments.m
    DART/trunk/DART_LAB/matlab/lorenz_63_adv_1step.m
    DART/trunk/DART_LAB/matlab/lorenz_63_static_init_model.m
    DART/trunk/DART_LAB/matlab/lorenz_96_adv_1step.m
    DART/trunk/DART_LAB/matlab/lorenz_96_static_init_model.m
    DART/trunk/DART_LAB/matlab/obs_increment_eakf.m
    DART/trunk/DART_LAB/matlab/obs_increment_enkf.m
    DART/trunk/DART_LAB/matlab/obs_increment_rhf.m
    DART/trunk/DART_LAB/matlab/oned_ensemble.m
    DART/trunk/DART_LAB/matlab/oned_model.m
    DART/trunk/DART_LAB/matlab/plot_gaussian.m
    DART/trunk/DART_LAB/matlab/plot_polar.m
    DART/trunk/DART_LAB/matlab/product_of_gaussians.m
    DART/trunk/DART_LAB/matlab/run_lorenz_63.m
    DART/trunk/DART_LAB/matlab/run_lorenz_96.m
    DART/trunk/DART_LAB/matlab/run_template.m
    DART/trunk/DART_LAB/matlab/twod_ensemble.m
    DART/trunk/README
    DART/trunk/adaptive_inflate/adaptive_inflate_mod.f90
    DART/trunk/adaptive_inflate/adaptive_inflate_mod.html
    DART/trunk/adaptive_inflate/fill_inflation_restart.f90
    DART/trunk/adaptive_inflate/fill_inflation_restart.html
    DART/trunk/assim_model/assim_model_mod.f90
    DART/trunk/assim_tools/assim_tools_mod.f90
    DART/trunk/assim_tools/assim_tools_mod.html
    DART/trunk/assim_tools/assim_tools_mod.nml
    DART/trunk/assim_tools/option7.m
    DART/trunk/common/types_mod.f90
    DART/trunk/cov_cutoff/cov_cutoff_mod.f90
    DART/trunk/diagnostics/matlab/PlotObsLocs.m
    DART/trunk/diagnostics/matlab/PlotWindObs.m
    DART/trunk/diagnostics/matlab/get_varnames.m
    DART/trunk/diagnostics/matlab/get_varsNdims.m
    DART/trunk/diagnostics/matlab/link_obs.m
    DART/trunk/diagnostics/matlab/linked_observations.m
    DART/trunk/diagnostics/matlab/nc_var_dims.m
    DART/trunk/diagnostics/matlab/obs_num_time.m
    DART/trunk/diagnostics/matlab/plot_bias_xxx_profile.m
    DART/trunk/diagnostics/matlab/plot_coverage.m
    DART/trunk/diagnostics/matlab/plot_evolution.m
    DART/trunk/diagnostics/matlab/plot_obs_netcdf.m
    DART/trunk/diagnostics/matlab/plot_obs_netcdf_diffs.m
    DART/trunk/diagnostics/matlab/plot_observation_locations.m
    DART/trunk/diagnostics/matlab/plot_profile.m
    DART/trunk/diagnostics/matlab/plot_rank_histogram.m
    DART/trunk/diagnostics/matlab/plot_rmse_xxx_evolution.m
    DART/trunk/diagnostics/matlab/plot_rmse_xxx_profile.m
    DART/trunk/diagnostics/matlab/plot_wind_vectors.m
    DART/trunk/diagnostics/matlab/read_obs_netcdf.m
    DART/trunk/diagnostics/matlab/two_experiments_evolution.m
    DART/trunk/diagnostics/matlab/two_experiments_profile.m
    DART/trunk/diagnostics/oned/obs_diag.f90
    DART/trunk/diagnostics/oned/obs_diag.html
    DART/trunk/diagnostics/oned/obs_diag.nml
    DART/trunk/diagnostics/rms_diag.f90
    DART/trunk/diagnostics/threed_sphere/obs_diag.f90
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    DART/trunk/diagnostics/threed_sphere/obs_diag.nml
    DART/trunk/doc/html/doc.css
    DART/trunk/doc/html/html_function.f90
    DART/trunk/doc/html/html_namelist.f90
    DART/trunk/doc/html/html_subroutine.f90
    DART/trunk/doc/mpi/ctest.c
    DART/trunk/doc/mpi/ctest_mpi.c
    DART/trunk/doc/mpi/ctest_nc.c
    DART/trunk/doc/mpi/ftest_f90.f90
    DART/trunk/doc/mpi/ftest_go.f90
    DART/trunk/doc/mpi/ftest_mpi.f90
    DART/trunk/doc/mpi/ftest_nc.f90
    DART/trunk/doc/mpi/ftest_stop.f90
    DART/trunk/ensemble_manager/ensemble_manager_mod.f90
    DART/trunk/ensemble_manager/ensemble_manager_mod.html
    DART/trunk/ensemble_manager/ensemble_manager_mod.nml
    DART/trunk/filter/filter.dopplerfold.f90
    DART/trunk/filter/filter.f90
    DART/trunk/filter/filter.html
    DART/trunk/filter/filter.nml
    DART/trunk/filter/wakeup_filter.f90
    DART/trunk/index.html
    DART/trunk/integrate_model/integrate_model.f90
    DART/trunk/location/README
    DART/trunk/location/annulus/location_mod.f90
    DART/trunk/location/annulus/test/mkmf_location_test
    DART/trunk/location/annulus/test/path_names_location_test
    DART/trunk/location/column/location_mod.f90
    DART/trunk/location/column/test/mkmf_location_test
    DART/trunk/location/column/test/path_names_location_test
    DART/trunk/location/location_test.f90
    DART/trunk/location/location_test2.f90
    DART/trunk/location/oned/location_mod.f90
    DART/trunk/location/oned/test/mkmf_location2_test
    DART/trunk/location/oned/test/mkmf_location_test
    DART/trunk/location/oned/test/path_names_location2_test
    DART/trunk/location/oned/test/path_names_location_test
    DART/trunk/location/testall.csh
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    DART/trunk/location/threed_sphere/location_mod.html
    DART/trunk/location/threed_sphere/test/mkmf_location_test
    DART/trunk/location/threed_sphere/test/path_names_location_test
    DART/trunk/location/twod/location_mod.f90
    DART/trunk/location/twod/test/mkmf_location_test
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    DART/trunk/location/twod_sphere/location_mod.f90
    DART/trunk/location/twod_sphere/test/mkmf_location_test
    DART/trunk/location/twod_sphere/test/path_names_location_test
    DART/trunk/matlab/CheckModel.m
    DART/trunk/matlab/CheckModelCompatibility.m
    DART/trunk/matlab/ChecknetCDFuse.m
    DART/trunk/matlab/CombineStructs.m
    DART/trunk/matlab/DART.m
    DART/trunk/matlab/DiffnetCDFstate.m
    DART/trunk/matlab/GetBgridInfo.m
    DART/trunk/matlab/GetCalendarDate.m
    DART/trunk/matlab/GetCamInfo.m
    DART/trunk/matlab/GetMITgcm_oceanInfo.m
    DART/trunk/matlab/GetNCindices.m
    DART/trunk/matlab/GetPe2lyrInfo.m
    DART/trunk/matlab/GetTIEGCMInfo.m
    DART/trunk/matlab/GetWRFInfo.m
    DART/trunk/matlab/ParseAlphaNumerics.m
    DART/trunk/matlab/PlotBins.m
    DART/trunk/matlab/PlotCEnsErrSpread.m
    DART/trunk/matlab/PlotCorrel.m
    DART/trunk/matlab/PlotEnsErrSpread.m
    DART/trunk/matlab/PlotEnsMeanTimeSeries.m
    DART/trunk/matlab/PlotEnsTimeSeries.m
    DART/trunk/matlab/PlotJeffCorrel.m
    DART/trunk/matlab/PlotPhaseSpace.m
    DART/trunk/matlab/PlotRegFactor.m
    DART/trunk/matlab/PlotSawtooth.m
    DART/trunk/matlab/PlotTotalErr.m
    DART/trunk/matlab/PlotVarVarCorrel.m
    DART/trunk/matlab/Plot_network.m
    DART/trunk/matlab/Plot_obs.m
    DART/trunk/matlab/ReadASCIIObsSeq.m
    DART/trunk/matlab/ReadBinaryObsSeq.m
    DART/trunk/matlab/ReadObsSeq.m
    DART/trunk/matlab/SetCopyID.m
    DART/trunk/matlab/SetCopyID2.m
    DART/trunk/matlab/SetVariableID.m
    DART/trunk/matlab/SimpleMap.m
    DART/trunk/matlab/StatObsSeq.m
    DART/trunk/matlab/dbz_colors.m
    DART/trunk/matlab/ens_correl.m
    DART/trunk/matlab/ens_plot.m
    DART/trunk/matlab/get_DARTvars.m
    DART/trunk/matlab/get_copy_index.m
    DART/trunk/matlab/get_ens_series.m
    DART/trunk/matlab/get_ens_size.m
    DART/trunk/matlab/get_qc_index.m
    DART/trunk/matlab/get_state_copy.m
    DART/trunk/matlab/get_var_series.m
    DART/trunk/matlab/jeff_correl.m
    DART/trunk/matlab/locations_in_region.m
    DART/trunk/matlab/parse.m
    DART/trunk/matlab/plot_bins.m
    DART/trunk/matlab/plot_correl.m
    DART/trunk/matlab/plot_ens_err_spread.m
    DART/trunk/matlab/plot_ens_mean_time_series.m
    DART/trunk/matlab/plot_ens_time_series.m
    DART/trunk/matlab/plot_jeff_correl.m
    DART/trunk/matlab/plot_phase_space.m
    DART/trunk/matlab/plot_reg_factor.m
    DART/trunk/matlab/plot_sawtooth.m
    DART/trunk/matlab/plot_smoother_err.m
    DART/trunk/matlab/plot_total_err.m
    DART/trunk/matlab/plot_var_var_correl.m
    DART/trunk/matlab/rank_hist.m
    DART/trunk/matlab/read_state.m
    DART/trunk/matlab/scalebar.m
    DART/trunk/matlab/startup.m
    DART/trunk/matlab/state_diag.m
    DART/trunk/matlab/total_err.m
    DART/trunk/matlab/worldmap.m
    DART/trunk/matlab/wysiwyg.m
    DART/trunk/mkmf/mkmf
    DART/trunk/mkmf/mkmf.html
    DART/trunk/mkmf/mkmf.template
    DART/trunk/mkmf/mkmf.template.absoft.osx
    DART/trunk/mkmf/mkmf.template.g95
    DART/trunk/mkmf/mkmf.template.gfortran
    DART/trunk/mkmf/mkmf.template.intel.linux
    DART/trunk/mkmf/mkmf.template.intel.osx
    DART/trunk/mkmf/mkmf.template.lahey.linux
    DART/trunk/mkmf/mkmf.template.pathscale.linux
    DART/trunk/mkmf/mkmf.template.pgi.cray
    DART/trunk/mkmf/mkmf.template.pgi.linux
    DART/trunk/mkmf/mkmf.template.pgi.osx
    DART/trunk/mkmf/mkmf.template.sgi.altix
    DART/trunk/mkmf/mkmf.template.xlf.aix
    DART/trunk/models/9var/matlab/RunAllTests.m
    DART/trunk/models/9var/model_mod.f90
    DART/trunk/models/9var/work/input.nml
    DART/trunk/models/9var/work/mkmf_create_fixed_network_seq
    DART/trunk/models/9var/work/mkmf_create_obs_sequence
    DART/trunk/models/9var/work/mkmf_filter
    DART/trunk/models/9var/work/mkmf_obs_diag
    DART/trunk/models/9var/work/mkmf_obs_sequence_tool
    DART/trunk/models/9var/work/mkmf_perfect_model_obs
    DART/trunk/models/9var/work/mkmf_preprocess
    DART/trunk/models/9var/work/mkmf_restart_file_tool
    DART/trunk/models/9var/work/mkmf_wakeup_filter
    DART/trunk/models/9var/work/path_names_create_fixed_network_seq
    DART/trunk/models/9var/work/path_names_create_obs_sequence
    DART/trunk/models/9var/work/path_names_filter
    DART/trunk/models/9var/work/path_names_obs_diag
    DART/trunk/models/9var/work/path_names_obs_sequence_tool
    DART/trunk/models/9var/work/path_names_perfect_model_obs
    DART/trunk/models/9var/work/path_names_preprocess
    DART/trunk/models/9var/work/path_names_restart_file_tool
    DART/trunk/models/9var/work/path_names_wakeup_filter
    DART/trunk/models/9var/work/quickbuild.csh
    DART/trunk/models/9var/work/workshop_setup.csh
    DART/trunk/models/MITgcm_annulus/model_mod.f90
    DART/trunk/models/MITgcm_annulus/shell_scripts/advance_model.csh
    DART/trunk/models/MITgcm_annulus/shell_scripts/byteswap.c
    DART/trunk/models/MITgcm_annulus/shell_scripts/coseq.pl
    DART/trunk/models/MITgcm_annulus/trans_MITgcm_to_dart.f90
    DART/trunk/models/MITgcm_annulus/trans_dart_to_MITgcm.f90
    DART/trunk/models/MITgcm_annulus/trans_perfect_ics.f90
    DART/trunk/models/MITgcm_annulus/work/input.nml
    DART/trunk/models/MITgcm_annulus/work/mkmf_MITgcm_to_dart
    DART/trunk/models/MITgcm_annulus/work/mkmf_create_fixed_network_seq
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    DART/trunk/models/MITgcm_annulus/work/mkmf_dart_to_MITgcm
    DART/trunk/models/MITgcm_annulus/work/mkmf_filter
    DART/trunk/models/MITgcm_annulus/work/mkmf_perfect_ics
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    DART/trunk/models/MITgcm_annulus/work/mkmf_preprocess
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    DART/trunk/models/MITgcm_annulus/work/path_names_perfect_model_obs
    DART/trunk/models/MITgcm_annulus/work/path_names_preprocess
    DART/trunk/models/MITgcm_annulus/work/path_names_restart_file_tool
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    DART/trunk/models/MITgcm_ocean/matlab/VerifyNetCDF.m
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    DART/trunk/models/MITgcm_ocean/work/path_names_restart_file_tool
    DART/trunk/models/MITgcm_ocean/work/path_names_trans_pv_sv
    DART/trunk/models/MITgcm_ocean/work/path_names_trans_sv_pv
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    DART/trunk/models/NCOMMAS/work/mkmf_preprocess
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    DART/trunk/models/NCOMMAS/work/path_names_dart_to_ncommas
    DART/trunk/models/NCOMMAS/work/path_names_filter
    DART/trunk/models/NCOMMAS/work/path_names_ncommas_to_dart
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    DART/trunk/models/NCOMMAS/work/path_names_obs_seq_to_netcdf
    DART/trunk/models/NCOMMAS/work/path_names_obs_sequence_tool
    DART/trunk/models/NCOMMAS/work/path_names_perfect_model_obs
    DART/trunk/models/NCOMMAS/work/path_names_restart_file_tool
    DART/trunk/models/NCOMMAS/work/quickbuild.csh
    DART/trunk/models/POP/dart_pop_mod.f90
    DART/trunk/models/POP/dart_to_pop.f90
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    DART/trunk/models/POP/matlab/Check_ud.m
    DART/trunk/models/POP/matlab/plot_evolution.m
    DART/trunk/models/POP/matlab/plot_global_grid.m
    DART/trunk/models/POP/matlab/plot_grid.m
    DART/trunk/models/POP/matlab/plot_interp_diffs.m
    DART/trunk/models/POP/matlab/plot_rmse_xxx_evolution.m
    DART/trunk/models/POP/matlab/plot_spread_xxx_evolution.m
    DART/trunk/models/POP/matlab/two_experiments_evolution.m
    DART/trunk/models/POP/model_mod.f90
    DART/trunk/models/POP/pop_to_dart.f90
    DART/trunk/models/POP/shell_scripts/MakeInitialEnsemble.csh
    DART/trunk/models/POP/shell_scripts/advance_model.csh
    DART/trunk/models/POP/shell_scripts/assimilate.csh
    DART/trunk/models/POP/test_dipole_interp.f90
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    DART/trunk/models/noah/work/mkmf_wakeup_filter
    DART/trunk/models/noah/work/namelist.hrldas
    DART/trunk/models/noah/work/obs_seq.in
    DART/trunk/models/noah/work/path_names_create_fixed_network_seq
    DART/trunk/models/noah/work/path_names_create_obs_sequence
    DART/trunk/models/noah/work/path_names_dart_to_noah
    DART/trunk/models/noah/work/path_names_filter
    DART/trunk/models/noah/work/path_names_model_mod_check
    DART/trunk/models/noah/work/path_names_noah_to_dart
    DART/trunk/models/noah/work/path_names_obs_diag
    DART/trunk/models/noah/work/path_names_obs_seq_to_netcdf
    DART/trunk/models/noah/work/path_names_obs_sequence_tool
    DART/trunk/models/noah/work/path_names_perfect_model_obs
    DART/trunk/models/noah/work/path_names_preprocess
    DART/trunk/models/noah/work/path_names_restart_file_tool
    DART/trunk/models/noah/work/path_names_wakeup_filter
    DART/trunk/models/noah/work/quickbuild.csh
    DART/trunk/models/noah/work/set_def.out
    DART/trunk/models/pe2lyr/matlab/RunAllTests.m
    DART/trunk/models/sqg/fft.f90
    DART/trunk/models/sqg/model_description
    DART/trunk/models/sqg/model_mod.f90
    DART/trunk/models/sqg/spectral_mod.f90
    DART/trunk/models/sqg/sqg.f90
    DART/trunk/models/sqg/sqg_mod.f90
    DART/trunk/models/sqg/work/
    DART/trunk/models/sqg/work/input.nml
    DART/trunk/models/sqg/work/mkmf_closest_member_tool
    DART/trunk/models/sqg/work/mkmf_create_fixed_network_seq
    DART/trunk/models/sqg/work/mkmf_create_obs_sequence
    DART/trunk/models/sqg/work/mkmf_filter
    DART/trunk/models/sqg/work/mkmf_integrate_model
    DART/trunk/models/sqg/work/mkmf_obs_diag
    DART/trunk/models/sqg/work/mkmf_obs_seq_to_netcdf
    DART/trunk/models/sqg/work/mkmf_obs_sequence_tool
    DART/trunk/models/sqg/work/mkmf_perfect_model_obs
    DART/trunk/models/sqg/work/mkmf_preprocess
    DART/trunk/models/sqg/work/mkmf_restart_file_tool
    DART/trunk/models/sqg/work/mkmf_sqg
    DART/trunk/models/sqg/work/mkmf_wakeup_filter
    DART/trunk/models/sqg/work/mkmf_write_sqg_restart
    DART/trunk/models/sqg/work/obs_network.py
    DART/trunk/models/sqg/work/obs_seq.in
    DART/trunk/models/sqg/work/obs_seq.out
    DART/trunk/models/sqg/work/path_names_closest_member_tool
    DART/trunk/models/sqg/work/path_names_create_fixed_network_seq
    DART/trunk/models/sqg/work/path_names_create_obs_sequence
    DART/trunk/models/sqg/work/path_names_filter
    DART/trunk/models/sqg/work/path_names_integrate_model
    DART/trunk/models/sqg/work/path_names_obs_diag
    DART/trunk/models/sqg/work/path_names_obs_seq_to_netcdf
    DART/trunk/models/sqg/work/path_names_obs_sequence_tool
    DART/trunk/models/sqg/work/path_names_perfect_model_obs
    DART/trunk/models/sqg/work/path_names_preprocess
    DART/trunk/models/sqg/work/path_names_restart_file_tool
    DART/trunk/models/sqg/work/path_names_sqg
    DART/trunk/models/sqg/work/path_names_wakeup_filter
    DART/trunk/models/sqg/work/path_names_write_sqg_restart
    DART/trunk/models/sqg/work/quickbuild.csh
    DART/trunk/models/sqg/work/sqgRestart.nc
    DART/trunk/models/sqg/write_sqg_restart.f90
    DART/trunk/models/template/utils/
    DART/trunk/obs_def/obs_def_tpw_mod.f90
    DART/trunk/obs_def/obs_def_tpw_mod.nml
    DART/trunk/observations/AURA/convert_all_aura.pro
    DART/trunk/observations/AURA/convert_aura.f90
    DART/trunk/observations/AURA/convert_hdf_to_netcdf.pro
    DART/trunk/observations/AURA/data/
    DART/trunk/observations/AURA/data/MLS-Aura_L2GP-Temperature_v03-33-c01_2011d244.he5
    DART/trunk/observations/AURA/work/
    DART/trunk/observations/AURA/work/input.nml
    DART/trunk/observations/AURA/work/inputDOY244.nml
    DART/trunk/observations/AURA/work/mkmf_advance_time
    DART/trunk/observations/AURA/work/mkmf_convert_aura
    DART/trunk/observations/AURA/work/mkmf_obs_sequence_tool
    DART/trunk/observations/AURA/work/mkmf_preprocess
    DART/trunk/observations/AURA/work/path_names_advance_time
    DART/trunk/observations/AURA/work/path_names_convert_aura
    DART/trunk/observations/AURA/work/path_names_obs_sequence_tool
    DART/trunk/observations/AURA/work/path_names_preprocess
    DART/trunk/observations/AURA/work/quickbuild.csh
    DART/trunk/observations/AURA/work/run_sept.csh
    DART/trunk/observations/Ameriflux/level4_to_obs.f90
    DART/trunk/observations/Ameriflux/level4_to_obs.html
    DART/trunk/observations/Ameriflux/level4_to_obs.nml
    DART/trunk/observations/Ameriflux/shell_scripts/
    DART/trunk/observations/Ameriflux/shell_scripts/CreateObs.csh
    DART/trunk/observations/Ameriflux/work/
    DART/trunk/observations/Ameriflux/work/input.nml
    DART/trunk/observations/Ameriflux/work/mkmf_level4_to_obs
    DART/trunk/observations/Ameriflux/work/mkmf_obs_sequence_tool
    DART/trunk/observations/Ameriflux/work/mkmf_preprocess
    DART/trunk/observations/Ameriflux/work/path_names_level4_to_obs
    DART/trunk/observations/Ameriflux/work/path_names_obs_sequence_tool
    DART/trunk/observations/Ameriflux/work/path_names_preprocess
    DART/trunk/observations/Ameriflux/work/quickbuild.csh
    DART/trunk/observations/COSMOS/COSMOS_development.f90
    DART/trunk/observations/COSMOS/COSMOS_development.html
    DART/trunk/observations/COSMOS/COSMOS_development.nml
    DART/trunk/observations/COSMOS/COSMOS_to_obs.f90
    DART/trunk/observations/COSMOS/COSMOS_to_obs.html
    DART/trunk/observations/COSMOS/COSMOS_to_obs.nml
    DART/trunk/observations/COSMOS/data/
    DART/trunk/observations/COSMOS/data/COSMIC_parlist.nc
    DART/trunk/observations/COSMOS/data/COSMIC_parlist.netCDF.txt
    DART/trunk/observations/COSMOS/data/COSMIC_parlist_station.txt
    DART/trunk/observations/COSMOS/data/COSMOS_SantaRita_2010.txt
    DART/trunk/observations/COSMOS/work/
    DART/trunk/observations/COSMOS/work/input.nml
    DART/trunk/observations/COSMOS/work/mkmf_COSMOS_development
    DART/trunk/observations/COSMOS/work/mkmf_COSMOS_to_obs
    DART/trunk/observations/COSMOS/work/mkmf_obs_sequence_tool
    DART/trunk/observations/COSMOS/work/mkmf_preprocess
    DART/trunk/observations/COSMOS/work/path_names_COSMOS_development
    DART/trunk/observations/COSMOS/work/path_names_COSMOS_to_obs
    DART/trunk/observations/COSMOS/work/path_names_obs_sequence_tool
    DART/trunk/observations/COSMOS/work/path_names_preprocess
    DART/trunk/observations/COSMOS/work/quickbuild.csh
    DART/trunk/observations/MIDAS/MIDAS_to_obs.f90
    DART/trunk/observations/MIDAS/MIDAS_to_obs.html
    DART/trunk/observations/MIDAS/MIDAS_to_obs_nml
    DART/trunk/observations/MIDAS/data/
    DART/trunk/observations/MIDAS/data/Test.nc
    DART/trunk/observations/MIDAS/work/
    DART/trunk/observations/MIDAS/work/input.nml
    DART/trunk/observations/MIDAS/work/mkmf_MIDAS_to_obs
    DART/trunk/observations/MIDAS/work/mkmf_obs_sequence_tool
    DART/trunk/observations/MIDAS/work/mkmf_preprocess
    DART/trunk/observations/MIDAS/work/path_names_MIDAS_to_obs
    DART/trunk/observations/MIDAS/work/path_names_obs_sequence_tool
    DART/trunk/observations/MIDAS/work/path_names_preprocess
    DART/trunk/observations/MIDAS/work/quickbuild.csh
    DART/trunk/observations/MODIS/SnglResSubsetter.v1.2.tar.gz
    DART/trunk/observations/MODIS/convert_tpw.f90
    DART/trunk/observations/MODIS/data/
    DART/trunk/observations/MODIS/data/README
    DART/trunk/observations/MODIS/doc/
    DART/trunk/observations/MODIS/doc/MOD_05.pdf
    DART/trunk/observations/MODIS/work/
    DART/trunk/observations/MODIS/work/input.nml
    DART/trunk/observations/MODIS/work/mkmf_convert_tpw
    DART/trunk/observations/MODIS/work/mkmf_preprocess
    DART/trunk/observations/MODIS/work/path_names_convert_tpw
    DART/trunk/observations/MODIS/work/path_names_preprocess
    DART/trunk/observations/MODIS/work/quickbuild.csh
    DART/trunk/observations/SABER/convert_saber_cdf.f90
    DART/trunk/observations/SABER/data/
    DART/trunk/observations/SABER/data/README
    DART/trunk/observations/SABER/error_prof.ps
    DART/trunk/observations/SABER/work/
    DART/trunk/observations/SABER/work/input.nml
    DART/trunk/observations/SABER/work/mkmf_advance_time
    DART/trunk/observations/SABER/work/mkmf_convert_saber_cdf
    DART/trunk/observations/SABER/work/mkmf_obs_sequence_tool
    DART/trunk/observations/SABER/work/mkmf_preprocess
    DART/trunk/observations/SABER/work/path_names_advance_time
    DART/trunk/observations/SABER/work/path_names_convert_saber_cdf
    DART/trunk/observations/SABER/work/path_names_obs_sequence_tool
    DART/trunk/observations/SABER/work/path_names_preprocess
    DART/trunk/observations/SABER/work/quickbuild.csh
    DART/trunk/observations/even_sphere/README
    DART/trunk/observations/even_sphere/even_sphere.m
    DART/trunk/observations/even_sphere/even_sphere_dense.m
    DART/trunk/observations/even_sphere/even_sphere_pe2lyr.m
    DART/trunk/observations/even_sphere/run_fixed_network_daily.csh
    DART/trunk/observations/even_sphere/run_fixed_network_seq.csh
    DART/trunk/observations/gps/shell_scripts/cosmic_to_obsseq.csh
    DART/trunk/observations/snow/data/
    DART/trunk/observations/snow/data/2006_222.txt
    DART/trunk/observations/snow/data/README
    DART/trunk/observations/snow/shell_scripts/
    DART/trunk/observations/snow/shell_scripts/hour_time_loop.csh
    DART/trunk/observations/snow/shell_scripts/input.nml
    DART/trunk/observations/snow/shell_scripts/input.nml.template
    DART/trunk/observations/snow/snow_to_obs.f90
    DART/trunk/observations/snow/snow_to_obs.html
    DART/trunk/observations/snow/snow_to_obs_netcdf.f90
    DART/trunk/observations/snow/work/
    DART/trunk/observations/snow/work/input.nml
    DART/trunk/observations/snow/work/mkmf_advance_time
    DART/trunk/observations/snow/work/mkmf_obs_sequence_tool
    DART/trunk/observations/snow/work/mkmf_preprocess
    DART/trunk/observations/snow/work/mkmf_snow_to_obs
    DART/trunk/observations/snow/work/mkmf_snow_to_obs_netcdf
    DART/trunk/observations/snow/work/path_names_advance_time
    DART/trunk/observations/snow/work/path_names_obs_sequence_tool
    DART/trunk/observations/snow/work/path_names_preprocess
    DART/trunk/observations/snow/work/path_names_snow_to_obs
    DART/trunk/observations/snow/work/path_names_snow_to_obs_netcdf
    DART/trunk/observations/snow/work/quickbuild.csh
    DART/trunk/random_nr/input.nml
    DART/trunk/random_nr/mkmf_test_random_nr
    DART/trunk/random_nr/path_names_test_random_nr
    DART/trunk/random_nr/random_nr_mod.html
    DART/trunk/random_nr/test_random_nr.f90
    DART/trunk/random_seq/input.nml
    DART/trunk/random_seq/mkmf_test_diff
    DART/trunk/random_seq/path_names_test_diff
    DART/trunk/random_seq/test/input.nml
    DART/trunk/random_seq/test/mkmf_test_corr
    DART/trunk/random_seq/test/mkmf_test_diff
    DART/trunk/random_seq/test/mkmf_test_random_gsl
    DART/trunk/random_seq/test/mkmf_test_reseed
    DART/trunk/random_seq/test/path_names_test_corr
    DART/trunk/random_seq/test/path_names_test_diff
    DART/trunk/random_seq/test/path_names_test_gsl_dart
    DART/trunk/random_seq/test/path_names_test_gsl_native
    DART/trunk/random_seq/test/path_names_test_random_gsl
    DART/trunk/random_seq/test/path_names_test_reseed
    DART/trunk/tutorial/building_blocks/
    DART/trunk/tutorial/index.fm
    DART/trunk/tutorial/section1/
    DART/trunk/tutorial/section10/
    DART/trunk/tutorial/section11/
    DART/trunk/tutorial/section12/
    DART/trunk/tutorial/section13/
    DART/trunk/tutorial/section14/
    DART/trunk/tutorial/section15/
    DART/trunk/tutorial/section16/
    DART/trunk/tutorial/section17/
    DART/trunk/tutorial/section18/
    DART/trunk/tutorial/section19/
    DART/trunk/tutorial/section2/
    DART/trunk/tutorial/section20/
    DART/trunk/tutorial/section21/
    DART/trunk/tutorial/section22/
    DART/trunk/tutorial/section3/
    DART/trunk/tutorial/section4/
    DART/trunk/tutorial/section5/
    DART/trunk/tutorial/section6/
    DART/trunk/tutorial/section7/
    DART/trunk/tutorial/section8/
    DART/trunk/tutorial/section9/
    DART/trunk/tutorial/section_carbon/

Property Changed:
----------------
    DART/trunk/
    DART/trunk/adaptive_inflate/
    DART/trunk/adaptive_inflate/adaptive_inflate_mod.f90
    DART/trunk/assim_tools/
    DART/trunk/assim_tools/assim_tools_mod.f90
    DART/trunk/mkmf/mkmf.template
    DART/trunk/mkmf/mkmf.template.absoft.osx
    DART/trunk/mkmf/mkmf.template.g95
    DART/trunk/mkmf/mkmf.template.gfortran
    DART/trunk/mkmf/mkmf.template.intel.linux
    DART/trunk/mkmf/mkmf.template.intel.osx
    DART/trunk/mkmf/mkmf.template.lahey.linux
    DART/trunk/mkmf/mkmf.template.pathscale.linux
    DART/trunk/mkmf/mkmf.template.pgi.cray
    DART/trunk/mkmf/mkmf.template.pgi.linux
    DART/trunk/mkmf/mkmf.template.pgi.osx
    DART/trunk/mkmf/mkmf.template.sgi.altix
    DART/trunk/mkmf/mkmf.template.xlf.aix
    DART/trunk/models/bgrid_solo/model_mod.f90
    DART/trunk/models/cam/
    DART/trunk/models/tiegcm/dart_to_model.f90
    DART/trunk/models/tiegcm/model_mod.f90
    DART/trunk/models/tiegcm/model_to_dart.f90
    DART/trunk/models/tiegcm/shell_scripts/advance_model.csh
    DART/trunk/models/tiegcm/shell_scripts/run_filter.csh
    DART/trunk/models/tiegcm/shell_scripts/run_filter_async4.csh
    DART/trunk/models/tiegcm/shell_scripts/run_perfect_model_obs.csh
    DART/trunk/models/tiegcm/work/mkmf_create_fixed_network_seq
    DART/trunk/models/tiegcm/work/mkmf_create_obs_sequence
    DART/trunk/models/tiegcm/work/mkmf_dart_to_model
    DART/trunk/models/tiegcm/work/mkmf_filter
    DART/trunk/models/tiegcm/work/mkmf_model_mod_check
    DART/trunk/models/tiegcm/work/mkmf_model_to_dart
    DART/trunk/models/tiegcm/work/mkmf_obs_diag
    DART/trunk/models/tiegcm/work/mkmf_perfect_model_obs
    DART/trunk/models/tiegcm/work/mkmf_preprocess
    DART/trunk/models/tiegcm/work/mkmf_wakeup_filter
    DART/trunk/models/tiegcm/work/path_names_create_fixed_network_seq
    DART/trunk/models/tiegcm/work/path_names_create_obs_sequence
    DART/trunk/models/tiegcm/work/path_names_dart_to_model
    DART/trunk/models/tiegcm/work/path_names_filter
    DART/trunk/models/tiegcm/work/path_names_model_mod_check
    DART/trunk/models/tiegcm/work/path_names_model_to_dart
    DART/trunk/models/tiegcm/work/path_names_obs_diag
    DART/trunk/models/tiegcm/work/path_names_obs_seq_to_netcdf
    DART/trunk/models/tiegcm/work/path_names_perfect_model_obs
    DART/trunk/models/tiegcm/work/path_names_preprocess
    DART/trunk/models/tiegcm/work/path_names_restart_file_tool
    DART/trunk/models/tiegcm/work/path_names_wakeup_filter
    DART/trunk/models/tiegcm/work/quickbuild.csh
    DART/trunk/models/wrf/model_mod.f90
    DART/trunk/models/wrf/work/path_names_obs_seq_verify
    DART/trunk/obs_kind/DEFAULT_obs_kind_mod.F90
    DART/trunk/obs_sequence/obs_seq_verify.f90
    DART/trunk/observations/AIRS/
    DART/trunk/observations/MADIS/
    DART/trunk/observations/NCEP/ascii_to_obs/real_obs_mod.f90
    DART/trunk/utilities/
    DART/trunk/utilities/closest_member_tool.f90

-------------- next part --------------

Property changes on: DART/trunk
___________________________________________________________________
Added: svn:mergeinfo
   + /DART/branches/development:4680-6255
/DART/branches/gitm:5143-6215
/DART/branches/helen:5995-6161

Modified: DART/trunk/DART_LAB/matlab/advance_oned.m
===================================================================
--- DART/trunk/DART_LAB/matlab/advance_oned.m	2013-06-12 15:51:42 UTC (rev 6255)
+++ DART/trunk/DART_LAB/matlab/advance_oned.m	2013-06-12 16:19:10 UTC (rev 6256)
@@ -1,15 +1,11 @@
 function x_new = advance_oned(x, alpha, model_bias)
 %% advance_oned(x, alpha, model_bias)
 
-%% DART software - Copyright 2004 - 2011 UCAR. This open source software is
+%% DART software - Copyright 2004 - 2013 UCAR. This open source software is
 % provided by UCAR, "as is", without charge, subject to all terms of use at
 % http://www.image.ucar.edu/DAReS/DART/DART_download
 %
-% <next few lines under version control, do not edit>
-% $URL$
 % $Id$
-% $Revision$
-% $Date$
 
 x_new = x + comp_dt(x, alpha, model_bias);
 end
@@ -24,3 +20,9 @@
 dx = (x + model_bias) + alpha .* x .* abs(x);
 
 end
+
+% <next few lines under version control, do not edit>
+% $URL$
+% $Id$
+% $Revision$
+% $Date$

Modified: DART/trunk/DART_LAB/matlab/comp_cov_factor.m
===================================================================
--- DART/trunk/DART_LAB/matlab/comp_cov_factor.m	2013-06-12 15:51:42 UTC (rev 6255)
+++ DART/trunk/DART_LAB/matlab/comp_cov_factor.m	2013-06-12 16:19:10 UTC (rev 6256)
@@ -1,15 +1,11 @@
 function cov_factor = comp_cov_factor(z_in, c)
 %% comp_cov_factor Gaspari Cohn cutoff, z_in is the distance while c is the cutoff
 
-%% DART software - Copyright 2004 - 2011 UCAR. This open source software is
+%% DART software - Copyright 2004 - 2013 UCAR. This open source software is
 % provided by UCAR, "as is", without charge, subject to all terms of use at
 % http://www.image.ucar.edu/DAReS/DART/DART_download
 %
-% <next few lines under version control, do not edit>
-% $URL$
 % $Id$
-% $Revision$
-% $Date$
 
 z = abs(z_in);
 
@@ -23,3 +19,8 @@
    cov_factor = ((((r/12 -0.5)*r +0.625)*r +5.0/3.0)*r -5.0)*r + 4.0 - 2.0 / (3.0 * r);
 end
 
+% <next few lines under version control, do not edit>
+% $URL$
+% $Id$
+% $Revision$
+% $Date$

Modified: DART/trunk/DART_LAB/matlab/g_prod_plot.m
===================================================================
--- DART/trunk/DART_LAB/matlab/g_prod_plot.m	2013-06-12 15:51:42 UTC (rev 6255)
+++ DART/trunk/DART_LAB/matlab/g_prod_plot.m	2013-06-12 16:19:10 UTC (rev 6256)
@@ -1,15 +1,11 @@
 function [prior_mean, prior_sd, obs_mean, obs_err_sd, is_err] = g_prod_plot(h)
 %% g_prod_plot Updates the plot of the prior and observation gaussians
 
-%% DART software - Copyright 2004 - 2011 UCAR. This open source software is
+%% DART software - Copyright 2004 - 2013 UCAR. This open source software is
 % provided by UCAR, "as is", without charge, subject to all terms of use at
 % http://www.image.ucar.edu/DAReS/DART/DART_download
 %
-% <next few lines under version control, do not edit>
-% $URL$
 % $Id$
-% $Revision$
-% $Date$
 
 % Successful return as default
 is_err = false;
@@ -104,3 +100,9 @@
    return; 
 
 end
+
+% <next few lines under version control, do not edit>
+% $URL$
+% $Id$
+% $Revision$
+% $Date$

Modified: DART/trunk/DART_LAB/matlab/gaussian_product.m
===================================================================
--- DART/trunk/DART_LAB/matlab/gaussian_product.m	2013-06-12 15:51:42 UTC (rev 6255)
+++ DART/trunk/DART_LAB/matlab/gaussian_product.m	2013-06-12 16:19:10 UTC (rev 6256)
@@ -13,15 +13,11 @@
 % See also: oned_model, oned_ensemble, twod_ensemble, run_lorenz_63, 
 %           run_lorenz_96
 
-%% DART software - Copyright 2004 - 2011 UCAR. This open source software is
+%% DART software - Copyright 2004 - 2013 UCAR. This open source software is
 % provided by UCAR, "as is", without charge, subject to all terms of use at
 % http://www.image.ucar.edu/DAReS/DART/DART_download
 %
-% <next few lines under version control, do not edit>
-% $URL$
 % $Id$
-% $Revision$
-% $Date$
 
 % Begin initialization code - DO NOT EDIT
 gui_Singleton = 1;
@@ -210,3 +206,8 @@
 legend('Prior', 'Obs. Likelihood', 'Posterior', 'Weighted Posterior');
 
 
+% <next few lines under version control, do not edit>
+% $URL$
+% $Id$
+% $Revision$
+% $Date$

Modified: DART/trunk/DART_LAB/matlab/get_ens_rank.m
===================================================================
--- DART/trunk/DART_LAB/matlab/get_ens_rank.m	2013-06-12 15:51:42 UTC (rev 6255)
+++ DART/trunk/DART_LAB/matlab/get_ens_rank.m	2013-06-12 16:19:10 UTC (rev 6256)
@@ -1,15 +1,11 @@
 function [rank] = get_ens_rank(ens, x)
 %% get_ens_rank
 
-%% DART software - Copyright 2004 - 2011 UCAR. This open source software is
+%% DART software - Copyright 2004 - 2013 UCAR. This open source software is
 % provided by UCAR, "as is", without charge, subject to all terms of use at
 % http://www.image.ucar.edu/DAReS/DART/DART_download
 %
-% <next few lines under version control, do not edit>
-% $URL$
 % $Id$
-% $Revision$
-% $Date$
 
 s_ens = sort(ens);
 rank = max(find(s_ens < squeeze(x))) + 1;;
@@ -18,3 +14,9 @@
 end
 
 end
+
+% <next few lines under version control, do not edit>
+% $URL$
+% $Id$
+% $Revision$
+% $Date$

Modified: DART/trunk/DART_LAB/matlab/get_state_increments.m
===================================================================
--- DART/trunk/DART_LAB/matlab/get_state_increments.m	2013-06-12 15:51:42 UTC (rev 6255)
+++ DART/trunk/DART_LAB/matlab/get_state_increments.m	2013-06-12 16:19:10 UTC (rev 6256)
@@ -2,15 +2,11 @@
 %% get_state_increments Computes state increments given observation increments and
 % the state and obs prior ensembles
 
-%% DART software - Copyright 2004 - 2011 UCAR. This open source software is
+%% DART software - Copyright 2004 - 2013 UCAR. This open source software is
 % provided by UCAR, "as is", without charge, subject to all terms of use at
 % http://www.image.ucar.edu/DAReS/DART/DART_download
 %
-% <next few lines under version control, do not edit>
-% $URL$
 % $Id$
-% $Revision$
-% $Date$
 
 % Compute state variance and covariance
 covar = cov(state_ens, obs_ens);
@@ -18,3 +14,8 @@
 
 state_incs = obs_incs * covar(1, 2) / covar(2, 2);
 
+% <next few lines under version control, do not edit>
+% $URL$
+% $Id$
+% $Revision$
+% $Date$

Modified: DART/trunk/DART_LAB/matlab/lorenz_63_adv_1step.m
===================================================================
--- DART/trunk/DART_LAB/matlab/lorenz_63_adv_1step.m	2013-06-12 15:51:42 UTC (rev 6255)
+++ DART/trunk/DART_LAB/matlab/lorenz_63_adv_1step.m	2013-06-12 16:19:10 UTC (rev 6256)
@@ -4,15 +4,11 @@
 %
 % x is the 3-vector state, time is the 2-vector days and seconds time
 
-%% DART software - Copyright 2004 - 2011 UCAR. This open source software is
+%% DART software - Copyright 2004 - 2013 UCAR. This open source software is
 % provided by UCAR, "as is", without charge, subject to all terms of use at
 % http://www.image.ucar.edu/DAReS/DART/DART_download
 %
-% <next few lines under version control, do not edit>
-% $URL$
 % $Id$
-% $Revision$
-% $Date$
 
 global DELTAT
 
@@ -48,3 +44,8 @@
 
 end
 
+% <next few lines under version control, do not edit>
+% $URL$
+% $Id$
+% $Revision$
+% $Date$

Modified: DART/trunk/DART_LAB/matlab/lorenz_63_static_init_model.m
===================================================================
--- DART/trunk/DART_LAB/matlab/lorenz_63_static_init_model.m	2013-06-12 15:51:42 UTC (rev 6255)
+++ DART/trunk/DART_LAB/matlab/lorenz_63_static_init_model.m	2013-06-12 16:19:10 UTC (rev 6256)
@@ -1,15 +1,11 @@
 %% lorenz_63_static_init_model Initializes class data for L63, sets up global storage
 % and reads in control data from input file
 
-%% DART software - Copyright 2004 - 2011 UCAR. This open source software is
+%% DART software - Copyright 2004 - 2013 UCAR. This open source software is
 % provided by UCAR, "as is", without charge, subject to all terms of use at
 % http://www.image.ucar.edu/DAReS/DART/DART_download
 %
-% <next few lines under version control, do not edit>
-% $URL$
 % $Id$
-% $Revision$
-% $Date$
 
 % Lorenz-63 model parameters
 global SIGMA
@@ -36,3 +32,9 @@
 global STATE_LOC
 
 STATE_LOC = (0:2) / 3;
+
+% <next few lines under version control, do not edit>
+% $URL$
+% $Id$
+% $Revision$
+% $Date$

Modified: DART/trunk/DART_LAB/matlab/lorenz_96_adv_1step.m
===================================================================
--- DART/trunk/DART_LAB/matlab/lorenz_96_adv_1step.m	2013-06-12 15:51:42 UTC (rev 6255)
+++ DART/trunk/DART_LAB/matlab/lorenz_96_adv_1step.m	2013-06-12 16:19:10 UTC (rev 6256)
@@ -3,15 +3,11 @@
 %
 % x is the 40-vector state, time is the 2-vector days and seconds time
 
-%% DART software - Copyright 2004 - 2011 UCAR. This open source software is
+%% DART software - Copyright 2004 - 2013 UCAR. This open source software is
 % provided by UCAR, "as is", without charge, subject to all terms of use at
 % http://www.image.ucar.edu/DAReS/DART/DART_download
 %
-% <next few lines under version control, do not edit>
-% $URL$
 % $Id$
-% $Revision$
-% $Date$
 
 global DELTA_T
 
@@ -63,3 +59,8 @@
 
 end
 
+% <next few lines under version control, do not edit>
+% $URL$
+% $Id$
+% $Revision$
+% $Date$

Modified: DART/trunk/DART_LAB/matlab/lorenz_96_static_init_model.m
===================================================================
--- DART/trunk/DART_LAB/matlab/lorenz_96_static_init_model.m	2013-06-12 15:51:42 UTC (rev 6255)
+++ DART/trunk/DART_LAB/matlab/lorenz_96_static_init_model.m	2013-06-12 16:19:10 UTC (rev 6256)
@@ -1,15 +1,11 @@
 %% lorenz_96_static_init_model Initializes class data for L96, sets up global storage
 % and reads in control data from input file
 
-%% DART software - Copyright 2004 - 2011 UCAR. This open source software is
+%% DART software - Copyright 2004 - 2013 UCAR. This open source software is
 % provided by UCAR, "as is", without charge, subject to all terms of use at
 % http://www.image.ucar.edu/DAReS/DART/DART_download
 %
-% <next few lines under version control, do not edit>
-% $URL$
 % $Id$
-% $Revision$
-% $Date$
 
 % Lorenz-96 model parameters
 global FORCING
@@ -32,3 +28,9 @@
 global STATE_LOC
 
 STATE_LOC = (0:MODEL_SIZE - 1) / MODEL_SIZE;
+
+% <next few lines under version control, do not edit>
+% $URL$
+% $Id$
+% $Revision$
+% $Date$

Modified: DART/trunk/DART_LAB/matlab/obs_increment_eakf.m
===================================================================
--- DART/trunk/DART_LAB/matlab/obs_increment_eakf.m	2013-06-12 15:51:42 UTC (rev 6255)
+++ DART/trunk/DART_LAB/matlab/obs_increment_eakf.m	2013-06-12 16:19:10 UTC (rev 6256)
@@ -1,15 +1,11 @@
 function [obs_increments, err] =  obs_increment_eakf(ensemble, observation, obs_error_var)
 %% obs_increment_eakf Computes increments for an ensemble adjustment filter
 
-%% DART software - Copyright 2004 - 2011 UCAR. This open source software is
+%% DART software - Copyright 2004 - 2013 UCAR. This open source software is
 % provided by UCAR, "as is", without charge, subject to all terms of use at
 % http://www.image.ucar.edu/DAReS/DART/DART_download
 %
-% <next few lines under version control, do not edit>
-% $URL$
 % $Id$
-% $Revision$
-% $Date$
 
 % Set error return to default successful
 err = 0;
@@ -53,4 +49,8 @@
 obs_increments = updated_ensemble - ensemble;
 
 
-
+% <next few lines under version control, do not edit>
+% $URL$
+% $Id$
+% $Revision$
+% $Date$

Modified: DART/trunk/DART_LAB/matlab/obs_increment_enkf.m
===================================================================
--- DART/trunk/DART_LAB/matlab/obs_increment_enkf.m	2013-06-12 15:51:42 UTC (rev 6255)
+++ DART/trunk/DART_LAB/matlab/obs_increment_enkf.m	2013-06-12 16:19:10 UTC (rev 6256)
@@ -1,15 +1,11 @@
 function [obs_increments, err] =  obs_increment_enkf(ensemble, observation, obs_error_var)
 %% obs_increment_enkf Computes increments for an ensemble Kalman filter with perturbed obs mean correction.
 
-%% DART software - Copyright 2004 - 2011 UCAR. This open source software is
+%% DART software - Copyright 2004 - 2013 UCAR. This open source software is
 % provided by UCAR, "as is", without charge, subject to all terms of use at
 % http://www.image.ucar.edu/DAReS/DART/DART_download
 %
-% <next few lines under version control, do not edit>
-% $URL$
 % $Id$
-% $Revision$
-% $Date$
 
 % Set error return to default successful
 err = 0;
@@ -71,3 +67,8 @@
 % Compute the increments
 %%%obs_increments = updated_ensemble - ensemble;
 
+% <next few lines under version control, do not edit>
+% $URL$
+% $Id$
+% $Revision$
+% $Date$

Modified: DART/trunk/DART_LAB/matlab/obs_increment_rhf.m
===================================================================
--- DART/trunk/DART_LAB/matlab/obs_increment_rhf.m	2013-06-12 15:51:42 UTC (rev 6255)
+++ DART/trunk/DART_LAB/matlab/obs_increment_rhf.m	2013-06-12 16:19:10 UTC (rev 6256)
@@ -3,15 +3,11 @@
 % Need to discuss the available options eventually
 % For now this implements the default options
 
-%% DART software - Copyright 2004 - 2011 UCAR. This open source software is
+%% DART software - Copyright 2004 - 2013 UCAR. This open source software is
 % provided by UCAR, "as is", without charge, subject to all terms of use at
 % http://www.image.ucar.edu/DAReS/DART/DART_download
 %
-% <next few lines under version control, do not edit>
-% $URL$
 % $Id$
-% $Revision$
-% $Date$
 
 % Set error return to default successful
 err = 0;
@@ -174,3 +170,8 @@
 % Add in the mean and normalize by sd
 x = mean + x * sd;
 
+% <next few lines under version control, do not edit>
+% $URL$
+% $Id$
+% $Revision$
+% $Date$

Modified: DART/trunk/DART_LAB/matlab/oned_ensemble.m
===================================================================
--- DART/trunk/DART_LAB/matlab/oned_ensemble.m	2013-06-12 15:51:42 UTC (rev 6255)
+++ DART/trunk/DART_LAB/matlab/oned_ensemble.m	2013-06-12 16:19:10 UTC (rev 6256)
@@ -32,15 +32,11 @@
 % See also: gaussian_product, oned_model, twod_ensemble, run_lorenz_63, 
 %           run_lorenz_96
 
-%% DART software - Copyright 2004 - 2011 UCAR. This open source software is
+%% DART software - Copyright 2004 - 2013 UCAR. This open source software is
 % provided by UCAR, "as is", without charge, subject to all terms of use at
 % http://www.image.ucar.edu/DAReS/DART/DART_download
 %
-% <next few lines under version control, do not edit>
-% $URL$
 % $Id$
-% $Revision$
-% $Date$
 
 % Last Modified by GUIDE v2.5 28-Aug-2009 16:29:57
 
@@ -723,3 +719,8 @@
 end
 
 
+% <next few lines under version control, do not edit>
+% $URL$
+% $Id$
+% $Revision$
+% $Date$

Modified: DART/trunk/DART_LAB/matlab/oned_model.m
===================================================================
--- DART/trunk/DART_LAB/matlab/oned_model.m	2013-06-12 15:51:42 UTC (rev 6255)
+++ DART/trunk/DART_LAB/matlab/oned_model.m	2013-06-12 16:19:10 UTC (rev 6256)
@@ -38,15 +38,11 @@
 % See also: gaussian_product, oned_ensemble, twod_ensemble, run_lorenz_63, 
 %           run_lorenz_96
 
-%% DART software - Copyright 2004 - 2011 UCAR. This open source software is
+%% DART software - Copyright 2004 - 2013 UCAR. This open source software is
 % provided by UCAR, "as is", without charge, subject to all terms of use at
 % http://www.image.ucar.edu/DAReS/DART/DART_download
 %
-% <next few lines under version control, do not edit>
-% $URL$
 % $Id$
-% $Revision$
-% $Date$
 
 % Last Modified by GUIDE v2.5 27-Aug-2009 08:54:05
 
@@ -632,6 +628,7 @@
 
    % Put on a legend
    legend('Error', 'Spread', 'Location', 'SouthWest');
+   legend boxoff
 
    % Want the lower y limit to stay 0 for error spread
    set(gca, 'YLimMode', 'Auto');
@@ -655,8 +652,9 @@
    % Update the rank data
    subplot(handles.r4);
    ens_rank = get_ens_rank(ens_new, 0);
-sort(ens_new)
-ens_rank
+   fprintf([sprintf('\ntimestep %d bin edges are ',handles.time_step), ...
+            num2str(sort([-Inf ens_new Inf]),'%10.4f'),'\n'])
+   fprintf('timestep %d bin/"rank" is %d\n',handles.time_step, ens_rank)
 
    % Plot the latest rank entry as a different color
    temp_rank(:, 1) = handles.prior_rank(1:handles.ens_size + 1);
@@ -1019,3 +1017,8 @@
 
 
 
+% <next few lines under version control, do not edit>
+% $URL$
+% $Id$
+% $Revision$
+% $Date$

Modified: DART/trunk/DART_LAB/matlab/plot_gaussian.m
===================================================================
--- DART/trunk/DART_LAB/matlab/plot_gaussian.m	2013-06-12 15:51:42 UTC (rev 6255)
+++ DART/trunk/DART_LAB/matlab/plot_gaussian.m	2013-06-12 16:19:10 UTC (rev 6256)
@@ -1,15 +1,11 @@
 function[plot_handle] = plot_gaussian(mean, sd, weight)
 %% plot_gaussian Plot gaussian over 5 standard deviations
 
-%% DART software - Copyright 2004 - 2011 UCAR. This open source software is
+%% DART software - Copyright 2004 - 2013 UCAR. This open source software is
 % provided by UCAR, "as is", without charge, subject to all terms of use at
 % http://www.image.ucar.edu/DAReS/DART/DART_download
 %
-% <next few lines under version control, do not edit>
-% $URL$
 % $Id$
-% $Revision$
-% $Date$
 
 x_min = mean - 5*sd;
 x_max = mean + 5*sd;
@@ -22,3 +18,9 @@
 y = weight * normpdf(x, mean, sd);
 
 plot_handle = plot(x, y);
+
+% <next few lines under version control, do not edit>
+% $URL$
+% $Id$
+% $Revision$
+% $Date$

Modified: DART/trunk/DART_LAB/matlab/plot_polar.m
===================================================================
--- DART/trunk/DART_LAB/matlab/plot_polar.m	2013-06-12 15:51:42 UTC (rev 6255)
+++ DART/trunk/DART_LAB/matlab/plot_polar.m	2013-06-12 16:19:10 UTC (rev 6256)
@@ -1,15 +1,11 @@
 function h = plot_polar(y, x, mean_dist, string, model_size)
 %% plot_polar
 
-%% DART software - Copyright 2004 - 2011 UCAR. This open source software is
+%% DART software - Copyright 2004 - 2013 UCAR. This open source software is
 % provided by UCAR, "as is", without charge, subject to all terms of use at
 % http://www.image.ucar.edu/DAReS/DART/DART_download
 %
-% <next few lines under version control, do not edit>
-% $URL$
 % $Id$
-% $Revision$
-% $Date$
 
 % Y includes a wraparound point, x does not
 x_t(model_size + 1) = x(1);
@@ -17,3 +13,9 @@
 h = polar(y, mean_dist + x_t, string);
 
 end
+
+% <next few lines under version control, do not edit>
+% $URL$
+% $Id$
+% $Revision$
+% $Date$

Modified: DART/trunk/DART_LAB/matlab/product_of_gaussians.m
===================================================================
--- DART/trunk/DART_LAB/matlab/product_of_gaussians.m	2013-06-12 15:51:42 UTC (rev 6255)
+++ DART/trunk/DART_LAB/matlab/product_of_gaussians.m	2013-06-12 16:19:10 UTC (rev 6256)
@@ -2,15 +2,11 @@
    product_of_gaussians(prior_mean, prior_sd, obs, obs_err_sd) 
 %% product_of_gaussians Computes mean, variance and weight of the product of two unit gaussians given the mean and standard deviation of each.
 
-%% DART software - Copyright 2004 - 2011 UCAR. This open source software is
+%% DART software - Copyright 2004 - 2013 UCAR. This open source software is
 % provided by UCAR, "as is", without charge, subject to all terms of use at
 % http://www.image.ucar.edu/DAReS/DART/DART_download
 %
-% <next few lines under version control, do not edit>
-% $URL$
 % $Id$
-% $Revision$
-% $Date$
 
 % Get the prior and observational error variance
 prior_var = prior_sd^2;
@@ -27,3 +23,8 @@
 weight = (1. / (sqrt(2. * pi) * sqrt(prior_var + obs_err_var))) *...
    exp(-0.5 * (obs - prior_mean).^2 ./ (prior_var + obs_err_var));
 
+% <next few lines under version control, do not edit>
+% $URL$
+% $Id$
+% $Revision$
+% $Date$

Modified: DART/trunk/DART_LAB/matlab/run_lorenz_63.m
===================================================================
--- DART/trunk/DART_LAB/matlab/run_lorenz_63.m	2013-06-12 15:51:42 UTC (rev 6255)
+++ DART/trunk/DART_LAB/matlab/run_lorenz_63.m	2013-06-12 16:19:10 UTC (rev 6256)
@@ -33,15 +33,11 @@
 % See also: gaussian_product, oned_model, oned_ensemble, twod_ensemble, 
 %           run_lorenz_96
 
-%% DART software - Copyright 2004 - 2011 UCAR. This open source software is
+%% DART software - Copyright 2004 - 2013 UCAR. This open source software is
 % provided by UCAR, "as is", without charge, subject to all terms of use at
 % http://www.image.ucar.edu/DAReS/DART/DART_download
 %
-% <next few lines under version control, do not edit>
-% $URL$
 % $Id$
-% $Revision$
-% $Date$
 
 % Begin initialization code - DO NOT EDIT
 gui_Singleton = 1;
@@ -447,3 +443,8 @@
 end
 
 
+% <next few lines under version control, do not edit>
+% $URL$
+% $Id$
+% $Revision$
+% $Date$

Modified: DART/trunk/DART_LAB/matlab/run_lorenz_96.m
===================================================================
--- DART/trunk/DART_LAB/matlab/run_lorenz_96.m	2013-06-12 15:51:42 UTC (rev 6255)
+++ DART/trunk/DART_LAB/matlab/run_lorenz_96.m	2013-06-12 16:19:10 UTC (rev 6256)
@@ -24,15 +24,11 @@
 % See also: gaussian_product, oned_model, oned_ensemble, twod_ensemble, 
 %           run_lorenz_63
 
-%% DART software - Copyright 2004 - 2011 UCAR. This open source software is
+%% DART software - Copyright 2004 - 2013 UCAR. This open source software is
 % provided by UCAR, "as is", without charge, subject to all terms of use at
 % http://www.image.ucar.edu/DAReS/DART/DART_download
 %
-% <next few lines under version control, do not edit>
-% $URL$
 % $Id$
-% $Revision$
-% $Date$
 
 % Begin initialization code - DO NOT EDIT
 gui_Singleton = 1;
@@ -757,3 +753,8 @@
 ens_mean = mean(squeeze(ens)');
 ens_mean_rms = sqrt(sum((truth - ens_mean).^2) / size(truth, 2));
 
+% <next few lines under version control, do not edit>
+% $URL$
+% $Id$
+% $Revision$
+% $Date$

Modified: DART/trunk/DART_LAB/matlab/run_template.m
===================================================================
--- DART/trunk/DART_LAB/matlab/run_template.m	2013-06-12 15:51:42 UTC (rev 6255)
+++ DART/trunk/DART_LAB/matlab/run_template.m	2013-06-12 16:19:10 UTC (rev 6256)
@@ -22,15 +22,11 @@
 
 % Edit the above text to modify the response to help run_template
 
-%% DART software - Copyright 2004 - 2011 UCAR. This open source software is
+%% DART software - Copyright 2004 - 2013 UCAR. This open source software is
 % provided by UCAR, "as is", without charge, subject to all terms of use at
 % http://www.image.ucar.edu/DAReS/DART/DART_download
 %
-% <next few lines under version control, do not edit>
-% $URL$
 % $Id$
-% $Revision$
-% $Date$
 
 % Begin initialization code - DO NOT EDIT
 gui_Singleton = 1;
@@ -203,3 +199,8 @@
 % Update the global storage and return
 guidata(hObject, handles);
 
+% <next few lines under version control, do not edit>
+% $URL$
+% $Id$
+% $Revision$
+% $Date$

Modified: DART/trunk/DART_LAB/matlab/twod_ensemble.m
===================================================================
--- DART/trunk/DART_LAB/matlab/twod_ensemble.m	2013-06-12 15:51:42 UTC (rev 6255)
+++ DART/trunk/DART_LAB/matlab/twod_ensemble.m	2013-06-12 16:19:10 UTC (rev 6256)
@@ -22,15 +22,11 @@
 % See also: gaussian_product, oned_model, oned_ensemble, run_lorenz_63, 
 %           run_lorenz_96
 
-%% DART software - Copyright 2004 - 2011 UCAR. This open source software is
+%% DART software - Copyright 2004 - 2013 UCAR. This open source software is
 % provided by UCAR, "as is", without charge, subject to all terms of use at
 % http://www.image.ucar.edu/DAReS/DART/DART_download
 %
-% <next few lines under version control, do not edit>
-% $URL$
 % $Id$
-% $Revision$
-% $Date$
 
 % Begin initialization code - DO NOT EDIT
 gui_Singleton = 1;
@@ -661,3 +657,8 @@
 [gcbo_h, gcbo_fig] = gcbo;
 figure(gcbo_fig);
 
+% <next few lines under version control, do not edit>
+% $URL$
+% $Id$
+% $Revision$
+% $Date$

Modified: DART/trunk/README
===================================================================
--- DART/trunk/README	2013-06-12 15:51:42 UTC (rev 6255)
+++ DART/trunk/README	2013-06-12 16:19:10 UTC (rev 6256)
@@ -69,3 +69,4 @@
 DART project web page listed above for very detailed instructions that
 should get you over any bumps in the process.
 
+


Property changes on: DART/trunk/adaptive_inflate
___________________________________________________________________
Modified: svn:mergeinfo
   - /DART/branches/inf_restart:4784-4812
   + /DART/branches/development/adaptive_inflate:4680-6255
/DART/branches/gitm/adaptive_inflate:5143-6215
/DART/branches/helen/adaptive_inflate:5995-6161
/DART/branches/inf_restart:4784-4812

Modified: DART/trunk/adaptive_inflate/adaptive_inflate_mod.f90
===================================================================
--- DART/trunk/adaptive_inflate/adaptive_inflate_mod.f90	2013-06-12 15:51:42 UTC (rev 6255)
+++ DART/trunk/adaptive_inflate/adaptive_inflate_mod.f90	2013-06-12 16:19:10 UTC (rev 6256)
@@ -1,24 +1,21 @@
-! DART software - Copyright 2004 - 2011 UCAR. This open source software is
+! DART software - Copyright 2004 - 2013 UCAR. This open source software is
 ! provided by UCAR, "as is", without charge, subject to all terms of use at
 ! http://www.image.ucar.edu/DAReS/DART/DART_download
+!
+! $Id$ 
 
 module adaptive_inflate_mod
 
-! <next few lines under version control, do not edit>
-! $URL$ 
-! $Id$ 
-! $Revision$ 
-! $Date$ 
-!
 ! Operations and storage required for various adaptive inflation algorithms
 
-use types_mod,            only : r8, PI
+use types_mod,            only : r8, PI, missing_r8
 use time_manager_mod,     only : time_type, get_time, set_time
-use utilities_mod,        only : file_exist, get_unit, register_module, &
+use utilities_mod,        only : register_module, open_file, close_file, &
                                  error_handler, E_ERR, E_MSG
 use random_seq_mod,       only : random_seq_type, random_gaussian, init_random_seq
-use ensemble_manager_mod, only : ensemble_type, all_vars_to_all_copies, all_copies_to_all_vars, &
-                                 read_ensemble_restart, write_ensemble_restart, get_copy_owner_index
+use ensemble_manager_mod, only : ensemble_type, read_ensemble_restart, write_ensemble_restart,  &
+                                 get_copy_owner_index, prepare_to_write_to_vars,                &
+                                 prepare_to_read_from_vars, prepare_to_update_vars, map_pe_to_task
 use mpi_utilities_mod,    only : my_task_id, send_to, receive_from
 
 implicit none
@@ -32,10 +29,10 @@
 
 
 ! version controlled file description for error handling, do not edit
-character(len=128), parameter :: &
-   source   = "$URL$", &
-   revision = "$Revision$", &
-   revdate  = "$Date$"
+character(len=256), parameter :: source   = &
+   "$URL$"
+character(len=32 ), parameter :: revision = "$Revision$"
+character(len=128), parameter :: revdate  = "$Date$"
 
 ! Manages both observation space and state space inflation
 ! Handles initial values and restarts, diagnostic output, and computations
@@ -57,7 +54,7 @@
 end type adaptive_inflate_type
 
 ! Module storage for writing error messages
-character(len = 129) :: errstring
+character(len = 255) :: msgstring
 
 ! Flag indicating whether module has been initialized
 logical :: initialized = .false.
@@ -99,11 +96,13 @@
 if(.not. initialized) then
    initialized = .true.
    call register_module(source, revision, revdate)
+endif
 
-   ! If non-deterministic inflation is being done, need to initialize random sequence.
-   ! use the task id number (plus 1 since they start at 0) to set the initial seed.
-   ! NOTE: non-deterministic inflation does NOT reproduce as process count is varied!
-   if(.not. deterministic) call init_random_seq(inflate_handle%ran_seq, my_task_id()+1)
+! If non-deterministic inflation is being done, need to initialize random sequence.
+! use the task id number (plus 1 since they start at 0) to set the initial seed.
+! NOTE: non-deterministic inflation does NOT reproduce as process count is varied!
+if(.not. deterministic) then
+   call init_random_seq(inflate_handle%ran_seq, my_task_id()+1)
 endif
 
 ! more information for users to document what they selected in the nml:
@@ -155,14 +154,14 @@
 
 ! Cannot support non-determistic inflation and an inf_lower_bound < 1
 if(.not. deterministic .and. inf_lower_bound < 1.0_r8) then
-   write(errstring, *) 'Cannot have non-deterministic inflation and inf_lower_bound < 1'
-   call error_handler(E_ERR, 'adaptive_inflate_init', errstring, source, revision, revdate)
+   write(msgstring, *) 'Cannot have non-deterministic inflation and inf_lower_bound < 1'
+   call error_handler(E_ERR, 'adaptive_inflate_init', msgstring, source, revision, revdate)
 endif
 
-! give this an initial value which defaults to time-constant inflation
-! change it below if the value(s) are > 0
-minmax_mean(:) = 0.0_r8
-minmax_sd(:)   = 0.0_r8
+! give these distinctive values; if inflation is being used
+! (e.g. inf_flavor > 0) then they should be set in all cases.
+minmax_mean(:) = missing_r8
+minmax_sd(:)   = missing_r8
 
 !------ Block for state space inflation initialization ------
 
@@ -173,16 +172,12 @@
 
    ! Verify that indices are contiguous
    if(ss_inflate_sd_index /= ss_inflate_index + 1) then
-      write(errstring, *) 'ss_inflate_index = ', ss_inflate_index, &
+      write(msgstring, *) 'ss_inflate_index = ', ss_inflate_index, &
          ' and ss_inflate_sd_index = ', ss_inflate_sd_index, ' must be continguous'
       call error_handler(E_ERR, 'adaptive_inflate_init', &
-         errstring, source, revision, revdate)
+         msgstring, source, revision, revdate)
    endif
 
-   ! set this, and then below if sd values are from a file, compute them
-   ! and send the value to PE0 if not already there.
-   minmax_sd = sd_initial
-
    ! Read in initial values from file OR get from namelist arguments
 
    ! If either mean, sd, or both are to be read from the restart file, read them in.
@@ -205,14 +200,39 @@
       ! a transpose.
       if (.not. mean_from_restart) then
          call get_copy_owner_index(ss_inflate_index, owner, owners_index)
-         if (owner == my_task_id()) ens_handle%vars(:, owners_index) = inf_initial
+         if (owner == ens_handle%my_pe) then
+            call prepare_to_write_to_vars(ens_handle)
+            ens_handle%vars(:, owners_index) = inf_initial
+         endif
       endif
       if (.not. sd_from_restart) then
          call get_copy_owner_index(ss_inflate_sd_index, owner, owners_index)
-         if (owner == my_task_id()) ens_handle%vars(:, owners_index) = sd_initial
+         if (owner == ens_handle%my_pe)  then
+            call prepare_to_write_to_vars(ens_handle)
+            ens_handle%vars(:, owners_index) = sd_initial
+         endif
       endif
    endif
 
+   ! Inflation type 3 is spatially-constant.  Make sure the entire array is set to that
+   ! value. the computation only uses index 1, but the diagnostics write out the entire
+   ! array and it will be misleading if not constant.  the inf values were set above.  
+   ! if they were set by namelist, this code changes nothing.  but if they were read in
+   ! from a file, then it is possible the values vary across the array.  these lines
+   ! ensure the entire array contains a single constant value to match what the code uses.
+   if(inf_flavor == 3) then
+      call get_copy_owner_index(ss_inflate_index, owner, owners_index)
+      if (owner == ens_handle%my_pe) then
+         call prepare_to_update_vars(ens_handle)
+         ens_handle%vars(:, owners_index) = ens_handle%vars(1, owners_index)
+      endif
+      call get_copy_owner_index(ss_inflate_sd_index, owner, owners_index)
+      if (owner == ens_handle%my_pe) then
+         call prepare_to_update_vars(ens_handle)
+         ens_handle%vars(:, owners_index) = ens_handle%vars(1, owners_index)
+      endif
+   endif
+
    ! this block figures out what the min/max value of the mean/sd is
    ! if we are reading in the values from a restart file.  it is used
    ! in diagnostic output so it needs to get to PE0.  we also could check it
@@ -224,18 +244,20 @@
       ! if inflation array is already on PE0, just figure out the
       ! largest value in the array and we're done.
       if (owner == 0) then
+         call prepare_to_read_from_vars(ens_handle)
          minmax_mean(1) = minval(ens_handle%vars(:, owners_index))
          minmax_mean(2) = maxval(ens_handle%vars(:, owners_index))
       else
          ! someone else has the inf array.  have the owner send the min/max
          ! values to PE0.  after this point only PE0 has the right value
          ! in minmax_mean, but it is the only one who is going to print below.
-         if (my_task_id() == 0) then
-            call receive_from(owner, minmax_mean)
-         else if (my_task_id() == owner) then
+         if (ens_handle%my_pe == 0) then
+            call receive_from(map_pe_to_task(ens_handle, owner), minmax_mean)
+         else if (ens_handle%my_pe == owner) then
+            call prepare_to_read_from_vars(ens_handle)
             minmax_mean(1) = minval(ens_handle%vars(:, owners_index))
             minmax_mean(2) = maxval(ens_handle%vars(:, owners_index))
-            call send_to(0, minmax_mean)
+            call send_to(map_pe_to_task(ens_handle, 0), minmax_mean)
          endif
       endif
    endif
@@ -244,34 +266,24 @@
       ! if inflation sd array is already on PE0, just figure out the
       ! largest value in the array and we're done.
       if (owner == 0) then
+         call prepare_to_read_from_vars(ens_handle)
          minmax_sd(1) = minval(ens_handle%vars(:, owners_index))
          minmax_sd(2) = maxval(ens_handle%vars(:, owners_index))
       else
          ! someone else has the sd array.  have the owner send the min/max
          ! values to PE0.  after this point only PE0 has the right value
          ! in minmax_sd, but it is the only one who is going to print below.
-         if (my_task_id() == 0) then
-            call receive_from(owner, minmax_sd)
-         else if (my_task_id() == owner) then
+         if (ens_handle%my_pe == 0) then
+            call receive_from(map_pe_to_task(ens_handle, owner), minmax_sd)
+         else if (ens_handle%my_pe == owner) then 
+            call prepare_to_read_from_vars(ens_handle)
             minmax_sd(1) = minval(ens_handle%vars(:, owners_index))
             minmax_sd(2) = maxval(ens_handle%vars(:, owners_index))
-            call send_to(0, minmax_sd)
+            call send_to(map_pe_to_task(ens_handle, 0), minmax_sd)
          endif
       endif
    endif
    
-   ! Inflation type 3 is spatially-constant.  Make sure the entire array is set to that
-   ! value. the computation only uses index 1, but the diagnostics write out the entire
-   ! array and it will be misleading if not constant.  the inf values were set above.  
-   ! if they were set by namelist, this code changes nothing.  but if they were read in
-   ! from a file, then it is possible the values vary across the array.  these lines
-   ! ensure the entire array contains a single constant value to match what the code uses.
-   if(inf_flavor == 3) then
-      call get_copy_owner_index(ss_inflate_index, owner, owners_index)
-      if (owner == my_task_id()) ens_handle%vars(:, owners_index) = ens_handle%vars(1, owners_index)
-      call get_copy_owner_index(ss_inflate_sd_index, owner, owners_index)
-      if (owner == my_task_id()) ens_handle%vars(:, owners_index) = ens_handle%vars(1, owners_index)
-   endif
 
 !------ Block for obs. space inflation initialization ------
 
@@ -282,28 +294,22 @@
    ! Only single values for inflation, inflation_sd (not arrays)
    if(mean_from_restart .or. sd_from_restart) then
       ! Open the file
-      restart_unit = get_unit()
-      open(unit = restart_unit, file = in_file_name, action = 'read', &
-           form = 'formatted', iostat = io)
-      if (io /= 0) then
-         write(errstring, *) 'unable to open inflation restart file ', &
-                              trim(in_file_name), ' for reading'
-         call error_handler(E_ERR, 'adaptive_inflate_init', &
-            errstring, source, revision, revdate)
-      endif
+      restart_unit = open_file(in_file_name, form='formatted', action='read')
       read(restart_unit, *, iostat = io) inflate_handle%inflate, inflate_handle%sd
       if (io /= 0) then
-         write(errstring, *) 'unable to read inflation restart values from ', &
+         write(msgstring, *) 'unable to read inflation restart values from ', &
                               trim(in_file_name)
          call error_handler(E_ERR, 'adaptive_inflate_init', &
-            errstring, source, revision, revdate)
+            msgstring, source, revision, revdate)
       endif
-      close(restart_unit)
+      call close_file(restart_unit)
    endif
    ! If using the namelist values, set (or overwrite) them here.
    if (.not. mean_from_restart) inflate_handle%inflate = inf_initial
    if (.not.   sd_from_restart) inflate_handle%sd      = sd_initial
 
+   minmax_mean(:) = inflate_handle%inflate
+   minmax_sd(:)   = inflate_handle%sd
 endif
 
 ! Write to log file what kind of inflation is being used.
@@ -342,25 +348,40 @@
       sadapt = ' spatially-constant,'
       akind = ' state-space'
    case default
-      write(errstring, *) 'Illegal inflation value for ', label
-      call error_handler(E_ERR, 'adaptive_inflate_init', errstring, source, revision, revdate)
+      write(msgstring, *) 'Illegal inflation value for ', label
+      call error_handler(E_ERR, 'adaptive_inflate_init', msgstring, source, revision, revdate)
 end select
 
 ! say in plain english what kind of inflation was selected.
-write(errstring, '(4A)') &
+write(msgstring, '(4A)') &
    trim(det), trim(tadapt), trim(sadapt), trim(akind)
-call error_handler(E_MSG, trim(label) // ' inflation:', errstring, source, revision, revdate)
+call error_handler(E_MSG, trim(label) // ' inflation:', msgstring, source, revision, revdate)
 
+! if inflation was set from a namelist, that message has already been
+! printed (further up in this routine).  for values set from a restart
+! file, if the inflation flavor is 2, the values printed are the min and
+! max from the entire array.  for flavors 1 and 3 there is only a single
+! value to print out.
 if (inf_flavor > 0) then
    if (mean_from_restart) then
-      write(errstring, '(A, F8.3, A, F8.3)') &
-         'inf mean   from restart file: min value: ', minmax_mean(1), ' max value: ', minmax_mean(2)
-      call error_handler(E_MSG, trim(label) // ' inflation:', errstring, source, revision, revdate)
+      if (inf_flavor == 2) then
+         write(msgstring, '(A, F8.3, A, F8.3)') &
+            'inf mean   from restart file: min value: ', minmax_mean(1), ' max value: ', minmax_mean(2)
+      else
+         write(msgstring, '(A, F8.3, A, F8.3)') &
+            'inf mean   from restart file: value: ', minmax_mean(1)
+      endif
+      call error_handler(E_MSG, trim(label) // ' inflation:', msgstring, source, revision, revdate)
    endif
    if (sd_from_restart) then
-      write(errstring, '(A, F8.3, A, F8.3)') &
-         'inf stddev from restart file: min value: ', minmax_sd(1), ' max value: ', minmax_sd(2)
-      call error_handler(E_MSG, trim(label) // ' inflation:', errstring, source, revision, revdate)
+      if (inf_flavor == 2) then
+         write(msgstring, '(A, F8.3, A, F8.3)') &
+            'inf stddev from restart file: min value: ', minmax_sd(1), ' max value: ', minmax_sd(2)
+      else
+         write(msgstring, '(A, F8.3, A, F8.3)') &
+            'inf stddev from restart file: value: ', minmax_sd(1)
+      endif
+      call error_handler(E_MSG, trim(label) // ' inflation:', msgstring, source, revision, revdate)
    endif
 endif
 
@@ -382,10 +403,10 @@
    if(do_varying_ss_inflate(inflate_handle) .or. do_single_ss_inflate(inflate_handle)) then
       ! Verify that indices are contiguous
       if(ss_inflate_sd_index /= ss_inflate_index + 1) then
-         write(errstring, *) 'ss_inflate_index = ', ss_inflate_index, &
+         write(msgstring, *) 'ss_inflate_index = ', ss_inflate_index, &
             ' and ss_inflate_sd_index = ', ss_inflate_sd_index, ' must be continguous'
          call error_handler(E_ERR, 'adaptive_inflate_end', &
-            errstring, source, revision, revdate)
+            msgstring, source, revision, revdate)
       endif
 
       ! Write the inflate and inflate_sd as two copies for a restart
@@ -395,28 +416,21 @@
    ! Flavor 1 is observation space, write its restart directly
    else if(do_obs_inflate(inflate_handle)) then
       ! Open the restart file
-      restart_unit = get_unit()
-      open(unit = restart_unit, file = inflate_handle%out_file_name, &
-         action = 'write', form = 'formatted', iostat = io)
-      if (io /= 0) then
-         write(errstring, *) 'unable to open inflation restart file ', &
-                              trim(inflate_handle%out_file_name), ' for writing'
-         call error_handler(E_ERR, 'adaptive_inflate_end', &
-            errstring, source, revision, revdate)
-      endif
+      restart_unit = open_file(inflate_handle%out_file_name, &
+                               form = 'formatted', action='write')

@@ Diff output truncated at 40000 characters. @@