From 0a1f3b4cd893ab7abc58b37893d84a6127e6dd41 Mon Sep 17 00:00:00 2001 From: kdraeder Date: Wed, 8 Jan 2025 09:06:06 -0700 Subject: [PATCH 1/7] Updated RDA addresses and dataset names Did not update ./CHANGELOG.rst ./_build/html/CHANGELOG.html ./_build/html/_sources/CHANGELOG.rst.txt These substitutions were made: sed \ -e "s#glade\/collections#glade\/campaign\/collections#" \ -e "s#edu\/ds\/#edu\/datasets\/ds#g" \ -e "s#ds345.0#d345000#g" \ -e "s#ds199.1#d199001#g" \ -e "s#ds090.0#d090000#g" \ -e "s#ds337.0#d337000#g" \ -e "s#ds285.0#d285000#g" \ --- models/POP/readme.rst | 4 ++-- ..._datm.streams.txt.CPLHISTForcing.Solar_template | 10 +++++----- ...tm.streams.txt.CPLHISTForcing.State1hr_template | 10 +++++----- ...tm.streams.txt.CPLHISTForcing.State3hr_template | 10 +++++----- ...treams.txt.CPLHISTForcing.nonSolarFlux_template | 10 +++++----- models/cam-fv/readme.rst | 10 +++++----- models/cice/shell_scripts/CESM1_5_setup_ensemble | 0 .../datm.streams.txt.CPLHIST3HrWx.Precip_template | 4 ++-- .../datm.streams.txt.CPLHIST3HrWx.Solar_template | 4 ++-- ...ams.txt.CPLHIST3HrWx.nonSolarNonPrecip_template | 4 ++-- ...atm.streams.txt.CPLHISTForcing.Solar_2005to2010 | 4 ++-- .../datm.streams.txt.CPLHISTForcing.Solar_complete | 4 ++-- .../datm.streams.txt.CPLHISTForcing.Solar_single | 4 ++-- .../datm.streams.txt.CPLHISTForcing.Solar_template | 4 ++-- ....streams.txt.CPLHISTForcing.State1hr_2005to2010 | 4 ++-- ...tm.streams.txt.CPLHISTForcing.State1hr_complete | 4 ++-- ...datm.streams.txt.CPLHISTForcing.State1hr_single | 4 ++-- ...tm.streams.txt.CPLHISTForcing.State1hr_template | 4 ++-- ....streams.txt.CPLHISTForcing.State3hr_2005to2010 | 4 ++-- .../datm.streams.txt.CPLHISTForcing.State3hr_3hr | 4 ++-- ...tm.streams.txt.CPLHISTForcing.State3hr_complete | 4 ++-- ...datm.streams.txt.CPLHISTForcing.State3hr_single | 4 ++-- ...tm.streams.txt.CPLHISTForcing.State3hr_template | 4 ++-- ...eams.txt.CPLHISTForcing.nonSolarFlux_2005to2010 | 4 ++-- ...atm.streams.txt.CPLHISTForcing.nonSolarFlux_3hr | 4 ++-- ...treams.txt.CPLHISTForcing.nonSolarFlux_complete | 4 ++-- ....streams.txt.CPLHISTForcing.nonSolarFlux_single | 4 ++-- ...treams.txt.CPLHISTForcing.nonSolarFlux_template | 4 ++-- models/clm/CAM_bias_correction/CAM4_site_grid.sh | 2 +- models/clm/CAM_bias_correction/CAM6_site_grid.sh | 2 +- models/clm/CAM_bias_correction/README | 6 +++--- models/clm/matlab/CheckDATM.m | 2 +- .../shell_scripts/cesm1_x/CESM1_1_1_setup_hybrid | 0 .../clm/shell_scripts/cesm1_x/CESM1_1_1_setup_pmo | 0 .../shell_scripts/cesm1_x/CESM1_2_1_setup_hybrid | 0 models/clm/shell_scripts/cesm2_2/DART_params.csh | 0 .../datm.streams.txt.CPLHISTForcing.Solar_complete | 12 ++++++------ ...tm.streams.txt.CPLHISTForcing.Solar_single_year | 12 ++++++------ ...tm.streams.txt.CPLHISTForcing.State1hr_complete | 12 ++++++------ ...streams.txt.CPLHISTForcing.State1hr_single_year | 12 ++++++------ ...tm.streams.txt.CPLHISTForcing.State3hr_complete | 12 ++++++------ ...streams.txt.CPLHISTForcing.State3hr_single_year | 12 ++++++------ ...treams.txt.CPLHISTForcing.nonSolarFlux_complete | 12 ++++++------ ...ams.txt.CPLHISTForcing.nonSolarFlux_single_year | 12 ++++++------ models/clm/tutorial/README.rst | 14 +++++++------- models/wrf/tutorial/README.rst | 6 +++--- .../obs_converters/NCEP/prep_bufr/prep_bufr.rst | 4 ++-- observations/obs_converters/WOD/WOD.rst | 2 +- 48 files changed, 136 insertions(+), 136 deletions(-) mode change 100755 => 100644 models/cice/shell_scripts/CESM1_5_setup_ensemble mode change 100755 => 100644 models/clm/CAM_bias_correction/CAM4_site_grid.sh mode change 100755 => 100644 models/clm/CAM_bias_correction/CAM6_site_grid.sh mode change 100755 => 100644 models/clm/shell_scripts/cesm1_x/CESM1_1_1_setup_hybrid mode change 100755 => 100644 models/clm/shell_scripts/cesm1_x/CESM1_1_1_setup_pmo mode change 100755 => 100644 models/clm/shell_scripts/cesm1_x/CESM1_2_1_setup_hybrid mode change 100755 => 100644 models/clm/shell_scripts/cesm2_2/DART_params.csh diff --git a/models/POP/readme.rst b/models/POP/readme.rst index 3726297166..65f74d7914 100644 --- a/models/POP/readme.rst +++ b/models/POP/readme.rst @@ -62,7 +62,7 @@ making minor edits to set details that are specific to your project. The setup scripts create a CESM case in which POP is configured using a 1° horizontal grid, and uses the eddy parametrization of Gent and McWilliams (1990). [2]_ The CICE model is active and atmospheric forcing is provided by the `CAM6 DART -Reanalysis `_. +Reanalysis `_. The filesystem attached to NSF NCAR's supercomputer is known as the Globally Accessible Data Environment (GLADE). All filepaths on GLADE have the structure: @@ -285,7 +285,7 @@ Data atmosphere streams files ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ The setup scripts configure the CESM case with atmospheric forcing from the -`CAM6 DART Reanalysis `_. The coupler +`CAM6 DART Reanalysis `_. The coupler history files from this reanalysis are referenced in ``user_datm.streams*template`` files. These ``user_datm.streams*template`` files are contained in the same directory as the setup scripts and are diff --git a/models/POP/shell_scripts/cesm2_1/user_datm.streams.txt.CPLHISTForcing.Solar_template b/models/POP/shell_scripts/cesm2_1/user_datm.streams.txt.CPLHISTForcing.Solar_template index 8e6699a325..3f3af1304b 100644 --- a/models/POP/shell_scripts/cesm2_1/user_datm.streams.txt.CPLHISTForcing.Solar_template +++ b/models/POP/shell_scripts/cesm2_1/user_datm.streams.txt.CPLHISTForcing.Solar_template @@ -1,11 +1,11 @@ - The CAM6-DART Ensemble Reanalysis (NCAR RDA ds345.0) contains + The CAM6-DART Ensemble Reanalysis (NCAR RDA d345000) contains DATM forcing files particularly appropriate for CESM experiments. - https://rda.ucar.edu/datasets/ds345.0 + https://rda.ucar.edu/datasets/d345000 They are available on spinning disk (compressed) on the NCAR supercomputers at: - /glade/collections/rda/data/ds345.0/cpl_unzipped + /glade/campaign/collections/rda/data/d345000/cpl_unzipped @@ -16,7 +16,7 @@ doma_mask mask - /glade/collections/rda/data/ds345.0/cpl_unzipped/NINST + /glade/campaign/collections/rda/data/d345000/cpl_unzipped/NINST f.e21.FHIST_BGC.f09_025.CAM6assim.011.cpl_NINST.ha2x3h.2011.nc @@ -30,7 +30,7 @@ a2x3h_Faxa_swvdf swvdf - /glade/collections/rda/data/ds345.0/cpl_unzipped/NINST + /glade/campaign/collections/rda/data/d345000/cpl_unzipped/NINST f.e21.FHIST_BGC.f09_025.CAM6assim.011.cpl_NINST.ha2x3h.2011.nc diff --git a/models/POP/shell_scripts/cesm2_1/user_datm.streams.txt.CPLHISTForcing.State1hr_template b/models/POP/shell_scripts/cesm2_1/user_datm.streams.txt.CPLHISTForcing.State1hr_template index 434f5edf9b..db9a2b474d 100644 --- a/models/POP/shell_scripts/cesm2_1/user_datm.streams.txt.CPLHISTForcing.State1hr_template +++ b/models/POP/shell_scripts/cesm2_1/user_datm.streams.txt.CPLHISTForcing.State1hr_template @@ -1,11 +1,11 @@ - The CAM6-DART Ensemble Reanalysis (NCAR RDA ds345.0) contains + The CAM6-DART Ensemble Reanalysis (NCAR RDA d345000) contains DATM forcing files particularly appropriate for CESM experiments. - https://rda.ucar.edu/datasets/ds345.0 + https://rda.ucar.edu/datasets/d345000 They are available on spinning disk (compressed) on the NCAR supercomputers at: - /glade/collections/rda/data/ds345.0/cpl_unzipped + /glade/campaign/collections/rda/data/d345000/cpl_unzipped @@ -16,7 +16,7 @@ doma_mask mask - /glade/collections/rda/data/ds345.0/cpl_unzipped/NINST + /glade/campaign/collections/rda/data/d345000/cpl_unzipped/NINST f.e21.FHIST_BGC.f09_025.CAM6assim.011.cpl_NINST.ha2x1h.2011.nc @@ -28,7 +28,7 @@ a2x1h_Sa_v v - /glade/collections/rda/data/ds345.0/cpl_unzipped/NINST + /glade/campaign/collections/rda/data/d345000/cpl_unzipped/NINST linear diff --git a/models/POP/shell_scripts/cesm2_1/user_datm.streams.txt.CPLHISTForcing.State3hr_template b/models/POP/shell_scripts/cesm2_1/user_datm.streams.txt.CPLHISTForcing.State3hr_template index 5b1925c10e..cdc65f182e 100644 --- a/models/POP/shell_scripts/cesm2_1/user_datm.streams.txt.CPLHISTForcing.State3hr_template +++ b/models/POP/shell_scripts/cesm2_1/user_datm.streams.txt.CPLHISTForcing.State3hr_template @@ -1,11 +1,11 @@ - The CAM6-DART Ensemble Reanalysis (NCAR RDA ds345.0) contains + The CAM6-DART Ensemble Reanalysis (NCAR RDA d345000) contains DATM forcing files particularly appropriate for CESM experiments. - https://rda.ucar.edu/datasets/ds345.0 + https://rda.ucar.edu/datasets/d345000 They are available on spinning disk (compressed) on the NCAR supercomputers at: - /glade/collections/rda/data/ds345.0/cpl_unzipped + /glade/campaign/collections/rda/data/d345000/cpl_unzipped @@ -16,7 +16,7 @@ doma_mask mask - /glade/collections/rda/data/ds345.0/cpl_unzipped/NINST + /glade/campaign/collections/rda/data/d345000/cpl_unzipped/NINST f.e21.FHIST_BGC.f09_025.CAM6assim.011.cpl_NINST.ha2x3h.2011.nc @@ -34,7 +34,7 @@ a2x3h_Sa_pslv pslv - /glade/collections/rda/data/ds345.0/cpl_unzipped/NINST + /glade/campaign/collections/rda/data/d345000/cpl_unzipped/NINST linear diff --git a/models/POP/shell_scripts/cesm2_1/user_datm.streams.txt.CPLHISTForcing.nonSolarFlux_template b/models/POP/shell_scripts/cesm2_1/user_datm.streams.txt.CPLHISTForcing.nonSolarFlux_template index d1f6d75623..ee5513dc43 100644 --- a/models/POP/shell_scripts/cesm2_1/user_datm.streams.txt.CPLHISTForcing.nonSolarFlux_template +++ b/models/POP/shell_scripts/cesm2_1/user_datm.streams.txt.CPLHISTForcing.nonSolarFlux_template @@ -1,11 +1,11 @@ - The CAM6-DART Ensemble Reanalysis (NCAR RDA ds345.0) contains + The CAM6-DART Ensemble Reanalysis (NCAR RDA d345000) contains DATM forcing files particularly appropriate for CESM experiments. - https://rda.ucar.edu/datasets/ds345.0 + https://rda.ucar.edu/datasets/d345000 They are available on spinning disk (compressed) on the NCAR supercomputers at: - /glade/collections/rda/data/ds345.0/cpl_unzipped + /glade/campaign/collections/rda/data/d345000/cpl_unzipped @@ -16,7 +16,7 @@ doma_mask mask - /glade/collections/rda/data/ds345.0/cpl_unzipped/NINST + /glade/campaign/collections/rda/data/d345000/cpl_unzipped/NINST f.e21.FHIST_BGC.f09_025.CAM6assim.011.cpl_NINST.ha2x3h.2011.nc @@ -31,7 +31,7 @@ a2x3h_Faxa_lwdn lwdn - /glade/collections/rda/data/ds345.0/cpl_unzipped/NINST + /glade/campaign/collections/rda/data/d345000/cpl_unzipped/NINST f.e21.FHIST_BGC.f09_025.CAM6assim.011.cpl_NINST.ha2x3h.2011.nc diff --git a/models/cam-fv/readme.rst b/models/cam-fv/readme.rst index c47683c2b8..0585feb30d 100644 --- a/models/cam-fv/readme.rst +++ b/models/cam-fv/readme.rst @@ -118,7 +118,7 @@ Reanalyses There have been two large-scale reanalysis efforts using CAM-FV and DART. The **CAM6 Data Assimilation Research Testbed (DART) Reanalysis** is archived in the NSF NCAR Research Data Archive -`DS345.0 `__ . +`DS345.0 `__ . (See the |CAM6_Rean|_ ). It contains just under 120Tb (yes Tb) of data: @@ -139,7 +139,7 @@ An earlier, more limited dataset can be found in the `**Ensemble of Atmospheric Forcing Files from a CAM4-FV Reanalysis** `__ is archived in the NSF NCAR Research Data Archive -`DS199.1 `__ . +`DS199.1 `__ . It contains about 1.5Tb of data: This dataset contains files that are an ensemble of 'coupler history' @@ -154,7 +154,7 @@ It contains about 1.5Tb of data: for CESM component sets that require a data atmosphere. Some example stream text files are included in the RDA to illustrate how to use these data. -.. * CAM4, 2 degree, 2000-2010, `Reanalysis `__ +.. * CAM4, 2 degree, 2000-2010, `Reanalysis `__ .. * files from the old "large file site": http://www.image.ucar.edu/pub/DART/CAM/ Observations @@ -167,11 +167,11 @@ which contain the types of observations in the table below These files are available on NSF NCAR's glade file system: /glade/p/cisl/dares/Observations/NCEP+ACARS+GPS+AIRS/Thinned_x9x10. Versions of these files, which also have the results of the reanalysis in them, -are available from the RDA ds345.0 linked above. +are available from the RDA d345000 linked above. NCEP NCEP's PREPBUFR files (prepqm) in NSF NCAR's Research Data Archive: - (https://rda.ucar.edu/datasets/ds090.0/) + (https://rda.ucar.edu/datasets/d090000/) COSMIC This site (http://www.cosmic.ucar.edu/) provides atmospheric refractivity diff --git a/models/cice/shell_scripts/CESM1_5_setup_ensemble b/models/cice/shell_scripts/CESM1_5_setup_ensemble old mode 100755 new mode 100644 diff --git a/models/cice/shell_scripts/datm.streams.txt.CPLHIST3HrWx.Precip_template b/models/cice/shell_scripts/datm.streams.txt.CPLHIST3HrWx.Precip_template index 576d583bbe..a5c794b374 100644 --- a/models/cice/shell_scripts/datm.streams.txt.CPLHIST3HrWx.Precip_template +++ b/models/cice/shell_scripts/datm.streams.txt.CPLHIST3HrWx.Precip_template @@ -18,7 +18,7 @@ doma_mask mask - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 CAM_DATM.cpl_NINST.ha2x1dx6h.RUNYEAR.nc @@ -32,7 +32,7 @@ a2x6h_Faxa_snowl snowl - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 nearest diff --git a/models/cice/shell_scripts/datm.streams.txt.CPLHIST3HrWx.Solar_template b/models/cice/shell_scripts/datm.streams.txt.CPLHIST3HrWx.Solar_template index 969819950b..a63e7c2c48 100644 --- a/models/cice/shell_scripts/datm.streams.txt.CPLHIST3HrWx.Solar_template +++ b/models/cice/shell_scripts/datm.streams.txt.CPLHIST3HrWx.Solar_template @@ -18,7 +18,7 @@ doma_mask mask - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 CAM_DATM.cpl_NINST.ha2x1dx6h.RUNYEAR.nc @@ -32,7 +32,7 @@ a2x6h_Faxa_swvdf swvdf - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 coszen diff --git a/models/cice/shell_scripts/datm.streams.txt.CPLHIST3HrWx.nonSolarNonPrecip_template b/models/cice/shell_scripts/datm.streams.txt.CPLHIST3HrWx.nonSolarNonPrecip_template index feadcd5721..5a37e0bddf 100644 --- a/models/cice/shell_scripts/datm.streams.txt.CPLHIST3HrWx.nonSolarNonPrecip_template +++ b/models/cice/shell_scripts/datm.streams.txt.CPLHIST3HrWx.nonSolarNonPrecip_template @@ -18,7 +18,7 @@ doma_mask mask - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 CAM_DATM.cpl_NINST.ha2x1dx6h.RUNYEAR.nc @@ -38,7 +38,7 @@ a2x6h_Sa_pslv pslv - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 linear diff --git a/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.Solar_2005to2010 b/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.Solar_2005to2010 index 6fade7c355..427b2efe7c 100644 --- a/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.Solar_2005to2010 +++ b/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.Solar_2005to2010 @@ -18,7 +18,7 @@ doma_mask mask - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 CAM_DATM.cpl_NINST.ha2x1dx6h.RUNYEAR.nc @@ -32,7 +32,7 @@ a2x6h_Faxa_swvdf swvdf - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 coszen diff --git a/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.Solar_complete b/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.Solar_complete index 36846c7ae3..3e50d3ee65 100644 --- a/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.Solar_complete +++ b/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.Solar_complete @@ -18,7 +18,7 @@ doma_mask mask - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 CAM_DATM.cpl_NINST.ha2x1dx6h.RUNYEAR.nc @@ -32,7 +32,7 @@ a2x6h_Faxa_swvdf swvdf - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 coszen diff --git a/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.Solar_single b/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.Solar_single index 4ed9fd8509..ce5c1464d9 100644 --- a/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.Solar_single +++ b/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.Solar_single @@ -18,7 +18,7 @@ doma_mask mask - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 CAM_DATM.cpl_NINST.ha2x1dx6h.RUNYEAR.nc @@ -32,7 +32,7 @@ a2x6h_Faxa_swvdf swvdf - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 coszen diff --git a/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.Solar_template b/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.Solar_template index 969819950b..a63e7c2c48 100644 --- a/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.Solar_template +++ b/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.Solar_template @@ -18,7 +18,7 @@ doma_mask mask - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 CAM_DATM.cpl_NINST.ha2x1dx6h.RUNYEAR.nc @@ -32,7 +32,7 @@ a2x6h_Faxa_swvdf swvdf - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 coszen diff --git a/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.State1hr_2005to2010 b/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.State1hr_2005to2010 index 9dfddf64e2..138871c4ea 100644 --- a/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.State1hr_2005to2010 +++ b/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.State1hr_2005to2010 @@ -18,7 +18,7 @@ doma_mask mask - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 CAM_DATM.cpl_NINST.ha2x1dx6h.RUNYEAR.nc @@ -30,7 +30,7 @@ a2x6h_Sa_v v - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 linear diff --git a/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.State1hr_complete b/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.State1hr_complete index 3a8c0d7975..0faf17247c 100644 --- a/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.State1hr_complete +++ b/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.State1hr_complete @@ -18,7 +18,7 @@ doma_mask mask - /glade/p/collections/rda/data/ds199.1 + /glade/p/collections/rda/data/d199001 CAM_DATM.cpl_NINST.ha2x1dx6h.RUNYEAR.nc @@ -30,7 +30,7 @@ a2x6h_Sa_v v - /glade/p/collections/rda/data/ds199.1 + /glade/p/collections/rda/data/d199001 linear diff --git a/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.State1hr_single b/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.State1hr_single index 0cc35331e4..55ca97d04f 100644 --- a/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.State1hr_single +++ b/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.State1hr_single @@ -18,7 +18,7 @@ doma_mask mask - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 CAM_DATM.cpl_NINST.ha2x1dx6h.RUNYEAR.nc @@ -30,7 +30,7 @@ a2x6h_Sa_v v - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 linear diff --git a/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.State1hr_template b/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.State1hr_template index c03d2bed67..f6854820aa 100644 --- a/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.State1hr_template +++ b/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.State1hr_template @@ -18,7 +18,7 @@ doma_mask mask - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 CAM_DATM.cpl_NINST.ha2x1dx6h.RUNYEAR.nc @@ -30,7 +30,7 @@ a2x6h_Sa_v v - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 linear diff --git a/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.State3hr_2005to2010 b/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.State3hr_2005to2010 index e79be1cf9b..305a1059f2 100644 --- a/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.State3hr_2005to2010 +++ b/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.State3hr_2005to2010 @@ -18,7 +18,7 @@ doma_mask mask - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 CAM_DATM.cpl_NINST.ha2x1dx6h.RUNYEAR.nc @@ -36,7 +36,7 @@ a2x6h_Sa_pslv pslv - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 linear diff --git a/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.State3hr_3hr b/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.State3hr_3hr index 1b5fe2404a..3cec72e34a 100644 --- a/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.State3hr_3hr +++ b/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.State3hr_3hr @@ -18,7 +18,7 @@ doma_mask mask - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 CAM_DATM.cpl_NINST.ha2x1dx3h.RUNYEAR.nc @@ -36,7 +36,7 @@ a2x3h_Sa_pslv pslv - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 linear diff --git a/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.State3hr_complete b/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.State3hr_complete index 0f03f47ff0..4095317a03 100644 --- a/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.State3hr_complete +++ b/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.State3hr_complete @@ -18,7 +18,7 @@ doma_mask mask - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 CAM_DATM.cpl_NINST.ha2x1dx6h.RUNYEAR.nc @@ -36,7 +36,7 @@ a2x6h_Sa_pslv pslv - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 linear diff --git a/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.State3hr_single b/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.State3hr_single index 4bb162abbf..a8926c0484 100644 --- a/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.State3hr_single +++ b/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.State3hr_single @@ -18,7 +18,7 @@ doma_mask mask - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 CAM_DATM.cpl_NINST.ha2x1dx6h.RUNYEAR.nc @@ -36,7 +36,7 @@ a2x6h_Sa_pslv pslv - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 linear diff --git a/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.State3hr_template b/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.State3hr_template index e7dec9697a..9de092787a 100644 --- a/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.State3hr_template +++ b/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.State3hr_template @@ -18,7 +18,7 @@ doma_mask mask - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 CAM_DATM.cpl_NINST.ha2x1dx6h.RUNYEAR.nc @@ -36,7 +36,7 @@ a2x6h_Sa_pslv pslv - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 linear diff --git a/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.nonSolarFlux_2005to2010 b/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.nonSolarFlux_2005to2010 index f223eae38b..78d96eadb5 100644 --- a/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.nonSolarFlux_2005to2010 +++ b/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.nonSolarFlux_2005to2010 @@ -18,7 +18,7 @@ doma_mask mask - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 CAM_DATM.cpl_NINST.ha2x1dx6h.RUNYEAR.nc @@ -33,7 +33,7 @@ a2x6h_Faxa_lwdn lwdn - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 -10800 diff --git a/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.nonSolarFlux_3hr b/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.nonSolarFlux_3hr index bd8ecc3c00..b6a3333b66 100644 --- a/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.nonSolarFlux_3hr +++ b/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.nonSolarFlux_3hr @@ -18,7 +18,7 @@ doma_mask mask - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 CAM_DATM.cpl_NINST.ha2x1dx3h.RUNYEAR.nc @@ -33,7 +33,7 @@ a2x3h_Faxa_lwdn lwdn - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 -10800 diff --git a/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.nonSolarFlux_complete b/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.nonSolarFlux_complete index 25f2fd1f6c..0d52272e12 100644 --- a/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.nonSolarFlux_complete +++ b/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.nonSolarFlux_complete @@ -18,7 +18,7 @@ doma_mask mask - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 CAM_DATM.cpl_NINST.ha2x1dx6h.RUNYEAR.nc @@ -33,7 +33,7 @@ a2x6h_Faxa_lwdn lwdn - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 -10800 diff --git a/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.nonSolarFlux_single b/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.nonSolarFlux_single index 02d088af5b..efa27169a1 100644 --- a/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.nonSolarFlux_single +++ b/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.nonSolarFlux_single @@ -18,7 +18,7 @@ doma_mask mask - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 CAM_DATM.cpl_NINST.ha2x1dx6h.RUNYEAR.nc @@ -32,7 +32,7 @@ a2x6h_Faxa_snowl snowl - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 nearest diff --git a/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.nonSolarFlux_template b/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.nonSolarFlux_template index 16321df6a7..314bff3f1e 100644 --- a/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.nonSolarFlux_template +++ b/models/cice/shell_scripts/datm.streams.txt.CPLHISTForcing.nonSolarFlux_template @@ -18,7 +18,7 @@ doma_mask mask - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 CAM_DATM.cpl_NINST.ha2x1dx6h.RUNYEAR.nc @@ -33,7 +33,7 @@ a2x6h_Faxa_lwdn lwdn - /glade/collections/rda/data/ds199.1 + /glade/campaign/collections/rda/data/d199001 -10800 diff --git a/models/clm/CAM_bias_correction/CAM4_site_grid.sh b/models/clm/CAM_bias_correction/CAM4_site_grid.sh old mode 100755 new mode 100644 index 1ca0f8e47d..a80dd7d947 --- a/models/clm/CAM_bias_correction/CAM4_site_grid.sh +++ b/models/clm/CAM_bias_correction/CAM4_site_grid.sh @@ -3,7 +3,7 @@ # Extracts site level grid cell from CAM4 reanalysis # CAM4 reanalysis -CAM4_grid_path="/glade/collections/rda/data/ds199.1/" +CAM4_grid_path="/glade/campaign/collections/rda/data/d199001/" # Site Level grid cell from CAM4 renanalysis CAM4_site_path="/glade/work/bmraczka/CAM4_NR1/" diff --git a/models/clm/CAM_bias_correction/CAM6_site_grid.sh b/models/clm/CAM_bias_correction/CAM6_site_grid.sh old mode 100755 new mode 100644 index 29e7bd3459..3bdc1bacdc --- a/models/clm/CAM_bias_correction/CAM6_site_grid.sh +++ b/models/clm/CAM_bias_correction/CAM6_site_grid.sh @@ -4,7 +4,7 @@ # CAM6 Reanalysis -CAM6_grid_path="/glade/collections/rda/data/ds345.0/cpl_unzipped/" +CAM6_grid_path="/glade/campaign/collections/rda/data/d345000/cpl_unzipped/" # Site level grid cell from CAM6 reanalysis CAM6_site_path="/glade/work/bmraczka/CAM6_NR1/" diff --git a/models/clm/CAM_bias_correction/README b/models/clm/CAM_bias_correction/README index f516f6e298..53ec4bbd0a 100644 --- a/models/clm/CAM_bias_correction/README +++ b/models/clm/CAM_bias_correction/README @@ -3,7 +3,7 @@ Purpose: These scripts are designed to improve site level CLM-DART simulations. They remove -bias from the CAM6 (ds345.0) and CAM4 (ds199.1) reanalysis products. Meteorological bias +bias from the CAM6 (d345000) and CAM4 (d199001) reanalysis products. Meteorological bias is significant and detrimental for site level simulations because of the spatial mismatch between a reanalysis grid (1-2 degrees) and a land site (1x1 km). These scripts are designed to operate on the CAM6 or CAM4 reanalysis global gridded datasets @@ -13,8 +13,8 @@ See the following github issue for more information: https://github.com/NCAR/DAR Required Input: 1) CAM4 or CAM6 global datasets (80 members) Located on Cheyenne or archived at: - https://rda.ucar.edu/datasets/ds345-0/ - https://rda.ucar.edu/datasets/ds199-1/ + https://rda.ucar.edu/datasets/d345000/ + https://rda.ucar.edu/datasets/d199001/ 2) Site Level Meterological Forcing (e.g. Ameriflux, NEON) The scripts are designed for PLUMBER2 format w/ US-NR1 as example. diff --git a/models/clm/matlab/CheckDATM.m b/models/clm/matlab/CheckDATM.m index 4a422b88df..68c5b5e094 100644 --- a/models/clm/matlab/CheckDATM.m +++ b/models/clm/matlab/CheckDATM.m @@ -7,7 +7,7 @@ % characteristics for CAM reanalysis. This checks % for missing time steps or suspicious variance across members -dirname = '/glade/collections/rda/data/ds199.1'; +dirname = '/glade/campaign/collections/rda/data/d199001'; dirname = '/glade/p/cisl/dares/thoar/CAM_DATM/4xdaily'; % float a2x6h_Faxa_swndf(time, a2x6h_ny, a2x6h_nx) ; diff --git a/models/clm/shell_scripts/cesm1_x/CESM1_1_1_setup_hybrid b/models/clm/shell_scripts/cesm1_x/CESM1_1_1_setup_hybrid old mode 100755 new mode 100644 diff --git a/models/clm/shell_scripts/cesm1_x/CESM1_1_1_setup_pmo b/models/clm/shell_scripts/cesm1_x/CESM1_1_1_setup_pmo old mode 100755 new mode 100644 diff --git a/models/clm/shell_scripts/cesm1_x/CESM1_2_1_setup_hybrid b/models/clm/shell_scripts/cesm1_x/CESM1_2_1_setup_hybrid old mode 100755 new mode 100644 diff --git a/models/clm/shell_scripts/cesm2_2/DART_params.csh b/models/clm/shell_scripts/cesm2_2/DART_params.csh old mode 100755 new mode 100644 diff --git a/models/clm/shell_scripts/cesm2_2/datm.streams.txt.CPLHISTForcing.Solar_complete b/models/clm/shell_scripts/cesm2_2/datm.streams.txt.CPLHISTForcing.Solar_complete index 49d21c5121..bb11e80d9e 100644 --- a/models/clm/shell_scripts/cesm2_2/datm.streams.txt.CPLHISTForcing.Solar_complete +++ b/models/clm/shell_scripts/cesm2_2/datm.streams.txt.CPLHISTForcing.Solar_complete @@ -4,14 +4,14 @@ Two CAM-DART Ensemble Reanalysis efforts have been completed and provide DATM forcing files particularly appropriate for CESM experiments. - NSF NCAR RDA ds199.1 | DOI: 10.5065/38ED-RZ08 + NSF NCAR RDA d199001 | DOI: 10.5065/38ED-RZ08 Spans 1998_01-2010_12 at 1.875x2.5 degrees resolution every 6 hours a2x6h_Faxa_swndr long_name = "Direct near-infrared incident solar radiation" ; a2x6h_Faxa_swvdr long_name = "Direct visible incident solar radiation" ; a2x6h_Faxa_swndf long_name = "Diffuse near-infrared incident solar radiation" ; a2x6h_Faxa_swvdf long_name = "Diffuse visible incident solar radiation" ; - NSF NCAR RDA ds345.0 | DOI: 10.5065/JG1E-8525 + NSF NCAR RDA d345000 | DOI: 10.5065/JG1E-8525 Spans 2010_07-2019_12 at 0.9x1.25 degree resolution a2x1hi_Faxa_swndr long_name = "Direct near-infrared incident solar radiation" ; a2x1hi_Faxa_swvdr long_name = "Direct visible incident solar radiation" ; @@ -19,7 +19,7 @@ a2x1hi_Faxa_swvdf long_name = "Diffuse visible incident solar radiation" ; The NSF NCAR RDA collections are located: - /glade/campaign/collections/rda/data/ds345.0/cpl_unzipped/----/{CASENAME}.cpl_----.ha2x*.YYYY.nc + /glade/campaign/collections/rda/data/d345000/cpl_unzipped/----/{CASENAME}.cpl_----.ha2x*.YYYY.nc @@ -27,7 +27,7 @@ Raeder et al. 80 member CAM/DART reanalysis V2 - https://rda.ucar.edu/datasets/ds345.0 + https://rda.ucar.edu/datasets/d345000 https://doi.org/10.5065/JG1E-8525 @@ -39,7 +39,7 @@ doma_mask mask - /glade/campaign/collections/rda/data/ds345.0/cpl_unzipped/NINST + /glade/campaign/collections/rda/data/d345000/cpl_unzipped/NINST f.e21.FHIST_BGC.f09_025.CAM6assim.011.cpl_NINST.ha2x1hi.2011.nc @@ -53,7 +53,7 @@ a2x1hi_Faxa_swvdf swvdf - /glade/campaign/collections/rda/data/ds345.0/cpl_unzipped/NINST + /glade/campaign/collections/rda/data/d345000/cpl_unzipped/NINST 1800 diff --git a/models/clm/shell_scripts/cesm2_2/datm.streams.txt.CPLHISTForcing.Solar_single_year b/models/clm/shell_scripts/cesm2_2/datm.streams.txt.CPLHISTForcing.Solar_single_year index a295b392d3..675cf3c9cf 100644 --- a/models/clm/shell_scripts/cesm2_2/datm.streams.txt.CPLHISTForcing.Solar_single_year +++ b/models/clm/shell_scripts/cesm2_2/datm.streams.txt.CPLHISTForcing.Solar_single_year @@ -4,14 +4,14 @@ Two CAM-DART Ensemble Reanalysis efforts have been completed and provide DATM forcing files particularly appropriate for CESM experiments. - NSF NCAR RDA ds199.1 | DOI: 10.5065/38ED-RZ08 + NSF NCAR RDA d199001 | DOI: 10.5065/38ED-RZ08 Spans 1998_01-2010_12 at 1.875x2.5 degrees resolution every 6 hours a2x6h_Faxa_swndr long_name = "Direct near-infrared incident solar radiation" ; a2x6h_Faxa_swvdr long_name = "Direct visible incident solar radiation" ; a2x6h_Faxa_swndf long_name = "Diffuse near-infrared incident solar radiation" ; a2x6h_Faxa_swvdf long_name = "Diffuse visible incident solar radiation" ; - NSF NCAR RDA ds345.0 | DOI: 10.5065/JG1E-8525 + NSF NCAR RDA d345000 | DOI: 10.5065/JG1E-8525 Spans 2010_07-2019_12 at 0.9x1.25 degree resolution a2x1hi_Faxa_swndr long_name = "Direct near-infrared incident solar radiation" ; a2x1hi_Faxa_swvdr long_name = "Direct visible incident solar radiation" ; @@ -19,7 +19,7 @@ a2x1hi_Faxa_swvdf long_name = "Diffuse visible incident solar radiation" ; The NSF NCAR RDA collections are located: - /glade/campaign/collections/rda/data/ds345.0/cpl_unzipped/----/{CASENAME}.cpl_----.ha2x*.YYYY.nc + /glade/campaign/collections/rda/data/d345000/cpl_unzipped/----/{CASENAME}.cpl_----.ha2x*.YYYY.nc @@ -27,7 +27,7 @@ Raeder et al. 80 member CAM/DART reanalysis V2 - https://rda.ucar.edu/datasets/ds345.0 + https://rda.ucar.edu/datasets/d345000 https://doi.org/10.5065/JG1E-8525 @@ -39,7 +39,7 @@ doma_mask mask - /glade/campaign/collections/rda/data/ds345.0/cpl_unzipped/NINST + /glade/campaign/collections/rda/data/d345000/cpl_unzipped/NINST f.e21.FHIST_BGC.f09_025.CAM6assim.011.cpl_NINST.ha2x1hi.RUNYEAR.nc @@ -53,7 +53,7 @@ a2x1hi_Faxa_swvdf swvdf - /glade/campaign/collections/rda/data/ds345.0/cpl_unzipped/NINST + /glade/campaign/collections/rda/data/d345000/cpl_unzipped/NINST 1800 diff --git a/models/clm/shell_scripts/cesm2_2/datm.streams.txt.CPLHISTForcing.State1hr_complete b/models/clm/shell_scripts/cesm2_2/datm.streams.txt.CPLHISTForcing.State1hr_complete index ddf2f29f0e..ee292b7ede 100644 --- a/models/clm/shell_scripts/cesm2_2/datm.streams.txt.CPLHISTForcing.State1hr_complete +++ b/models/clm/shell_scripts/cesm2_2/datm.streams.txt.CPLHISTForcing.State1hr_complete @@ -4,18 +4,18 @@ Two CAM-DART Ensemble Reanalysis efforts have been completed and provide DATM forcing files particularly appropriate for CESM experiments. - NSF NCAR RDA ds199.1 | DOI: 10.5065/38ED-RZ08 + NSF NCAR RDA d199001 | DOI: 10.5065/38ED-RZ08 Spans 1998_01-2010_12 at 1.875x2.5 degrees resolution every 6 hours a2x6h_Sa_u long_name = "Zonal wind at the lowest model level" ; a2x6h_Sa_v long_name = "Meridional wind at the lowest model level" ; - NSF NCAR RDA ds345.0 | DOI: 10.5065/JG1E-8525 + NSF NCAR RDA d345000 | DOI: 10.5065/JG1E-8525 Spans 2010_07-2019_12 at 0.9x1.25 degree resolution every hour a2x1h_Sa_u long_name = "Zonal wind at the lowest model level" ; a2x1h_Sa_v long_name = "Meridional wind at the lowest model level" ; The NSF NCAR RDA collections are located: - /glade/campaign/collections/rda/data/ds345.0/cpl_unzipped/----/{CASENAME}.cpl_----.ha2x*.YYYY.nc + /glade/campaign/collections/rda/data/d345000/cpl_unzipped/----/{CASENAME}.cpl_----.ha2x*.YYYY.nc @@ -23,7 +23,7 @@ Raeder et al. 80 member CAM/DART reanalysis V2 - https://rda.ucar.edu/datasets/ds345.0 + https://rda.ucar.edu/datasets/d345000 https://doi.org/10.5065/JG1E-8525 @@ -35,7 +35,7 @@ doma_mask mask - /glade/campaign/collections/rda/data/ds345.0/cpl_unzipped/NINST + /glade/campaign/collections/rda/data/d345000/cpl_unzipped/NINST f.e21.FHIST_BGC.f09_025.CAM6assim.011.cpl_NINST.ha2x1h.2011.nc @@ -47,7 +47,7 @@ a2x1h_Sa_v v - /glade/campaign/collections/rda/data/ds345.0/cpl_unzipped/NINST + /glade/campaign/collections/rda/data/d345000/cpl_unzipped/NINST linear diff --git a/models/clm/shell_scripts/cesm2_2/datm.streams.txt.CPLHISTForcing.State1hr_single_year b/models/clm/shell_scripts/cesm2_2/datm.streams.txt.CPLHISTForcing.State1hr_single_year index a1e6821a42..5da488a084 100644 --- a/models/clm/shell_scripts/cesm2_2/datm.streams.txt.CPLHISTForcing.State1hr_single_year +++ b/models/clm/shell_scripts/cesm2_2/datm.streams.txt.CPLHISTForcing.State1hr_single_year @@ -4,18 +4,18 @@ Two CAM-DART Ensemble Reanalysis efforts have been completed and provide DATM forcing files particularly appropriate for CESM experiments. - NSF NCAR RDA ds199.1 | DOI: 10.5065/38ED-RZ08 + NSF NCAR RDA d199001 | DOI: 10.5065/38ED-RZ08 Spans 1998_01-2010_12 at 1.875x2.5 degrees resolution every 6 hours a2x6h_Sa_u long_name = "Zonal wind at the lowest model level" ; a2x6h_Sa_v long_name = "Meridional wind at the lowest model level" ; - NSF NCAR RDA ds345.0 | DOI: 10.5065/JG1E-8525 + NSF NCAR RDA d345000 | DOI: 10.5065/JG1E-8525 Spans 2010_07-2019_12 at 0.9x1.25 degree resolution every hour a2x1h_Sa_u long_name = "Zonal wind at the lowest model level" ; a2x1h_Sa_v long_name = "Meridional wind at the lowest model level" ; The NSF NCAR RDA collections are located: - /glade/campaign/collections/rda/data/ds345.0/cpl_unzipped/----/{CASENAME}.cpl_----.ha2x*.YYYY.nc + /glade/campaign/collections/rda/data/d345000/cpl_unzipped/----/{CASENAME}.cpl_----.ha2x*.YYYY.nc @@ -23,7 +23,7 @@ Raeder et al. 80 member CAM/DART reanalysis V2 - https://rda.ucar.edu/datasets/ds345.0 + https://rda.ucar.edu/datasets/d345000 https://doi.org/10.5065/JG1E-8525 @@ -35,7 +35,7 @@ doma_mask mask - /glade/campaign/collections/rda/data/ds345.0/cpl_unzipped/NINST + /glade/campaign/collections/rda/data/d345000/cpl_unzipped/NINST f.e21.FHIST_BGC.f09_025.CAM6assim.011.cpl_NINST.ha2x1h.RUNYEAR.nc @@ -47,7 +47,7 @@ a2x1h_Sa_v v - /glade/campaign/collections/rda/data/ds345.0/cpl_unzipped/NINST + /glade/campaign/collections/rda/data/d345000/cpl_unzipped/NINST linear diff --git a/models/clm/shell_scripts/cesm2_2/datm.streams.txt.CPLHISTForcing.State3hr_complete b/models/clm/shell_scripts/cesm2_2/datm.streams.txt.CPLHISTForcing.State3hr_complete index 5d5adc4a94..e4d4b3d9e6 100644 --- a/models/clm/shell_scripts/cesm2_2/datm.streams.txt.CPLHISTForcing.State3hr_complete +++ b/models/clm/shell_scripts/cesm2_2/datm.streams.txt.CPLHISTForcing.State3hr_complete @@ -4,7 +4,7 @@ Two CAM-DART Ensemble Reanalysis efforts have been completed and provide DATM forcing files particularly appropriate for CESM experiments. - NSF NCAR RDA ds199.1 | DOI: 10.5065/38ED-RZ08 + NSF NCAR RDA d199001 | DOI: 10.5065/38ED-RZ08 Spans 1998_01-2010_12 at 1.875x2.5 degrees resolution every 6 hours a2x6h_Sa_z long_name = "Height at the lowest model level" ; a2x6h_Sa_tbot long_name = "Temperature at the lowest model level" ; @@ -15,7 +15,7 @@ a2x6h_Sa_dens long_name = "Density at the lowest model level" ; a2x6h_Sa_pslv long_name = "Sea level pressure" ; - NSF NCAR RDA ds345.0 + NSF NCAR RDA d345000 Spans 2010_07-2019_12 at 0.9x1.25 degree resolution every 3 hours a2x3h_Sa_z long_name = "Height at the lowest model level" ; a2x3h_Sa_tbot long_name = "Temperature at the lowest model level" ; @@ -27,7 +27,7 @@ a2x3h_Sa_pslv long_name = "Sea level pressure" ; The NSF NCAR RDA collections are located: - /glade/campaign/collections/rda/data/ds345.0/cpl_unzipped/----/{CASENAME}.cpl_----.ha2x*.YYYY.nc + /glade/campaign/collections/rda/data/d345000/cpl_unzipped/----/{CASENAME}.cpl_----.ha2x*.YYYY.nc @@ -35,7 +35,7 @@ Raeder et al. 80 member CAM/DART reanalysis V2 - https://rda.ucar.edu/datasets/ds345.0 + https://rda.ucar.edu/datasets/d345000 https://doi.org/10.5065/JG1E-8525 @@ -47,7 +47,7 @@ doma_mask mask - /glade/campaign/collections/rda/data/ds345.0/cpl_unzipped/NINST + /glade/campaign/collections/rda/data/d345000/cpl_unzipped/NINST f.e21.FHIST_BGC.f09_025.CAM6assim.011.cpl_NINST.ha2x3h.2011.nc @@ -65,7 +65,7 @@ a2x3h_Sa_pslv pslv - /glade/campaign/collections/rda/data/ds345.0/cpl_unzipped/NINST + /glade/campaign/collections/rda/data/d345000/cpl_unzipped/NINST linear diff --git a/models/clm/shell_scripts/cesm2_2/datm.streams.txt.CPLHISTForcing.State3hr_single_year b/models/clm/shell_scripts/cesm2_2/datm.streams.txt.CPLHISTForcing.State3hr_single_year index 77e6c48090..2107cc7acf 100644 --- a/models/clm/shell_scripts/cesm2_2/datm.streams.txt.CPLHISTForcing.State3hr_single_year +++ b/models/clm/shell_scripts/cesm2_2/datm.streams.txt.CPLHISTForcing.State3hr_single_year @@ -4,7 +4,7 @@ Two CAM-DART Ensemble Reanalysis efforts have been completed and provide DATM forcing files particularly appropriate for CESM experiments. - NSF NCAR RDA ds199.1 | DOI: 10.5065/38ED-RZ08 + NSF NCAR RDA d199001 | DOI: 10.5065/38ED-RZ08 Spans 1998_01-2010_12 at 1.875x2.5 degrees resolution every 6 hours a2x6h_Sa_z long_name = "Height at the lowest model level" ; a2x6h_Sa_tbot long_name = "Temperature at the lowest model level" ; @@ -15,7 +15,7 @@ a2x6h_Sa_dens long_name = "Density at the lowest model level" ; a2x6h_Sa_pslv long_name = "Sea level pressure" ; - NSF NCAR RDA ds345.0 + NSF NCAR RDA d345000 Spans 2010_07-2019_12 at 0.9x1.25 degree resolution every 3 hours a2x3h_Sa_z long_name = "Height at the lowest model level" ; a2x3h_Sa_tbot long_name = "Temperature at the lowest model level" ; @@ -27,7 +27,7 @@ a2x3h_Sa_pslv long_name = "Sea level pressure" ; The NSF NCAR RDA collections are located: - /glade/campaign/collections/rda/data/ds345.0/cpl_unzipped/----/{CASENAME}.cpl_----.ha2x*.YYYY.nc + /glade/campaign/collections/rda/data/d345000/cpl_unzipped/----/{CASENAME}.cpl_----.ha2x*.YYYY.nc @@ -35,7 +35,7 @@ Raeder et al. 80 member CAM/DART reanalysis V2 - https://rda.ucar.edu/datasets/ds345.0 + https://rda.ucar.edu/datasets/d345000 https://doi.org/10.5065/JG1E-8525 @@ -47,7 +47,7 @@ doma_mask mask - /glade/campaign/collections/rda/data/ds345.0/cpl_unzipped/NINST + /glade/campaign/collections/rda/data/d345000/cpl_unzipped/NINST f.e21.FHIST_BGC.f09_025.CAM6assim.011.cpl_NINST.ha2x3h.RUNYEAR.nc @@ -65,7 +65,7 @@ a2x3h_Sa_pslv pslv - /glade/campaign/collections/rda/data/ds345.0/cpl_unzipped/NINST + /glade/campaign/collections/rda/data/d345000/cpl_unzipped/NINST linear diff --git a/models/clm/shell_scripts/cesm2_2/datm.streams.txt.CPLHISTForcing.nonSolarFlux_complete b/models/clm/shell_scripts/cesm2_2/datm.streams.txt.CPLHISTForcing.nonSolarFlux_complete index f1639d7623..4527f7d577 100644 --- a/models/clm/shell_scripts/cesm2_2/datm.streams.txt.CPLHISTForcing.nonSolarFlux_complete +++ b/models/clm/shell_scripts/cesm2_2/datm.streams.txt.CPLHISTForcing.nonSolarFlux_complete @@ -4,7 +4,7 @@ Two CAM-DART Ensemble Reanalysis efforts have been completed and provide DATM forcing files particularly appropriate for CESM experiments. - NSF NCAR RDA ds199.1 | DOI: 10.5065/38ED-RZ08 + NSF NCAR RDA d199001 | DOI: 10.5065/38ED-RZ08 Spans 1998_01-2010_12 at 1.875x2.5 degrees resolution every 6 hours a2x6h_Faxa_rainc long_name = "Convective precipitation rate" ; a2x6h_Faxa_rainl long_name = "Large-scale (stable) precipitation rate" ; @@ -12,7 +12,7 @@ a2x6h_Faxa_snowl long_name = "Large-scale (stable) snow rate (water equivalent)" ; a2x6h_Faxa_lwdn long_name = "Downward longwave heat flux" ; - NSF NCAR RDA ds345.0 | DOI: 10.5065/JG1E-8525 + NSF NCAR RDA d345000 | DOI: 10.5065/JG1E-8525 Spans 2010_07-2019_12 at 0.9x1.25 degree resolution a2x3h_Faxa_rainc long_name = "Convective precipitation rate" ; a2x3h_Faxa_rainl long_name = "Large-scale (stable) precipitation rate" ; @@ -21,7 +21,7 @@ a2x3h_Faxa_lwdn long_name = "Downward longwave heat flux" ; The NSF NCAR RDA collections are located: - /glade/campaign/collections/rda/data/ds345.0/cpl_unzipped/----/{CASENAME}.cpl_----.ha2x*.YYYY.nc + /glade/campaign/collections/rda/data/d345000/cpl_unzipped/----/{CASENAME}.cpl_----.ha2x*.YYYY.nc @@ -29,7 +29,7 @@ Raeder et al. 80 member CAM/DART reanalysis V2 - https://rda.ucar.edu/datasets/ds345.0 + https://rda.ucar.edu/datasets/d345000 https://doi.org/10.5065/JG1E-8525 @@ -41,7 +41,7 @@ doma_mask mask - /glade/campaign/collections/rda/data/ds345.0/cpl_unzipped/NINST + /glade/campaign/collections/rda/data/d345000/cpl_unzipped/NINST f.e21.FHIST_BGC.f09_025.CAM6assim.011.cpl_NINST.ha2x3h.2011.nc @@ -56,7 +56,7 @@ a2x3h_Faxa_lwdn lwdn - /glade/campaign/collections/rda/data/ds345.0/cpl_unzipped/NINST + /glade/campaign/collections/rda/data/d345000/cpl_unzipped/NINST 1800 diff --git a/models/clm/shell_scripts/cesm2_2/datm.streams.txt.CPLHISTForcing.nonSolarFlux_single_year b/models/clm/shell_scripts/cesm2_2/datm.streams.txt.CPLHISTForcing.nonSolarFlux_single_year index 69fc479604..262e10e419 100644 --- a/models/clm/shell_scripts/cesm2_2/datm.streams.txt.CPLHISTForcing.nonSolarFlux_single_year +++ b/models/clm/shell_scripts/cesm2_2/datm.streams.txt.CPLHISTForcing.nonSolarFlux_single_year @@ -4,7 +4,7 @@ Two CAM-DART Ensemble Reanalysis efforts have been completed and provide DATM forcing files particularly appropriate for CESM experiments. - NSF NCAR RDA ds199.1 | DOI: 10.5065/38ED-RZ08 + NSF NCAR RDA d199001 | DOI: 10.5065/38ED-RZ08 Spans 1998_01-2010_12 at 1.875x2.5 degrees resolution every 6 hours a2x6h_Faxa_rainc long_name = "Convective precipitation rate" ; a2x6h_Faxa_rainl long_name = "Large-scale (stable) precipitation rate" ; @@ -12,7 +12,7 @@ a2x6h_Faxa_snowl long_name = "Large-scale (stable) snow rate (water equivalent)" ; a2x6h_Faxa_lwdn long_name = "Downward longwave heat flux" ; - NSF NCAR RDA ds345.0 | DOI: 10.5065/JG1E-8525 + NSF NCAR RDA d345000 | DOI: 10.5065/JG1E-8525 Spans 2010_07-2019_12 at 0.9x1.25 degree resolution a2x3h_Faxa_rainc long_name = "Convective precipitation rate" ; a2x3h_Faxa_rainl long_name = "Large-scale (stable) precipitation rate" ; @@ -21,7 +21,7 @@ a2x3h_Faxa_lwdn long_name = "Downward longwave heat flux" ; The NSF NCAR RDA collections are located: - /glade/campaign/collections/rda/data/ds345.0/cpl_unzipped/----/{CASENAME}.cpl_----.ha2x*.YYYY.nc + /glade/campaign/collections/rda/data/d345000/cpl_unzipped/----/{CASENAME}.cpl_----.ha2x*.YYYY.nc @@ -29,7 +29,7 @@ Raeder et al. 80 member CAM/DART reanalysis V2 - https://rda.ucar.edu/datasets/ds345.0 + https://rda.ucar.edu/datasets/d345000 https://doi.org/10.5065/JG1E-8525 @@ -41,7 +41,7 @@ doma_mask mask - /glade/campaign/collections/rda/data/ds345.0/cpl_unzipped/NINST + /glade/campaign/collections/rda/data/d345000/cpl_unzipped/NINST f.e21.FHIST_BGC.f09_025.CAM6assim.011.cpl_NINST.ha2x3h.RUNYEAR.nc @@ -56,7 +56,7 @@ a2x3h_Faxa_lwdn lwdn - /glade/campaign/collections/rda/data/ds345.0/cpl_unzipped/NINST + /glade/campaign/collections/rda/data/d345000/cpl_unzipped/NINST 1800 diff --git a/models/clm/tutorial/README.rst b/models/clm/tutorial/README.rst index f9ed10818d..3f9c7f81c3 100644 --- a/models/clm/tutorial/README.rst +++ b/models/clm/tutorial/README.rst @@ -84,7 +84,7 @@ from near present day (January-2011) and is initalized in 'hybrid' mode from a set of CLM restart files generated from a previous CLM 5-member ensemble simulation. The atmospheric forcing used for the assimilation comes from the Community Atmospheric Model (CAM) reanalysis -(`ds199.1 `__ and `ds345.0 `__). +(`d199001 `__ and `d345000 `__). This reanalysis atmospheric data includes 80 total ensemble members in which the across-member variation represents atmospheric uncertainty. We use 5 different ensemble members from the CAM6 reanalysis to generate @@ -131,7 +131,7 @@ custom initial conditions and observation sequence files for your own work. if you are using Derecho. If you are using your own machine you need use the following links to download these files directly: - 1. `CAM6 Reanalysis Meteorology `__, + 1. `CAM6 Reanalysis Meteorology `__, Year 2011, ensemble members 1-5 for three separate file types: ``f.e21.FHIST_BGC.f09_025.CAM6assim.011.cpl_000{1-5}.ha2x3h.2011.nc`` ``f.e21.FHIST_BGC.f09_025.CAM6assim.011.cpl_000{1-5}.ha2x1hi.2011.nc`` @@ -368,10 +368,10 @@ multiple model simulations (i.e. a model ensemble) that quantifies 1) state vari and 2) correlation between state variables. Given the sensitivity of CLM to atmospheric conditions an established method to generate multi-instance CLM simulations is through weather reanalysis data generated from a CAM-DART assimilation. These -CAM-DART reanalyses are available from 1997-2010 `ds199.1 `__, -and 2011-2020 `ds345.0 `__. +CAM-DART reanalyses are available from 1997-2010 `d199001 `__, +and 2011-2020 `d345000 `__. -For this tutorial we will use the January 2011 CAM6 reanalysis (ds345.0) only. +For this tutorial we will use the January 2011 CAM6 reanalysis (d345000) only. To make sure the scripts can locate the weather data first make sure the ``DART_params.csh`` variable ``dartroot`` is set to the path of your DART installation. For example, if you have a Derecho account and you @@ -422,7 +422,7 @@ and ``State3hr``. doma_mask mask - /glade/campaign/collections/rda/data/ds345.0/cpl_unzipped/NINST + /glade/campaign/collections/rda/data/d345000/cpl_unzipped/NINST f.e21.FHIST_BGC.f09_025.CAM6assim.011.cpl_NINST.ha2x3h.RUNYEAR.nc @@ -440,7 +440,7 @@ and ``State3hr``. a2x3h_Faxa_lwdn lwdn - /glade/campaign/collections/rda/data/ds345.0/cpl_unzipped/NINST + /glade/campaign/collections/rda/data/d345000/cpl_unzipped/NINST 1800 diff --git a/models/wrf/tutorial/README.rst b/models/wrf/tutorial/README.rst index 6e3a7be73c..b88862096b 100644 --- a/models/wrf/tutorial/README.rst +++ b/models/wrf/tutorial/README.rst @@ -624,7 +624,7 @@ Step 3: Prepare observations [OPTIONAL] The remaining instructions provided below in Step 3 are meant as a guideline to converting raw PREPBUFR data files into the required ``obs_seq`` format required by DART. Be aware that there is ongoing discussion of the proper - archived data set (RDA ds090.0 or ds337.0) that should be used to obtain + archived data set (RDA d090000 or d337000) that should be used to obtain the PREPBUFR data. See the discussion in `bug report #634 `__. If you have questions please contact the DART team. @@ -651,7 +651,7 @@ generate an observation sequence file. The steps listed below to generate these observation sequence files are meant as a guideline for NSF NCAR Research Data -Archive data file ds090.0. **Be aware not all required software has been +Archive data file d090000. **Be aware not all required software has been migrated to Derecho to perform this conversion.** See `bug report #634 `__ for more updated information. @@ -682,7 +682,7 @@ you would do the following: - Download the PREPBUFR observations for your desired time. Go to the `NSF NCAR Research Data - Archive `__ page for the + Archive `__ page for the NCEP/NSF NCAR Global Reanalysis Products. Register on the site, click on the "Data Access" tab, and follow either the instructions for external users or NSF NCAR internal users. diff --git a/observations/obs_converters/NCEP/prep_bufr/prep_bufr.rst b/observations/obs_converters/NCEP/prep_bufr/prep_bufr.rst index 5b6b0aa022..d4f214ccb1 100644 --- a/observations/obs_converters/NCEP/prep_bufr/prep_bufr.rst +++ b/observations/obs_converters/NCEP/prep_bufr/prep_bufr.rst @@ -148,12 +148,12 @@ Note that if you can get the blocked file formats to begin with, this program is Getting the ncep reanalysis prepbufr format data from NSF NCAR HPSS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -The NCEP PREPBUFR files (prepqmYYMMDDHH) can be found within the NCEP reanalysis dataset, ds090.0, on NSF NCAR Mass Store +The NCEP PREPBUFR files (prepqmYYMMDDHH) can be found within the NCEP reanalysis dataset, d090000, on NSF NCAR Mass Store System (HPSS). To find the files: -- go to the `NSF NCAR/NCEP reanalysis archive. `__ +- go to the `NSF NCAR/NCEP reanalysis archive. `__ - Click on the "Inventories" tab. - Select the year you are interested in. - Search for files with the string "prepqm" in the name. diff --git a/observations/obs_converters/WOD/WOD.rst b/observations/obs_converters/WOD/WOD.rst index 97c66d25fd..31bd4ab46a 100644 --- a/observations/obs_converters/WOD/WOD.rst +++ b/observations/obs_converters/WOD/WOD.rst @@ -105,7 +105,7 @@ Download WOD from NSF NCAR ^^^^^^^^^^^^^^^^^^^^^^^^^^ WOD09 can also be downloaded from NSF NCAR's `research data archive (RDA) dataset -285.0 `__. +285.0 `__. Programs -------- From a67de0eac351e80b89456c07303539391cb1672e Mon Sep 17 00:00:00 2001 From: Helen Kershaw Date: Tue, 21 Jan 2025 14:00:14 -0500 Subject: [PATCH 2/7] doc: reference page, rda links for RDA datasets: - cam6 rean d345 - cam 4 rean d199 - prepbufr d09 - wod d285 --- conf.py | 8 +++++++- guide/references.rst | 17 +++++++++++++++++ index.rst | 1 + models/POP/readme.rst | 4 ++-- models/cam-fv/readme.rst | 6 +++--- models/clm/tutorial/README.rst | 8 ++++---- models/wrf/tutorial/README.rst | 2 +- .../obs_converters/NCEP/prep_bufr/prep_bufr.rst | 2 +- observations/obs_converters/WOD/WOD.rst | 2 +- 9 files changed, 37 insertions(+), 13 deletions(-) create mode 100644 guide/references.rst diff --git a/conf.py b/conf.py index 7f26293ab9..a557f423c0 100644 --- a/conf.py +++ b/conf.py @@ -10,7 +10,7 @@ # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. # -# import os +import os # import sys # sys.path.insert(0, os.path.abspath('.')) @@ -86,3 +86,9 @@ html_static_path = ['guide/_static'] html_css_files = ['css/custom.css'] + +# include references +with open(os.path.join(os.path.dirname(__file__), 'guide/references.rst')) as f: + references_content = f.read() + +rst_prolog = references_content diff --git a/guide/references.rst b/guide/references.rst new file mode 100644 index 0000000000..7514e72ef2 --- /dev/null +++ b/guide/references.rst @@ -0,0 +1,17 @@ + +.. CAM6 reanalysis + +.. _d345000: https://rda.ucar.edu/datasets/d345000/ + + +.. CAM4 reanalysis + +.. _d199001: https://rda.ucar.edu/datasets/d199001/ + +.. NCEP's PREPBUFR files (prepqm) in NSF NCAR's Research Data Archive + +.. _d090000: https://rda.ucar.edu/datasets/d090000/ + +.. WOD (World Ocean Database) + +.. _d285000: https://rda.ucar.edu/datasets/d285000/ \ No newline at end of file diff --git a/index.rst b/index.rst index 06b4686699..7baef1108c 100644 --- a/index.rst +++ b/index.rst @@ -621,3 +621,4 @@ References :hidden: guide/404 + guide/references diff --git a/models/POP/readme.rst b/models/POP/readme.rst index 65f74d7914..eb789cb770 100644 --- a/models/POP/readme.rst +++ b/models/POP/readme.rst @@ -62,7 +62,7 @@ making minor edits to set details that are specific to your project. The setup scripts create a CESM case in which POP is configured using a 1° horizontal grid, and uses the eddy parametrization of Gent and McWilliams (1990). [2]_ The CICE model is active and atmospheric forcing is provided by the `CAM6 DART -Reanalysis `_. +Reanalysis `_. The filesystem attached to NSF NCAR's supercomputer is known as the Globally Accessible Data Environment (GLADE). All filepaths on GLADE have the structure: @@ -285,7 +285,7 @@ Data atmosphere streams files ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ The setup scripts configure the CESM case with atmospheric forcing from the -`CAM6 DART Reanalysis `_. The coupler +CAM6 DART Reanalysis `d345000`_. The coupler history files from this reanalysis are referenced in ``user_datm.streams*template`` files. These ``user_datm.streams*template`` files are contained in the same directory as the setup scripts and are diff --git a/models/cam-fv/readme.rst b/models/cam-fv/readme.rst index 0585feb30d..15d649db4b 100644 --- a/models/cam-fv/readme.rst +++ b/models/cam-fv/readme.rst @@ -118,7 +118,7 @@ Reanalyses There have been two large-scale reanalysis efforts using CAM-FV and DART. The **CAM6 Data Assimilation Research Testbed (DART) Reanalysis** is archived in the NSF NCAR Research Data Archive -`DS345.0 `__ . +`d345000`_. (See the |CAM6_Rean|_ ). It contains just under 120Tb (yes Tb) of data: @@ -139,7 +139,7 @@ An earlier, more limited dataset can be found in the `**Ensemble of Atmospheric Forcing Files from a CAM4-FV Reanalysis** `__ is archived in the NSF NCAR Research Data Archive -`DS199.1 `__ . +`d199001`_ . It contains about 1.5Tb of data: This dataset contains files that are an ensemble of 'coupler history' @@ -171,7 +171,7 @@ are available from the RDA d345000 linked above. NCEP NCEP's PREPBUFR files (prepqm) in NSF NCAR's Research Data Archive: - (https://rda.ucar.edu/datasets/d090000/) + (`d090000`_) COSMIC This site (http://www.cosmic.ucar.edu/) provides atmospheric refractivity diff --git a/models/clm/tutorial/README.rst b/models/clm/tutorial/README.rst index 3f9c7f81c3..77e7e1cdf7 100644 --- a/models/clm/tutorial/README.rst +++ b/models/clm/tutorial/README.rst @@ -84,7 +84,7 @@ from near present day (January-2011) and is initalized in 'hybrid' mode from a set of CLM restart files generated from a previous CLM 5-member ensemble simulation. The atmospheric forcing used for the assimilation comes from the Community Atmospheric Model (CAM) reanalysis -(`d199001 `__ and `d345000 `__). +(`d199001`_ and `d345000`_). This reanalysis atmospheric data includes 80 total ensemble members in which the across-member variation represents atmospheric uncertainty. We use 5 different ensemble members from the CAM6 reanalysis to generate @@ -131,7 +131,7 @@ custom initial conditions and observation sequence files for your own work. if you are using Derecho. If you are using your own machine you need use the following links to download these files directly: - 1. `CAM6 Reanalysis Meteorology `__, + 1. `CAM6 Reanalysis Meteorology `_, Year 2011, ensemble members 1-5 for three separate file types: ``f.e21.FHIST_BGC.f09_025.CAM6assim.011.cpl_000{1-5}.ha2x3h.2011.nc`` ``f.e21.FHIST_BGC.f09_025.CAM6assim.011.cpl_000{1-5}.ha2x1hi.2011.nc`` @@ -368,8 +368,8 @@ multiple model simulations (i.e. a model ensemble) that quantifies 1) state vari and 2) correlation between state variables. Given the sensitivity of CLM to atmospheric conditions an established method to generate multi-instance CLM simulations is through weather reanalysis data generated from a CAM-DART assimilation. These -CAM-DART reanalyses are available from 1997-2010 `d199001 `__, -and 2011-2020 `d345000 `__. +CAM-DART reanalyses are available from 1997-2010 `d199001`_, +and 2011-2020 `d345000`_. For this tutorial we will use the January 2011 CAM6 reanalysis (d345000) only. To make sure the scripts can locate the weather data first make sure diff --git a/models/wrf/tutorial/README.rst b/models/wrf/tutorial/README.rst index b88862096b..ea00a15cbd 100644 --- a/models/wrf/tutorial/README.rst +++ b/models/wrf/tutorial/README.rst @@ -682,7 +682,7 @@ you would do the following: - Download the PREPBUFR observations for your desired time. Go to the `NSF NCAR Research Data - Archive `__ page for the + Archive `_ page for the NCEP/NSF NCAR Global Reanalysis Products. Register on the site, click on the "Data Access" tab, and follow either the instructions for external users or NSF NCAR internal users. diff --git a/observations/obs_converters/NCEP/prep_bufr/prep_bufr.rst b/observations/obs_converters/NCEP/prep_bufr/prep_bufr.rst index d4f214ccb1..ea3976e387 100644 --- a/observations/obs_converters/NCEP/prep_bufr/prep_bufr.rst +++ b/observations/obs_converters/NCEP/prep_bufr/prep_bufr.rst @@ -153,7 +153,7 @@ System (HPSS). To find the files: -- go to the `NSF NCAR/NCEP reanalysis archive. `__ +- go to the `NSF NCAR/NCEP reanalysis archive. `_ - Click on the "Inventories" tab. - Select the year you are interested in. - Search for files with the string "prepqm" in the name. diff --git a/observations/obs_converters/WOD/WOD.rst b/observations/obs_converters/WOD/WOD.rst index 31bd4ab46a..b5f430be56 100644 --- a/observations/obs_converters/WOD/WOD.rst +++ b/observations/obs_converters/WOD/WOD.rst @@ -105,7 +105,7 @@ Download WOD from NSF NCAR ^^^^^^^^^^^^^^^^^^^^^^^^^^ WOD09 can also be downloaded from NSF NCAR's `research data archive (RDA) dataset -285.0 `__. +285.0 `_. Programs -------- From 2c43158d3ae8da36e46406ba26291d344b349173 Mon Sep 17 00:00:00 2001 From: kdraeder Date: Tue, 21 Jan 2025 13:49:51 -0700 Subject: [PATCH 3/7] Added references.rst and changed other .rst to use it. guide/references.rst Collected frequently used web addresses for convenient updating. conf.py Added lines to make references.rst available in all .rst files. models/POP/readme.rst models/cam-fv/readme.rst observations/obs_converters/WOD/WOD.rst Updated to use references.rst links. --- conf.py | 14 ++++++--- guide/references.rst | 12 ++++++++ models/POP/readme.rst | 14 +++++---- models/cam-fv/readme.rst | 39 ++++++++++++++----------- observations/obs_converters/WOD/WOD.rst | 4 +-- 5 files changed, 55 insertions(+), 28 deletions(-) create mode 100644 guide/references.rst diff --git a/conf.py b/conf.py index cc3ff2fa1d..7b2e47263e 100644 --- a/conf.py +++ b/conf.py @@ -9,10 +9,10 @@ # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. -# -# import os -# import sys -# sys.path.insert(0, os.path.abspath('.')) +# KDR I uncommented all three lines after Helen's conf.py lines to activate references.rst failed +import os +import sys +sys.path.insert(0, os.path.abspath('.')) # -- Project information ----------------------------------------------------- @@ -86,3 +86,9 @@ html_static_path = ['guide/_static'] html_css_files = ['css/custom.css'] + +# include references +with open(os.path.join(os.path.dirname(__file__), 'guide/references.rst')) as f: + references_content = f.read() + +rst_prolog = references_content diff --git a/guide/references.rst b/guide/references.rst new file mode 100644 index 0000000000..e9d99df349 --- /dev/null +++ b/guide/references.rst @@ -0,0 +1,12 @@ +.. _CAM6rean_rda : https://rda.ucar.edu/datasets/d345000/ +.. _CAM4rean_rda : https://rda.ucar.edu/datasets/d199001/ +.. _CAM6rean_wiki : https://github.com/NCAR/DART/wiki/1-degree,-CAM6,-ensemble-reanalysis-for-CESM-experiments-(2011-thru-2019):-DATM,-hindcasts,-model-evaluation +.. _CAM4rean_wiki : https://github.com/NCAR/DART/wiki/2-degree-DATM-ensemble-for-CESM-experiments-(1998-thru-2010) + +.. _NCEP_obs : https://rda.ucar.edu/datasets/d337000/ +.. _NCEP+NCAR_obs : https://rda.ucar.edu/datasets/d090000/ +.. _WOD_obs : https://rda.ucar.edu/datasets/d285000/ +.. _DART_obs : http://www.image.ucar.edu/pub/DART/Obs_sets/ + +.. These should be referenced with the syntax + `text to appear in doc `_ diff --git a/models/POP/readme.rst b/models/POP/readme.rst index 65f74d7914..5c1f39791f 100644 --- a/models/POP/readme.rst +++ b/models/POP/readme.rst @@ -1,3 +1,7 @@ +.. Shouldn't be needed because of new os lines in conf.py: +.. .. include:: /Users/raeder/DAI/Manhattan/guide/references.rst +.. .. include:: ../../guide/references.rst + .. _POP: POP @@ -62,7 +66,7 @@ making minor edits to set details that are specific to your project. The setup scripts create a CESM case in which POP is configured using a 1° horizontal grid, and uses the eddy parametrization of Gent and McWilliams (1990). [2]_ The CICE model is active and atmospheric forcing is provided by the `CAM6 DART -Reanalysis `_. +Reanalysis `_. The filesystem attached to NSF NCAR's supercomputer is known as the Globally Accessible Data Environment (GLADE). All filepaths on GLADE have the structure: @@ -231,7 +235,7 @@ Observation sequence files When ``setup_CESM_hybrid_ensemble.csh`` is used to create an assimilation experiment, ``DART_params.csh`` configures the experiment to assimilate observation sequence files from the World Ocean Database 2013 (WOD13; Boyer et -al. 2013 [5]_). +al. 2013 [5]_, `NSF NCAR's Research Data Archive `_.). The WOD13 dataset comprises data from 2005-01-01 to 2016-12-31 and contains the following observation types: @@ -262,7 +266,7 @@ the following directory on GLADE: .. code-block:: - /glade/p/cisl/dares/Observations/WOD13 + /glade/campaign/cisl/fs1_p_relocation/dares/Observations/WOD13 The subdirectories are formatted in ``YYYYMM`` order. @@ -272,7 +276,7 @@ are also stored in the following directory on GLADE: .. code-block:: - /glade/p/cisl/dares/Observations/WOD09 + /glade/campaign/cisl/fs1_p_relocation/dares/WOD09 These observation sequence files can be assimilated by changing the ``BASEOBSDIR`` variable in ``DART_params.csh``. @@ -285,7 +289,7 @@ Data atmosphere streams files ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ The setup scripts configure the CESM case with atmospheric forcing from the -`CAM6 DART Reanalysis `_. The coupler +`CAM6 DART Reanalysis `_. The coupler history files from this reanalysis are referenced in ``user_datm.streams*template`` files. These ``user_datm.streams*template`` files are contained in the same directory as the setup scripts and are diff --git a/models/cam-fv/readme.rst b/models/cam-fv/readme.rst index 0585feb30d..4164065ec4 100644 --- a/models/cam-fv/readme.rst +++ b/models/cam-fv/readme.rst @@ -1,3 +1,7 @@ +.. Shouldn't be needed because of new os lines in conf.py: +.. .. include:: /Users/raeder/DAI/Manhattan/guide/references.rst +.. .. include:: ../../guide/references.rst + Atmospheric Models in CESM ========================== @@ -6,7 +10,7 @@ Overview The larger context of the Community Earth System Model and DART interactions is described in the `CESM readme <../CESM/readme.html>`_ -This document focuses on the several `atmospheric models `__ +This document focuses on the several `atmospheric models `_ that have been developed or adapted to run in the CESM environment. They are named according to their dynamical core ("dycore"). As of 2021 these include Finite Volume Community Atmosphere Model (CAM-FV), @@ -15,18 +19,19 @@ The DART system has supported data assimilation into CAM-FV continuously for man An interface to CAM-SE was added to DART in 2022. An interface to MPAS is being developed (contact us about the current status). -.. |CAM6_Rean| replace:: 1 degree reanalysis wiki -.. _CAM6_Rean: https://github.com/NCAR/DART/wiki/1-degree,-CAM6,-ensemble-reanalysis-for-CESM-experiments-(2011-thru-2019):-DATM,-hindcasts,-model-evaluation +.. replaced by references.rst CAM6Rean_wiki + _CAM6_Rean: https://github.com/NCAR/DART/wiki/1-degree,-CAM6,-ensemble-reanalysis-for-CESM-experiments-(2011-thru-2019):-DATM,-hindcasts,-model-evaluation The flexibility of the DART environment has led to its use by graduate students, post-graduates, and scientists at universities and research labs to conduct data assimilation research. Others are using the products of data assimilation (analyses), which were produced at NSF NCAR using CESM+DART, to conduct related research. -The latest reanalysis is described in the DART |CAM6_Rean|_ +The latest reanalysis is described in the `DART 1 degree reanalysis wiki `_ + The variety of research can be sampled on the DART -`Publications `__ page. +`Publications `_ page. Terminology ~~~~~~~~~~~ @@ -118,8 +123,9 @@ Reanalyses There have been two large-scale reanalysis efforts using CAM-FV and DART. The **CAM6 Data Assimilation Research Testbed (DART) Reanalysis** is archived in the NSF NCAR Research Data Archive -`DS345.0 `__ . -(See the |CAM6_Rean|_ ). +`d345000 `_ . +(See the `CAM6rean_wiki`_ for details). + It contains just under 120Tb (yes Tb) of data: These CAM6+DART Reanalysis data @@ -137,9 +143,9 @@ It contains just under 120Tb (yes Tb) of data: An earlier, more limited dataset can be found in the `**Ensemble of Atmospheric Forcing Files from a CAM4-FV Reanalysis** -`__ +`_ is archived in the NSF NCAR Research Data Archive -`DS199.1 `__ . +`d199001 `_ . It contains about 1.5Tb of data: This dataset contains files that are an ensemble of 'coupler history' @@ -165,16 +171,16 @@ which contain the types of observations in the table below ("T" = temperature, "U" = zonal wind, "V" = meridional wind, "Q" = specific humidity, "refractivity" = the bending of light by density variations). These files are available on NSF NCAR's glade file system: -/glade/p/cisl/dares/Observations/NCEP+ACARS+GPS+AIRS/Thinned_x9x10. +/glade/campaign/cisl/fs1_p_relocation/dares/Observations/NCEP+ACARS+GPS+AIRS/Thinned_x9x10. Versions of these files, which also have the results of the reanalysis in them, are available from the RDA d345000 linked above. NCEP NCEP's PREPBUFR files (prepqm) in NSF NCAR's Research Data Archive: - (https://rda.ucar.edu/datasets/d090000/) + `newer `_ or `older `_ COSMIC - This site (http://www.cosmic.ucar.edu/) provides atmospheric refractivity + `This site `_ provides atmospheric refractivity from a variety of satellites (including COSMIC), which receive Global Positioning System radio occultation signals. @@ -202,9 +208,8 @@ AIRS | altimeter | Radiosondes, bouys | global surface | NCEP | +----------------------+----------------------------------------+--------------------------+--------+ -Sample sets of observations, which can be used with CAM+DART assimilations, can -be found at http://www.image.ucar.edu/pub/DART/Obs_sets/ of which the NCEP BUFR -observations are the most widely used. +`Sample sets of observations `_ can be used with CAM+DART assimilations, +of which the NCEP BUFR observations are the most widely used. The CAM-FV DART Interface ========================= @@ -283,7 +288,7 @@ The scripts in cesm#_# will handle, for that CESM version; Physics variants of other dycores are handled in other "model" interfaces, such as models/cam-se. -.. _reanalysis: https://github.com/kdraeder/cesm}{github.com/kdraeder/cesm +.. _reanalysis: https://github.com/kdraeder/cesm .. _SourceMods: @@ -905,7 +910,7 @@ before each hindcast by: References and Acknowledgements ------------------------------- -- `CESM homepage `__ +- `CESM homepage `_ Ave Arellano did the first work with CAM-Chem, assimilating MOPPITT CO observations into CAM-Chem. Jerome Barre and Benjamin Gaubert took up the diff --git a/observations/obs_converters/WOD/WOD.rst b/observations/obs_converters/WOD/WOD.rst index 31bd4ab46a..2bba443b2a 100644 --- a/observations/obs_converters/WOD/WOD.rst +++ b/observations/obs_converters/WOD/WOD.rst @@ -104,8 +104,8 @@ Data from each of the WOD releases can be downloaded interactively from the Download WOD from NSF NCAR ^^^^^^^^^^^^^^^^^^^^^^^^^^ -WOD09 can also be downloaded from NSF NCAR's `research data archive (RDA) dataset -285.0 `__. +WOD09 can also be downloaded from NSF NCAR's `Research Data Archive (RDA) dataset +d285000 `_. Programs -------- From a255dfc8ac83d4eaaa8b2cd5146a6d5878e93e74 Mon Sep 17 00:00:00 2001 From: kdraeder Date: Tue, 21 Jan 2025 14:48:06 -0700 Subject: [PATCH 4/7] Merge branch 'rda_refs' of github.com:NCAR/DART into rda_refs WARNING: there are still many non-link references (d######) to RDA datasets. These will not be updated by changes to references.rst, if, for example, the RDA changes its dataset name convention again. Trying to continue the merge. I resolved the conflicts, ran `make html`, which noted undefined links to the entries in refs, because they used Helen's abbreviations. I fixed those ({clm,wrf}/tutorial/README.rst and prep_bufr.rst), and added them explicitly, since they weren't part of the 2 previous references.rst commits and didn't have any conflicts. --- CHANGELOG.rst | 12 ++ .../modules/assimilation/filter_mod.f90 | 6 + .../programs/obs_diag/oned/obs_diag.f90 | 83 +++++--- conf.py | 8 +- guide/qceff_probit.rst | 5 + guide/references.rst | 20 +- index.rst | 1 + models/MOM6/model_mod.f90 | 186 ++++++++++++++---- models/clm/tutorial/README.rst | 10 +- models/lorenz_63/work/input.workshop.nml | 19 +- models/lorenz_96/work/input.workshop.nml | 20 +- models/wrf/tutorial/README.rst | 2 +- .../NCEP/prep_bufr/prep_bufr.rst | 2 +- 13 files changed, 286 insertions(+), 88 deletions(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index e47a8f40b3..fe81722453 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -22,6 +22,18 @@ individual files. The changes are now listed with the most recent at the top. +**January 14 2025 :: Bug-fix MOM6 potential temperature. Tag v11.8.8** + +- MOM6 model_interpolate for potential temperature +- Update lorenz workshop input.nmls to v11 + +**January 9 2025 :: Bug-fix 1D obs_diag. Tag v11.8.7** + +- Added a dummy dimension so 1D obs_diag output can be used with + MATLAB diagnostic tools +- Added a notification that probit inflation QCEFF options are ignored + for RTPS + **December 6 2024 :: Developer tests. Tag v11.8.6** - Tests for distribution modules: normal, beta, gamma diff --git a/assimilation_code/modules/assimilation/filter_mod.f90 b/assimilation_code/modules/assimilation/filter_mod.f90 index 710091f33c..a107add915 100644 --- a/assimilation_code/modules/assimilation/filter_mod.f90 +++ b/assimilation_code/modules/assimilation/filter_mod.f90 @@ -438,6 +438,12 @@ subroutine filter_main() inf_damping(POSTERIOR_INF), ' will be used' call error_handler(E_MSG,'filter_main:', msgstring) endif + if (do_rtps_inflate(post_inflate)) then + write(msgstring, *) 'Posterior inflation is RTPS, QCEFF ', & + 'inflation options will be ignored for posterior inflation' + call error_handler(E_MSG,'filter_main:', msgstring) + endif + endif call trace_message('After initializing inflation') diff --git a/assimilation_code/programs/obs_diag/oned/obs_diag.f90 b/assimilation_code/programs/obs_diag/oned/obs_diag.f90 index 287f2605c7..e125871861 100644 --- a/assimilation_code/programs/obs_diag/oned/obs_diag.f90 +++ b/assimilation_code/programs/obs_diag/oned/obs_diag.f90 @@ -68,6 +68,8 @@ program obs_diag integer, parameter :: MaxRegions = 4 integer, parameter :: MaxTrusted = 5 integer, parameter :: stringlength = 32 +! Output files need a single level to be compatible with three D fields for plotting +integer, parameter :: Nlevels = 1 !--------------------------------------------------------------------- ! variables associated with the observation @@ -1728,6 +1730,7 @@ subroutine WriteNetCDF(fname) character(len=*), intent(in) :: fname integer :: ncid, i, nobs, typesdimlen + integer :: LevelDimID, LevelVarID integer :: RegionDimID, RegionVarID integer :: TimeDimID, TimeVarID integer :: CopyDimID, CopyVarID, CopyMetaVarID @@ -1880,6 +1883,7 @@ subroutine WriteNetCDF(fname) call nc_check(nf90_def_dim(ncid=ncid, & name='time', len = NF90_UNLIMITED, dimid = TimeDimID), & 'WriteNetCDF', 'time:def_dim '//trim(fname)) + call nc_check(nf90_def_dim(ncid=ncid, & name='bounds', len = 2, dimid = BoundsDimID), & 'WriteNetCDF', 'bounds:def_dim '//trim(fname)) @@ -1892,6 +1896,10 @@ subroutine WriteNetCDF(fname) name='obstypes', len = max_defined_types_of_obs, dimid = TypesDimID), & 'WriteNetCDF', 'types:def_dim '//trim(fname)) + call nc_check(nf90_def_dim(ncid=ncid, & + name='level', len = 1, dimid = LevelDimID), & + 'WriteNetCDF', 'level:def_dim '//trim(fname)) + call nc_check(nf90_def_dim(ncid=ncid, & name='region', len = Nregions, dimid = RegionDimID), & 'WriteNetCDF', 'region:def_dim '//trim(fname)) @@ -1926,6 +1934,22 @@ subroutine WriteNetCDF(fname) call nc_check(nf90_put_att(ncid, TypesVarID, 'explanation', 'see ObservationTypes'), & 'WriteNetCDF', 'types:explanation') + !---------------------------------------------------------------------------- + ! Define 'level' dimension + !---------------------------------------------------------------------------- + + call nc_check(nf90_def_var(ncid=ncid, name='level', xtype=nf90_int, & + dimids=LevelDimID, varid=LevelVarID), 'WriteNetCDF', 'level:def_var') + call nc_check(nf90_put_att(ncid, LevelVarID, 'long_name', 'model level'), & + 'WriteNetCDF', 'level:long_name') + call nc_check(nf90_put_att(ncid, LevelVarID, 'units', 'nondimensional'), & + 'WriteNetCDF', 'level:units') + ! Level values are -1 to reflect that they are not meaningful + call nc_check(nf90_put_att(ncid, LevelVarID, 'valid_range', (/-1, -1/)), & + 'WriteNetCDF', 'level:valid_range') + call nc_check(nf90_put_att(ncid, LevelVarID, 'explanation', 'needed for compatibility with 3D'), & + 'WriteNetCDF', 'level:explanation') + !---------------------------------------------------------------------------- ! Define the regions coordinate variable and attributes !---------------------------------------------------------------------------- @@ -1939,7 +1963,7 @@ subroutine WriteNetCDF(fname) call nc_check(nf90_put_att(ncid, RegionVarID, 'valid_range', (/1,Nregions/)), & 'WriteNetCDF', 'region:valid_range') call nc_check(nf90_put_att(ncid, RegionVarID, 'explanation', 'see region_names'), & - 'WriteNetCDF', 'types:explanation') + 'WriteNetCDF', 'region:explanation') !---------------------------------------------------------------------------- ! Define 'bounds' dimension @@ -2055,6 +2079,9 @@ subroutine WriteNetCDF(fname) call nc_check(nf90_put_var(ncid, TypesMetaVarID, obs_type_strings(1:max_defined_types_of_obs)), & 'WriteNetCDF', 'typesmeta:put_var') + call nc_check(nf90_put_var(ncid, LevelVarID, (/ -1 /)), & + 'WriteNetCDF', 'level:put_var') + call nc_check(nf90_put_var(ncid, RegionVarID, (/ (i,i=1,Nregions) /) ), & 'WriteNetCDF', 'region:put_var') @@ -2078,13 +2105,13 @@ subroutine WriteNetCDF(fname) if ( verbose ) write(*,*)'summary for Priors of time-region vars' if ( create_rank_histogram ) then - ierr = WriteTRV(ncid, prior, TimeDimID, CopyDimID, RegionDimID, RankDimID) + ierr = WriteTRV(ncid, prior, TimeDimID, CopyDimID, LevelDimID, RegionDimID, RankDimID) else - ierr = WriteTRV(ncid, prior, TimeDimID, CopyDimID, RegionDimID) + ierr = WriteTRV(ncid, prior, TimeDimID, CopyDimID, LevelDimID, RegionDimID) endif if ( verbose ) write(*,*) if ( verbose ) write(*,*)'summary for Posteriors of time-region vars' - ierr = WriteTRV(ncid, poste, TimeDimID, CopyDimID, RegionDimID) + ierr = WriteTRV(ncid, poste, TimeDimID, CopyDimID, LevelDimID, RegionDimID) if ( verbose ) write(*,*) !---------------------------------------------------------------------------- @@ -2100,10 +2127,10 @@ end subroutine WriteNetCDF !====================================================================== - function WriteTRV(ncid, vrbl, TimeDimID, CopyDimID, RegionDimID, RankDimID) + function WriteTRV(ncid, vrbl, TimeDimID, CopyDimID, LevelDimID, RegionDimID, RankDimID) integer, intent(in) :: ncid type(TRV_type), intent(in) :: vrbl - integer, intent(in) :: TimeDimID, CopyDimID, RegionDimID + integer, intent(in) :: TimeDimID, CopyDimID, RegionDimID, LevelDimID integer, optional, intent(in) :: RankDimID integer :: WriteTRV @@ -2112,7 +2139,7 @@ function WriteTRV(ncid, vrbl, TimeDimID, CopyDimID, RegionDimID, RankDimID) character(len=NF90_MAX_NAME) :: string1 integer :: VarID, VarID2, oldmode - real(r4), allocatable, dimension(:,:,:) :: rchunk + real(r4), allocatable, dimension(:,:,:, :) :: rchunk integer, allocatable, dimension(:,:,:) :: ichunk FLAVORS : do ivar = 1,num_obs_types @@ -2124,31 +2151,31 @@ function WriteTRV(ncid, vrbl, TimeDimID, CopyDimID, RegionDimID, RankDimID) write(*,'(i4,1x,A,1x,i8)') ivar, obs_type_strings(ivar), nobs endif - allocate(rchunk(Nregions,Ncopies,Nepochs)) + allocate(rchunk(Nregions,Nlevels, Ncopies, Nepochs)) rchunk = MISSING_R4 do itime = 1,Nepochs do iregion = 1,Nregions - rchunk(iregion, 1,itime) = vrbl%Nposs( itime,iregion,ivar) - rchunk(iregion, 2,itime) = vrbl%Nused( itime,iregion,ivar) - rchunk(iregion, 3,itime) = vrbl%rmse( itime,iregion,ivar) - rchunk(iregion, 4,itime) = vrbl%bias( itime,iregion,ivar) - rchunk(iregion, 5,itime) = vrbl%spread( itime,iregion,ivar) - rchunk(iregion, 6,itime) = vrbl%totspread( itime,iregion,ivar) - rchunk(iregion, 7,itime) = vrbl%NbadDartQC( itime,iregion,ivar) - rchunk(iregion, 8,itime) = vrbl%observation(itime,iregion,ivar) - rchunk(iregion, 9,itime) = vrbl%ens_mean( itime,iregion,ivar) - rchunk(iregion,10,itime) = vrbl%Ntrusted( itime,iregion,ivar) - rchunk(iregion,11,itime) = vrbl%NDartQC_0( itime,iregion,ivar) - rchunk(iregion,12,itime) = vrbl%NDartQC_1( itime,iregion,ivar) - rchunk(iregion,13,itime) = vrbl%NDartQC_2( itime,iregion,ivar) - rchunk(iregion,14,itime) = vrbl%NDartQC_3( itime,iregion,ivar) - rchunk(iregion,15,itime) = vrbl%NDartQC_4( itime,iregion,ivar) - rchunk(iregion,16,itime) = vrbl%NDartQC_5( itime,iregion,ivar) - rchunk(iregion,17,itime) = vrbl%NDartQC_6( itime,iregion,ivar) - rchunk(iregion,18,itime) = vrbl%NDartQC_7( itime,iregion,ivar) - rchunk(iregion,19,itime) = vrbl%NDartQC_8( itime,iregion,ivar) + rchunk(iregion, 1, 1,itime) = vrbl%Nposs( itime,iregion,ivar) + rchunk(iregion, 1, 2,itime) = vrbl%Nused( itime,iregion,ivar) + rchunk(iregion, 1, 3,itime) = vrbl%rmse( itime,iregion,ivar) + rchunk(iregion, 1, 4,itime) = vrbl%bias( itime,iregion,ivar) + rchunk(iregion, 1, 5,itime) = vrbl%spread( itime,iregion,ivar) + rchunk(iregion, 1, 6,itime) = vrbl%totspread( itime,iregion,ivar) + rchunk(iregion, 1, 7,itime) = vrbl%NbadDartQC( itime,iregion,ivar) + rchunk(iregion, 1, 8,itime) = vrbl%observation(itime,iregion,ivar) + rchunk(iregion, 1, 9,itime) = vrbl%ens_mean( itime,iregion,ivar) + rchunk(iregion,1, 10,itime) = vrbl%Ntrusted( itime,iregion,ivar) + rchunk(iregion,1, 11,itime) = vrbl%NDartQC_0( itime,iregion,ivar) + rchunk(iregion,1, 12,itime) = vrbl%NDartQC_1( itime,iregion,ivar) + rchunk(iregion,1, 13,itime) = vrbl%NDartQC_2( itime,iregion,ivar) + rchunk(iregion,1, 14,itime) = vrbl%NDartQC_3( itime,iregion,ivar) + rchunk(iregion,1, 15,itime) = vrbl%NDartQC_4( itime,iregion,ivar) + rchunk(iregion,1, 16,itime) = vrbl%NDartQC_5( itime,iregion,ivar) + rchunk(iregion,1, 17,itime) = vrbl%NDartQC_6( itime,iregion,ivar) + rchunk(iregion,1, 18,itime) = vrbl%NDartQC_7( itime,iregion,ivar) + rchunk(iregion,1, 19,itime) = vrbl%NDartQC_8( itime,iregion,ivar) enddo enddo @@ -2161,7 +2188,7 @@ function WriteTRV(ncid, vrbl, TimeDimID, CopyDimID, RegionDimID, RankDimID) string1 = trim(obsname)//'_'//adjustl(vrbl%string) call nc_check(nf90_def_var(ncid, name=string1, xtype=nf90_real, & - dimids=(/ RegionDimID, CopyDimID, TimeDimID /), & + dimids=(/ RegionDimID, LevelDimID, CopyDimID, TimeDimID /), & varid=VarID), 'WriteTRV', 'region:def_var') call nc_check(nf90_put_att(ncid, VarID, '_FillValue', MISSING_R4), & 'WriteTRV','put_att:fillvalue') diff --git a/conf.py b/conf.py index 7b2e47263e..a557f423c0 100644 --- a/conf.py +++ b/conf.py @@ -9,10 +9,10 @@ # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. -# KDR I uncommented all three lines after Helen's conf.py lines to activate references.rst failed +# import os -import sys -sys.path.insert(0, os.path.abspath('.')) +# import sys +# sys.path.insert(0, os.path.abspath('.')) # -- Project information ----------------------------------------------------- @@ -21,7 +21,7 @@ author = 'Data Assimilation Research Section' # The full version, including alpha/beta/rc tags -release = '11.8.7' +release = '11.8.9' root_doc = 'index' # -- General configuration --------------------------------------------------- diff --git a/guide/qceff_probit.rst b/guide/qceff_probit.rst index d1d8bea4ef..299dd58778 100644 --- a/guide/qceff_probit.rst +++ b/guide/qceff_probit.rst @@ -48,6 +48,11 @@ options as columns of the qceff_table: * lower_bound (default -888888) * upper_bound (default -888888) + .. note:: + + If using RTPS inflation, the probit distribution information is ignored for posterior + inflation. + * Observation increment information diff --git a/guide/references.rst b/guide/references.rst index e9d99df349..b9404fd008 100644 --- a/guide/references.rst +++ b/guide/references.rst @@ -1,12 +1,26 @@ +.. These should be referenced with the syntax + `text to appear in doc `_ + +.. CAM6 reanalysis data .. _CAM6rean_rda : https://rda.ucar.edu/datasets/d345000/ + +.. CAM4 reanalysis data .. _CAM4rean_rda : https://rda.ucar.edu/datasets/d199001/ + +.. CAM6 reanalysis wiki .. _CAM6rean_wiki : https://github.com/NCAR/DART/wiki/1-degree,-CAM6,-ensemble-reanalysis-for-CESM-experiments-(2011-thru-2019):-DATM,-hindcasts,-model-evaluation + +.. CAM4 reanalysis wiki .. _CAM4rean_wiki : https://github.com/NCAR/DART/wiki/2-degree-DATM-ensemble-for-CESM-experiments-(1998-thru-2010) +.. NCEP's PREPBUFR files (prepqm) in NSF NCAR's Research Data Archive .. _NCEP_obs : https://rda.ucar.edu/datasets/d337000/ + +.. NCEP+NCAR Reanalysis observations dataset .. _NCEP+NCAR_obs : https://rda.ucar.edu/datasets/d090000/ + +.. WOD (World Ocean Database) .. _WOD_obs : https://rda.ucar.edu/datasets/d285000/ -.. _DART_obs : http://www.image.ucar.edu/pub/DART/Obs_sets/ -.. These should be referenced with the syntax - `text to appear in doc `_ +.. Sample observation sequence files +.. _DART_obs : http://www.image.ucar.edu/pub/DART/Obs_sets/ diff --git a/index.rst b/index.rst index 06b4686699..7baef1108c 100644 --- a/index.rst +++ b/index.rst @@ -621,3 +621,4 @@ References :hidden: guide/404 + guide/references diff --git a/models/MOM6/model_mod.f90 b/models/MOM6/model_mod.f90 index e6ebcd03f3..e0b88ae288 100644 --- a/models/MOM6/model_mod.f90 +++ b/models/MOM6/model_mod.f90 @@ -49,7 +49,8 @@ module model_mod use obs_kind_mod, only : get_index_for_quantity, QTY_U_CURRENT_COMPONENT, & QTY_V_CURRENT_COMPONENT, QTY_LAYER_THICKNESS, & - QTY_DRY_LAND, QTY_SALINITY + QTY_DRY_LAND, QTY_SALINITY, QTY_TEMPERATURE, & + QTY_POTENTIAL_TEMPERATURE use ensemble_manager_mod, only : ensemble_type @@ -113,8 +114,8 @@ module model_mod integer, parameter :: NOT_IN_STATE = 12 integer, parameter :: THICKNESS_NOT_IN_STATE = 13 integer, parameter :: QUAD_LOCATE_FAILED = 14 -integer, parameter :: THICKNESS_QUAD_EVALUTATE_FAILED = 15 -integer, parameter :: QUAD_EVALUTATE_FAILED = 16 +integer, parameter :: THICKNESS_QUAD_EVALUATE_FAILED = 15 +integer, parameter :: QUAD_EVALUATE_FAILED = 16 integer, parameter :: QUAD_ON_LAND = 17 integer, parameter :: QUAD_ON_BASIN_EDGE = 18 integer, parameter :: OBS_ABOVE_SURFACE = 20 @@ -220,25 +221,29 @@ end function get_model_size ! 0 unless there is some problem in computing the interpolation in ! which case a positive istatus should be returned. -subroutine model_interpolate(state_handle, ens_size, location, qty, expected_obs, istatus) +subroutine model_interpolate(state_handle, ens_size, location, qty_in, expected_obs, istatus) type(ensemble_type), intent(in) :: state_handle integer, intent(in) :: ens_size type(location_type), intent(in) :: location -integer, intent(in) :: qty +integer, intent(in) :: qty_in real(r8), intent(out) :: expected_obs(ens_size) !< array of interpolated values integer, intent(out) :: istatus(ens_size) +real(r8), parameter :: CONCENTRATION_TO_PPT = 1000.0_r8 + +integer :: qty ! local qty integer :: which_vert, four_ilons(4), four_ilats(4), lev(ens_size,2) integer :: locate_status, quad_status real(r8) :: lev_fract(ens_size) real(r8) :: lon_lat_vert(3) real(r8) :: quad_vals(4, ens_size) real(r8) :: expected(ens_size, 2) ! level below and above obs +real(r8) :: expected_pot_temp(ens_size), expected_salinity(ens_size), pressure_dbars(ens_size) type(quad_interp_handle) :: interp integer :: varid, i, e, thick_id -integer(i8) :: th_indx, indx(ens_size) +integer(i8) :: th_indx real(r8) :: depth_at_x(ens_size), thick_at_x(ens_size) ! depth, layer thickness at obs lat lon logical :: found(ens_size) @@ -247,6 +252,16 @@ subroutine model_interpolate(state_handle, ens_size, location, qty, expected_obs expected_obs(:) = MISSING_R8 istatus(:) = 1 +if (qty_in == QTY_TEMPERATURE) then + qty = QTY_POTENTIAL_TEMPERATURE ! model has potential temperature + if (get_varid_from_kind(dom_id, QTY_SALINITY) < 0) then ! Require salinity to convert to temperature + istatus = NOT_IN_STATE + return + end if +else + qty = qty_in +endif + varid = get_varid_from_kind(dom_id, qty) if (varid < 0) then ! not in state istatus = NOT_IN_STATE @@ -310,7 +325,7 @@ subroutine model_interpolate(state_handle, ens_size, location, qty, expected_obs thick_at_x, & quad_status) if (quad_status /= 0) then - istatus(:) = THICKNESS_QUAD_EVALUTATE_FAILED + istatus(:) = THICKNESS_QUAD_EVALUATE_FAILED return endif @@ -338,6 +353,66 @@ subroutine model_interpolate(state_handle, ens_size, location, qty, expected_obs return endif + +select case (qty_in) + case (QTY_TEMPERATURE) + ! convert from potential temperature to temperature + + call state_on_quad(four_ilons, four_ilats, lon_lat_vert, ens_size, lev, lev_fract, interp, state_handle, varid, expected_pot_temp, quad_status) + if (quad_status /= 0) then + istatus(:) = QUAD_EVALUATE_FAILED + return + endif + call state_on_quad(four_ilons, four_ilats, lon_lat_vert, ens_size, lev, lev_fract, interp, state_handle, get_varid_from_kind(dom_id, QTY_SALINITY), expected_salinity, quad_status) + if (quad_status /= 0) then + istatus(:) = QUAD_EVALUATE_FAILED + return + endif + + pressure_dbars = 0.059808_r8*(exp(-0.025_r8*depth_at_x) - 1.0_r8) & + + 0.100766_r8*depth_at_x + 2.28405e-7_r8*lon_lat_vert(3)**2 + expected_obs = sensible_temp(expected_pot_temp, expected_salinity, pressure_dbars) + + case (QTY_SALINITY) ! convert from g of salt per kg of seawater (model) to kg of salt per kg of seawater (observation) + call state_on_quad(four_ilons, four_ilats, lon_lat_vert, ens_size, lev, lev_fract, interp, state_handle, varid, expected_obs, quad_status) + if (quad_status /= 0) then + istatus(:) = QUAD_EVALUATE_FAILED + return + endif + expected_obs = expected_obs/CONCENTRATION_TO_PPT + + case default + call state_on_quad(four_ilons, four_ilats, lon_lat_vert, ens_size, lev, lev_fract, interp, state_handle, varid, expected_obs, quad_status) + if (quad_status /= 0) then + istatus(:) = QUAD_EVALUATE_FAILED + return + endif +end select + +istatus(:) = 0 + +end subroutine model_interpolate + +!------------------------------------------------------------------ +! Interpolate on the quad, between two levels +subroutine state_on_quad(four_ilons, four_ilats, lon_lat_vert, ens_size, lev, lev_fract, interp, state_handle, varid, expected_obs, quad_status) + +integer, intent(in) :: four_ilons(4), four_ilats(4) ! indices into lon, lat +real(r8), intent(in) :: lon_lat_vert(3) ! lon, lat, vert of obs +integer, intent(in) :: ens_size +integer, intent(in) :: lev(ens_size,2) ! levels below and above obs +real(r8), intent(in) :: lev_fract(ens_size) +type(quad_interp_handle), intent(in) :: interp +type(ensemble_type), intent(in) :: state_handle +integer, intent(in) :: varid ! which state variable +real(r8), intent(out) :: expected_obs(ens_size) +integer, intent(out) :: quad_status + +integer :: i, e +integer(i8) :: indx(ens_size) +real(r8) :: quad_vals(4, ens_size) +real(r8) :: expected(ens_size, 2) ! state value at level below and above obs + do i = 1, 2 !HK which corner of the quad is which? ! corner1 @@ -371,12 +446,7 @@ subroutine model_interpolate(state_handle, ens_size, location, qty, expected_obs quad_vals, & ! 4 corners x ens_size expected(:,i), & quad_status) - if (quad_status /= 0) then - istatus(:) = QUAD_EVALUTATE_FAILED - return - else - istatus = 0 - endif + if (quad_status /= 0) return enddo @@ -384,14 +454,7 @@ subroutine model_interpolate(state_handle, ens_size, location, qty, expected_obs ! expected_obs = bot_val + lev_fract * (top_val - bot_val) expected_obs = expected(:,1) + lev_fract(:) * (expected(:,2) - expected(:,1)) -if (qty == QTY_SALINITY) then ! convert from PSU (model) to MSU (obersvation) - expected_obs = expected_obs/1000.0_r8 -endif - - -end subroutine model_interpolate - - +end subroutine state_on_quad !------------------------------------------------------------------ ! Returns the smallest increment in time that the model is capable @@ -627,28 +690,28 @@ subroutine read_horizontal_grid() mask_v(:,:) = .false. call nc_get_attribute_from_variable(ncid, 'geolon', '_FillValue', fillval) where (geolon == fillval) mask = .true. -where (geolon == fillval) geolon = 72.51 -where (geolat == fillval) geolat = 42.56 +where (geolon == fillval) geolon = 72.51_r8 +where (geolat == fillval) geolat = 42.56_r8 call nc_get_attribute_from_variable(ncid, 'geolon_u', '_FillValue', fillval) where (geolon_u == fillval) mask_u = .true. -where (geolon_u == fillval) geolon_u = 72.51 -where (geolat_u == fillval) geolat_u = 42.56 +where (geolon_u == fillval) geolon_u = 72.51_r8 +where (geolat_u == fillval) geolat_u = 42.56_r8 call nc_get_attribute_from_variable(ncid, 'geolon_v', '_FillValue', fillval) where (geolon_v == fillval) mask_v = .true. -where (geolon_v == fillval) geolon_v = 72.51 -where (geolat_v == fillval) geolat_v = 42.56 +where (geolon_v == fillval) geolon_v = 72.51_r8 +where (geolat_v == fillval) geolat_v = 42.56_r8 ! mom6 example files have longitude > 360 and longitudes < 0 ! DART uses [0,360] -geolon = mod(geolon, 360.0) -geolon_u = mod(geolon_u, 360.0) -geolon_v = mod(geolon_v, 360.0) +geolon = mod(geolon, 360.0_r8) +geolon_u = mod(geolon_u, 360.0_r8) +geolon_v = mod(geolon_v, 360.0_r8) -where (geolon < 0.0) geolon = geolon + 360 -where (geolon_u < 0.0) geolon_u = geolon_u + 360 -where (geolon_v < 0.0) geolon_v = geolon_v + 360 +where (geolon < 0.0) geolon = geolon + 360.0_r8 +where (geolon_u < 0.0) geolon_u = geolon_u + 360.0_r8 +where (geolon_v < 0.0) geolon_v = geolon_v + 360.0_r8 call nc_close_file(ncid) @@ -897,6 +960,63 @@ function get_interp_handle(qty) end function +!------------------------------------------------------------ +! calculate sensible (in-situ) temperature from +! local pressure, salinity, and potential temperature +elemental function sensible_temp(potemp, s, lpres) + +real(r8), intent(in) :: potemp ! potential temperature in C +real(r8), intent(in) :: s ! salinity Practical Salinity Scale 1978 (PSS-78) +real(r8), intent(in) :: lpres ! pressure in decibars +real(r8) :: sensible_temp ! in-situ (sensible) temperature (C) + +integer :: i,j,n +real(r8) :: dp,p,q,r1,r2,r3,r4,r5,s1,t,x + +s1 = s - 35.0_r8 +p = 0.0_r8 +t = potemp + +dp = lpres - p +n = int (abs(dp)/1000.0_r8) + 1 +dp = dp/n + +do i=1,n + do j=1,4 + + r1 = ((-2.1687e-16_r8 * t + 1.8676e-14_r8) * t - 4.6206e-13_r8) * p + r2 = (2.7759e-12_r8*t - 1.1351e-10_r8) * s1 + r3 = ((-5.4481e-14_r8 * t + 8.733e-12_r8) * t - 6.7795e-10_r8) * t + r4 = (r1 + (r2 + r3 + 1.8741e-8_r8)) * p + (-4.2393e-8_r8 * t+1.8932e-6_r8) * s1 + r5 = r4 + ((6.6228e-10_r8 * t-6.836e-8_r8) * t + 8.5258e-6_r8) * t + 3.5803e-5_r8 + + x = dp*r5 + + if (j == 1) then + t = t + 0.5_r8 * x + q = x + p = p + 0.5_r8 * dp + + else if (j == 2) then + t = t + 0.29298322_r8 * (x-q) + q = 0.58578644_r8 * x + 0.121320344_r8 * q + + else if (j == 3) then + t = t + 1.707106781_r8 * (x-q) + q = 3.414213562_r8*x - 4.121320344_r8*q + p = p + 0.5_r8*dp + + else ! j must == 4 + t = t + (x - 2.0_r8 * q) / 6.0_r8 + + endif + + enddo ! j loop +enddo ! i loop + +sensible_temp = t + +end function sensible_temp !------------------------------------------------------------------ ! Verify that the namelist was filled in correctly, and check diff --git a/models/clm/tutorial/README.rst b/models/clm/tutorial/README.rst index 3f9c7f81c3..e01398b73f 100644 --- a/models/clm/tutorial/README.rst +++ b/models/clm/tutorial/README.rst @@ -83,8 +83,8 @@ a set of observations. The beginning of the assimilation starts from near present day (January-2011) and is initalized in 'hybrid' mode from a set of CLM restart files generated from a previous CLM 5-member ensemble simulation. The atmospheric forcing used for the assimilation -comes from the Community Atmospheric Model (CAM) reanalysis -(`d199001 `__ and `d345000 `__). +comes from the Community Atmospheric Model (CAM) reanalyses +(`CAM6 `_ and `CAM4 `_). This reanalysis atmospheric data includes 80 total ensemble members in which the across-member variation represents atmospheric uncertainty. We use 5 different ensemble members from the CAM6 reanalysis to generate @@ -131,7 +131,7 @@ custom initial conditions and observation sequence files for your own work. if you are using Derecho. If you are using your own machine you need use the following links to download these files directly: - 1. `CAM6 Reanalysis Meteorology `__, + 1. `CAM6 Reanalysis Meteorology `CAM6 `_, Year 2011, ensemble members 1-5 for three separate file types: ``f.e21.FHIST_BGC.f09_025.CAM6assim.011.cpl_000{1-5}.ha2x3h.2011.nc`` ``f.e21.FHIST_BGC.f09_025.CAM6assim.011.cpl_000{1-5}.ha2x1hi.2011.nc`` @@ -368,8 +368,8 @@ multiple model simulations (i.e. a model ensemble) that quantifies 1) state vari and 2) correlation between state variables. Given the sensitivity of CLM to atmospheric conditions an established method to generate multi-instance CLM simulations is through weather reanalysis data generated from a CAM-DART assimilation. These -CAM-DART reanalyses are available from 1997-2010 `d199001 `__, -and 2011-2020 `d345000 `__. +CAM-DART reanalyses are available from 1997-2010 `CAM4 `_, +and 2011-2020 `CAM6 `. For this tutorial we will use the January 2011 CAM6 reanalysis (d345000) only. To make sure the scripts can locate the weather data first make sure diff --git a/models/lorenz_63/work/input.workshop.nml b/models/lorenz_63/work/input.workshop.nml index 9313ee23c7..260278969a 100644 --- a/models/lorenz_63/work/input.workshop.nml +++ b/models/lorenz_63/work/input.workshop.nml @@ -1,3 +1,10 @@ +&probit_transform_nml + / + +&algorithm_info_nml + qceff_table_filename = '' + / + &perfect_model_obs_nml read_input_state_from_file = .true., single_file_in = .true. @@ -86,7 +93,6 @@ / &assim_tools_nml - filter_kind = 1, cutoff = 0.00001, sort_obs_inc = .false., spread_restoration = .false., @@ -135,11 +141,12 @@ / &preprocess_nml - input_obs_def_mod_file = '../../../observations/forward_operators/DEFAULT_obs_def_mod.F90', - output_obs_def_mod_file = '../../../observations/forward_operators/obs_def_mod.f90', - input_obs_kind_mod_file = '../../../assimilation_code/modules/observations/DEFAULT_obs_kind_mod.F90', - output_obs_kind_mod_file = '../../../assimilation_code/modules/observations/obs_kind_mod.f90', - input_files = '../../../observations/forward_operators/obs_def_1d_state_mod.f90' + input_obs_def_mod_file = '../../../observations/forward_operators/DEFAULT_obs_def_mod.F90' + output_obs_def_mod_file = '../../../observations/forward_operators/obs_def_mod.f90' + input_obs_qty_mod_file = '../../../assimilation_code/modules/observations/DEFAULT_obs_kind_mod.F90' + output_obs_qty_mod_file = '../../../assimilation_code/modules/observations/obs_kind_mod.f90' + obs_type_files = '../../../observations/forward_operators/obs_def_1d_state_mod.f90' + quantity_files = '../../../assimilation_code/modules/observations/oned_quantities_mod.f90' / &obs_sequence_tool_nml diff --git a/models/lorenz_96/work/input.workshop.nml b/models/lorenz_96/work/input.workshop.nml index 38de9f869b..db9da26e05 100644 --- a/models/lorenz_96/work/input.workshop.nml +++ b/models/lorenz_96/work/input.workshop.nml @@ -1,3 +1,10 @@ +&probit_transform_nml + / + +&algorithm_info_nml + qceff_table_filename = '' + / + &perfect_model_obs_nml read_input_state_from_file = .true., single_file_in = .true. @@ -89,7 +96,6 @@ # large for the model to converge. to test that the model is # doing a successful assimilation, change cutoff to 0.02 and rerun. &assim_tools_nml - filter_kind = 1, cutoff = 1000000.0, sort_obs_inc = .false., spread_restoration = .false., @@ -145,12 +151,12 @@ / &preprocess_nml - overwrite_output = .true., - input_obs_def_mod_file = '../../../observations/forward_operators/DEFAULT_obs_def_mod.F90', - output_obs_def_mod_file = '../../../observations/forward_operators/obs_def_mod.f90', - input_obs_kind_mod_file = '../../../assimilation_code/modules/observations/DEFAULT_obs_kind_mod.F90', - output_obs_kind_mod_file = '../../../assimilation_code/modules/observations/obs_kind_mod.f90', - input_files = '../../../observations/forward_operators/obs_def_1d_state_mod.f90', + input_obs_def_mod_file = '../../../observations/forward_operators/DEFAULT_obs_def_mod.F90' + output_obs_def_mod_file = '../../../observations/forward_operators/obs_def_mod.f90' + input_obs_qty_mod_file = '../../../assimilation_code/modules/observations/DEFAULT_obs_kind_mod.F90' + output_obs_qty_mod_file = '../../../assimilation_code/modules/observations/obs_kind_mod.f90' + obs_type_files = '../../../observations/forward_operators/obs_def_1d_state_mod.f90' + quantity_files = '../../../assimilation_code/modules/observations/oned_quantities_mod.f90' / &obs_sequence_tool_nml diff --git a/models/wrf/tutorial/README.rst b/models/wrf/tutorial/README.rst index b88862096b..cbae90f0e0 100644 --- a/models/wrf/tutorial/README.rst +++ b/models/wrf/tutorial/README.rst @@ -682,7 +682,7 @@ you would do the following: - Download the PREPBUFR observations for your desired time. Go to the `NSF NCAR Research Data - Archive `__ page for the + Archive `_ page for the NCEP/NSF NCAR Global Reanalysis Products. Register on the site, click on the "Data Access" tab, and follow either the instructions for external users or NSF NCAR internal users. diff --git a/observations/obs_converters/NCEP/prep_bufr/prep_bufr.rst b/observations/obs_converters/NCEP/prep_bufr/prep_bufr.rst index d4f214ccb1..67b95df11c 100644 --- a/observations/obs_converters/NCEP/prep_bufr/prep_bufr.rst +++ b/observations/obs_converters/NCEP/prep_bufr/prep_bufr.rst @@ -153,7 +153,7 @@ System (HPSS). To find the files: -- go to the `NSF NCAR/NCEP reanalysis archive. `__ +- go to the `NSF NCAR/NCEP reanalysis archive. `_ - Click on the "Inventories" tab. - Select the year you are interested in. - Search for files with the string "prepqm" in the name. From 56e01d28c9996b5f5b1a21fcc6632997e50d0e42 Mon Sep 17 00:00:00 2001 From: kdraeder Date: Wed, 22 Jan 2025 16:53:51 -0700 Subject: [PATCH 5/7] Tidied comments and link formatting and naming based on review. Removed mistaken `include` rst commands. models/cam-fv/readme.rst There is a "Publications" link, so Removed the related ISSUE. models/POP/readme.rst --- models/POP/readme.rst | 4 ---- models/cam-fv/readme.rst | 35 ++++++++++++----------------------- 2 files changed, 12 insertions(+), 27 deletions(-) diff --git a/models/POP/readme.rst b/models/POP/readme.rst index 5c1f39791f..dd5eed8015 100644 --- a/models/POP/readme.rst +++ b/models/POP/readme.rst @@ -1,7 +1,3 @@ -.. Shouldn't be needed because of new os lines in conf.py: -.. .. include:: /Users/raeder/DAI/Manhattan/guide/references.rst -.. .. include:: ../../guide/references.rst - .. _POP: POP diff --git a/models/cam-fv/readme.rst b/models/cam-fv/readme.rst index 4164065ec4..e5e5776fa4 100644 --- a/models/cam-fv/readme.rst +++ b/models/cam-fv/readme.rst @@ -1,7 +1,3 @@ -.. Shouldn't be needed because of new os lines in conf.py: -.. .. include:: /Users/raeder/DAI/Manhattan/guide/references.rst -.. .. include:: ../../guide/references.rst - Atmospheric Models in CESM ========================== @@ -9,7 +5,7 @@ Overview -------- The larger context of the Community Earth System Model and DART interactions -is described in the `CESM readme <../CESM/readme.html>`_ +is described in the :doc:`CESM readme <../CESM/readme>` This document focuses on the several `atmospheric models `_ that have been developed or adapted to run in the CESM environment. They are named according to their dynamical core ("dycore"). @@ -19,19 +15,16 @@ The DART system has supported data assimilation into CAM-FV continuously for man An interface to CAM-SE was added to DART in 2022. An interface to MPAS is being developed (contact us about the current status). -.. replaced by references.rst CAM6Rean_wiki - _CAM6_Rean: https://github.com/NCAR/DART/wiki/1-degree,-CAM6,-ensemble-reanalysis-for-CESM-experiments-(2011-thru-2019):-DATM,-hindcasts,-model-evaluation - The flexibility of the DART environment has led to its use by graduate students, post-graduates, and scientists at universities and research labs to conduct data assimilation research. Others are using the products of data assimilation (analyses), which were produced at NSF NCAR using CESM+DART, to conduct related research. -The latest reanalysis is described in the `DART 1 degree reanalysis wiki `_ +The latest reanalysis is described in the `CAM6 Reanalysis wiki `_ The variety of research can be sampled on the DART -`Publications `_ page. +`Publications page `__ . Terminology ~~~~~~~~~~~ @@ -61,7 +54,7 @@ with two independent main characteristics. CESM labels these as: model domain vary with those choices. - The combinations of parameterizations and vertical grids are named: CAM3.5, CAM5, CAM#, ... WACCM, WACCM#, WACCM-X, CAM-Chem. - - The compset is specified as described in the `CESM readme <../CESM/readme.html>`_. + - The compset is specified as described in the :doc:`CESM readme <../CESM/readme>`. **ensemble, multi-instance, and multidriver** @@ -121,11 +114,11 @@ Reanalyses ~~~~~~~~~~ There have been two large-scale reanalysis efforts using CAM-FV and DART. -The **CAM6 Data Assimilation Research Testbed (DART) Reanalysis** -is archived in the NSF NCAR Research Data Archive -`d345000 `_ . -(See the `CAM6rean_wiki`_ for details). +The **CAM6 Data Assimilation Research Testbed (DART) Reanalysis** +is archived in the NSF NCAR Research Data Archive (RDA) +`d345000 `_. +(See the `wiki `_ for details). It contains just under 120Tb (yes Tb) of data: These CAM6+DART Reanalysis data @@ -142,7 +135,7 @@ It contains just under 120Tb (yes Tb) of data: An earlier, more limited dataset can be found in the -`**Ensemble of Atmospheric Forcing Files from a CAM4-FV Reanalysis** +`Ensemble of Atmospheric Forcing Files from a CAM4-FV Reanalysis `_ is archived in the NSF NCAR Research Data Archive `d199001 `_ . @@ -160,9 +153,6 @@ It contains about 1.5Tb of data: for CESM component sets that require a data atmosphere. Some example stream text files are included in the RDA to illustrate how to use these data. -.. * CAM4, 2 degree, 2000-2010, `Reanalysis `__ -.. * files from the old "large file site": http://www.image.ucar.edu/pub/DART/CAM/ - Observations ------------ @@ -173,14 +163,14 @@ which contain the types of observations in the table below These files are available on NSF NCAR's glade file system: /glade/campaign/cisl/fs1_p_relocation/dares/Observations/NCEP+ACARS+GPS+AIRS/Thinned_x9x10. Versions of these files, which also have the results of the reanalysis in them, -are available from the RDA d345000 linked above. +are available from the `RDA d345000 `_ . NCEP NCEP's PREPBUFR files (prepqm) in NSF NCAR's Research Data Archive: `newer `_ or `older `_ COSMIC - `This site `_ provides atmospheric refractivity + `UCAR's COSMIC program `_ provides atmospheric refractivity from a variety of satellites (including COSMIC), which receive Global Positioning System radio occultation signals. @@ -233,7 +223,7 @@ Setup Scripts Unlike pre-Manhattan versions of DART-CAM, CESM (CAM) runs using its normal scripts, then stops and calls a DART script, which does the desired assimilation tasks, then returns to the CESM run script for the next model advance. See the CESM -interface documentation in the `CESM readme <../CESM/readme.html>`_ +interface documentation in the :doc:`CESM readme <../CESM/readme>` for more general information about running DART with CESM. Due to the complexity of the CESM software environment, the versions of CESM which can be used for assimilation are more restricted than @@ -891,7 +881,6 @@ before each hindcast by: - ISSUE: Improve this page * Add links and references to this document. - * Publications web page. * CAM-chem; link? More description? - ISSUE?; ``model_interpolate`` assumes that obs with a vertical location have From a705c561c91320015014f884a75189f1842dfc59 Mon Sep 17 00:00:00 2001 From: Helen Kershaw Date: Thu, 23 Jan 2025 13:50:35 -0500 Subject: [PATCH 6/7] fix: link missing _ --- models/clm/tutorial/README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/models/clm/tutorial/README.rst b/models/clm/tutorial/README.rst index e01398b73f..2fc6ae30b8 100644 --- a/models/clm/tutorial/README.rst +++ b/models/clm/tutorial/README.rst @@ -369,7 +369,7 @@ and 2) correlation between state variables. Given the sensitivity of CLM to atmospheric conditions an established method to generate multi-instance CLM simulations is through weather reanalysis data generated from a CAM-DART assimilation. These CAM-DART reanalyses are available from 1997-2010 `CAM4 `_, -and 2011-2020 `CAM6 `. +and 2011-2020 `CAM6 `_. For this tutorial we will use the January 2011 CAM6 reanalysis (d345000) only. To make sure the scripts can locate the weather data first make sure From 4c49aeaf80c87922036cbd31440c230b793185ec Mon Sep 17 00:00:00 2001 From: Helen Kershaw Date: Thu, 23 Jan 2025 10:38:04 -0500 Subject: [PATCH 7/7] doc: copy button for documnentation --- conf.py | 1 + guide/requirements.txt | 1 + 2 files changed, 2 insertions(+) diff --git a/conf.py b/conf.py index 6910cb5f0a..335f9c7925 100644 --- a/conf.py +++ b/conf.py @@ -30,6 +30,7 @@ # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ + 'sphinx_copybutton', 'sphinx_rtd_theme', 'sphinx.ext.autodoc', 'sphinx.ext.mathjax' diff --git a/guide/requirements.txt b/guide/requirements.txt index 254085495f..a600036f67 100644 --- a/guide/requirements.txt +++ b/guide/requirements.txt @@ -1,2 +1,3 @@ Sphinx==6.2.1 sphinx-rtd-theme==1.2.2 +sphinx_copybutton