From cc0c6056d8f34715516894af78948492336e0bbb Mon Sep 17 00:00:00 2001 From: Joshua Kublnick Date: Fri, 20 Mar 2026 14:21:56 -0400 Subject: [PATCH 1/4] purging hycom from the User's Guide --- doc/UsersGuide/source/BuildingAndRunning.rst | 3 +- doc/UsersGuide/source/CodeOverview.rst | 6 - doc/UsersGuide/source/Glossary.rst | 5 +- doc/UsersGuide/source/InputsOutputs.rst | 232 +------------------ 4 files changed, 5 insertions(+), 241 deletions(-) diff --git a/doc/UsersGuide/source/BuildingAndRunning.rst b/doc/UsersGuide/source/BuildingAndRunning.rst index 4cab058c0b..abdf9506e3 100644 --- a/doc/UsersGuide/source/BuildingAndRunning.rst +++ b/doc/UsersGuide/source/BuildingAndRunning.rst @@ -378,7 +378,6 @@ Lastly, the :wm-repo:`test configuration file `_. DOCN - DOCN is the *Data Ocean* component of :term:`CDEPS`. It uses static ocean forcing files (derived from observations or previous ocean model runs) instead of output from an active ocean model. This reduces the complexity and computational cost associated with coupling to an active ocean model. The *Data Ocean* component is particularly useful when employing computationally intensive Data Assimilation (DA) techniques to update atmospheric fields in a coupled model. In general, use of DOCN in place of :term:`MOM6` or :term:`HYCOM` can be appropriate when users are running a coupled model and only want certain components of the model to be active. More information about DOCN is available in the `CDEPS DOCN Documentation `_. + DOCN is the *Data Ocean* component of :term:`CDEPS`. It uses static ocean forcing files (derived from observations or previous ocean model runs) instead of output from an active ocean model. This reduces the complexity and computational cost associated with coupling to an active ocean model. The *Data Ocean* component is particularly useful when employing computationally intensive Data Assimilation (DA) techniques to update atmospheric fields in a coupled model. In general, use of DOCN in place of :term:`MOM6` can be appropriate when users are running a coupled model and only want certain components of the model to be active. More information about DOCN is available in the `CDEPS DOCN Documentation `_. dycore dynamical core @@ -111,9 +111,6 @@ Glossary HPSS High Performance Storage System (HPSS). - HYCOM - The HYbrid Coordinate Ocean Model (`HYCOM `_) was developed to address known shortcomings in the vertical coordinate scheme of the Miami Isopycnic-Coordinate Ocean Model (MICOM). HYCOM is a primitive equation, general circulation model with vertical coordinates that remain isopycnic in the open, stratified ocean. However, the isopycnal vertical coordinates smoothly transition to z-coordinates in the weakly stratified upper-ocean mixed layer, to terrain-following sigma coordinates in shallow water regions, and back to z-level coordinates in very shallow water. The latter transition prevents layers from becoming too thin where the water is very shallow. See the `HYCOM User's Guide `_ for more information on using the model. The `HYCOM model code `_ is publicly available on GitHub. - ICs Initial conditions diff --git a/doc/UsersGuide/source/InputsOutputs.rst b/doc/UsersGuide/source/InputsOutputs.rst index 16651c6444..cf4aa2a324 100644 --- a/doc/UsersGuide/source/InputsOutputs.rst +++ b/doc/UsersGuide/source/InputsOutputs.rst @@ -54,13 +54,13 @@ mediator). Currently, supported configurations include: * - LND-LM4 - Coupled :term:`CDEPS` - :term:`DATM` - :term:`LM4` * - HAFS - - Coupled :term:`ATM` - :term:`HYCOM` - :term:`CMEPS` + - Coupled :term:`ATM` - :term:`CMEPS` * - HAFSW - - Coupled :term:`ATM` - :term:`HYCOM` - :term:`WW3` - :term:`CMEPS` + - Coupled :term:`ATM` - :term:`WW3` - :term:`CMEPS` * - HAFS-MOM6W - Coupled :term:`ATM` - :term:`MOM6`- :term:`WW3` - :term:`CMEPS` * - HAFS-ALL - - Coupled :term:`CDEPS` - :term:`ATM` - :term:`HYCOM` - :term:`WW3` - :term:`CMEPS` + - Coupled :term:`CDEPS` - :term:`ATM` - :term:`WW3` - :term:`CMEPS` .. COMMENT: Should HAFS-ALL be DATM instead of ATM? .. COMMENT: No RTs for these apps: ATMWM, S2SL, S2SWL, HAFS-MOM6 @@ -350,14 +350,6 @@ The input files containing grid information and the initial conditions for globa - ocean basin classification grid - 0.50 - - * - hycom1_25.nc - - vertical coordinate thickness defining 25 vertical levels - - 9.00, 5.00 - - - * - hycom1_75_800m.nc - - vertical coordinate level thickness - - 1.00, 0.50, 0.25 - - * - layer_coord.nc - vertical layer target potential density - 1.00, 0.50, 0.25 @@ -427,166 +419,6 @@ The input files containing grid information and the initial conditions for globa - 1.00 - ✔ -.. _hycom-in: - -------- -HYCOM -------- - -.. _hycom-fix-files: - -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Static Datasets (i.e., *fix files*) -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -Static input files have been created for several regional domains. These domains are listed and described in :numref:`Table %s `. - -.. _HYCOM_DomainIdentifiers: - -.. list-table:: *The following table describes each domain identifier.* - :widths: 10 20 - :header-rows: 1 - - * - Identifier - - Description - * - hat10 - - Hurricane North Atlantic (1/12 degree) - * - hep20 - - Hurricane Eastern North Pacific (1/12 degree) - * - hwp30 - - Hurricane Western North Pacific (1/12 degree) - * - hcp70 - - Hurricane Central North Pacific (1/12 degree) - -Static input files are listed and described in :numref:`Table %s `. Several datasets contain both dot-a (.a) and dot-b (.b) files. Dot-a files contain data written as 32-bit IEEE real values (idm*jdm) and dot-b files contain plain text metadata for each field in the dot-a file. - -.. COMMENT: What is (idm*jdm)? - -.. _HYCOM_FixFiles: - -.. list-table:: *Fix files containing climatological information* - :widths: 15 30 15 - :header-rows: 1 - - * - Filename - - Description - - Domain - * - :ref:`blkdat.input` - - Model input parameters - - - * - patch.input - - Tile description - - - * - ports.input - - Open boundary cells - - - * - forcing.chl.(a,b) - - Chlorophyll (monthly climatology) - - hat10, hep20, hwp30, hcp70 - * - forcing.rivers.(a,b) - - River discharge (monthly climatology) - - hat10, hep20, hwp30, hcp70 - * - iso.sigma.(a,b) - - Fixed sigma thickness - - hat10, hep20, hwp30, hcp70 - * - regional.depth.(a,b) - - Total depth of ocean - - hat10, hep20, hwp30, hcp70 - * - regional.grid.(a,b) - - Grid information for HYCOM "C" grid - - hat10, hep20, hwp30, hcp70 - * - relax.rmu.(a,b) - - Open boundary nudging value - - hat10, hep20, hwp30, hcp70 - * - relax.ssh.(a,b) - - Surface height nudging value (monthly climatology) - - hat10, hep20, hwp30, hcp70 - * - tbaric.(a,b) - - Thermobaricity correction - - hat10, hep20, hwp30, hcp70 - * - thkdf4.(a,b) - - Diffusion velocity (m/s) for Laplacian thickness diffusivity - - hat10, hep20, hwp30, hcp70 - * - veldf2.(a,b) - - Diffusion velocity (m/s) for biharmonic momentum dissipation - - hat10, hep20, hwp30, hcp70 - * - veldf4.(a,b) - - Diffusion velocity (m/s) for Laplacian momentum dissipation - - hat10, hep20, hwp30, hcp70 - -.. _hycom-grid-ic-files: - -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Grid Description and Initial Condition Files -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -The input files containing time dependent configuration and forcing data are listed and described in :numref:`Table %s `. These files are generated for specific regional domains (see :numref:`Table %s `) during ocean prep. When uncoupled, the the forcing data drives the ocean model. When coupled, the forcing data is used to fill in unmapped grid cells. Several datasets contain both dot-a (.a) and dot-b (.b) files. Dot-a files contain data written as 32-bit IEEE real values (idm*jdm) and dot-b files contain plain text metadata for each field in the dot-a file. - -.. COMMENT: What is (idm*jdm)? - -.. _HYCOM_GridICFiles: - -.. list-table:: *Input files containing grid information, initial conditions, and forcing data for regional configurations.* - :widths: 12 30 18 5 - :header-rows: 1 - - * - Filename - - Description - - Domain - - Date-dependent - * - limits - - Model begin and end time (since HYCOM epoch) - - - - ✔ - * - forcing.airtmp.(a,b) - - GFS forcing data for 2m air temperature - - hat10, hep20, hwp30, hcp70 - - ✔ - * - forcing.mslprs.(a,b) - - GFS forcing data for mean sea level pressure (symlink) - - hat10, hep20, hwp30, hcp70 - - ✔ - * - forcing.precip.(a,b) - - GFS forcing data for precipitation rate - - hat10, hep20, hwp30, hcp70 - - ✔ - * - forcing.presur.(a,b) - - GFS forcing data for mean sea level pressure - - hat10, hep20, hwp30, hcp70 - - ✔ - * - forcing.radflx.(a,b) - - GFS forcing data for total radiation flux - - hat10, hep20, hwp30, hcp70 - - ✔ - * - forcing.shwflx.(a,b) - - GFS forcing data for net downward shortwave radiation flux - - hat10, hep20, hwp30, hcp70 - - ✔ - * - forcing.surtmp.(a,b) - - GFS forcing data for surface temperature - - hat10, hep20, hwp30, hcp70 - - ✔ - * - forcing.tauewd.(a,b) - - GFS forcing data for eastward momentum flux - - hat10, hep20, hwp30, hcp70 - - ✔ - * - forcing.taunwd.(a,b) - - GFS forcing data for northward momentum flux - - hat10, hep20, hwp30, hcp70 - - ✔ - * - forcing.vapmix.(a,b) - - GFS forcing data for 2m vapor mixing ratio - - hat10, hep20, hwp30, hcp70 - - ✔ - * - forcing.wndspd.(a,b) - - GFS forcing data for 10m wind speed - - hat10, hep20, hwp30, hcp70 - - ✔ - * - restart_in.(a,b) - - Restart file for ocean state variables - - hat10, hep20, hwp30, hcp70 - - ✔ - .. _cice-in: ------- @@ -955,9 +787,6 @@ The input files containing grid information and the time-varying forcing files f * - GHRSST_mesh.nc - ESMF mesh file for GHRSST data source - - * - hycom_YYYYMM_surf_nolev.nc - - MOM6 forcing file for year YYYY and month MM - - ✔ * - ghrsst_YYYYMMDD.nc - GHRSST forcing file for year YYYY, month MM and day DD - ✔ @@ -1277,7 +1106,6 @@ The configuration files used by the UFS Weather Model are listed here and descri * ``suite_[suite_name].xml`` (used only at build time) * ``datm.streams`` (used by CDEPS) * ``datm_in`` (used by CDEPS) - * ``blkdat.input`` (used by HYCOM) While the ``input.nml`` file is also a configuration file used by the UFS Weather Model, it is described in :numref:`Section %s `. The run-time configuration of model output fields is controlled by the combination of ``diag_table`` and ``model_configure``, and is described in detail in :numref:`Section %s `. @@ -1966,14 +1794,6 @@ A sample of the data stream namelist file is shown below: restfilm = "null" / -.. _HYCOM_BlkdatInput: - ---------------------------------------- -``blkdat.input`` ---------------------------------------- - -The HYCOM model reads parameters from a custom formatted configuraiton file, blkdat.input. The `HYCOM User's Guide `_ provides an in depth description of the configuration settings. - .. _InputNML: ----------------------------- @@ -2376,52 +2196,6 @@ A brief example of the diag_table is shown below. ``"..."`` denotes where lines "ocean_model", "tauy", "tauy", "ocn%4yr%2mo%2dy%2hr","all",.true.,"none",2 ... -.. _hycom-out: - -------- -HYCOM -------- - -HYCOM output configuration is set in the :ref:`blkdat.input` file. A few common configuration options are described in :numref:`Table %s ` - -.. _HYCOM_OutputConfig: - -.. list-table:: *The following table describes HYCOM output configuration.* - :widths: 10 25 - :header-rows: 1 - - * - Parameter - - Description - * - dsurfq - - Number of days between model diagnostics at the surface - * - diagfq - - Number of days between model diagnostics - * - meanfq - - Number of days between model time averaged diagnostics - * - rstrfq - - Number of days between model restart output - * - itest - - i grid point where detailed diagnostics are desired - * - jtest - - j grid point where detailed diagnostics are desired - -HYCOM outpus multiple datasets. These datasets contain both dot-a (.a), dot-b (.b), and dot-txt (.txt) files. Dot-a files contain data written as 32-bit IEEE real values (idm*jdm). Dot-b files contain plain text metadata for each field in the dot-a file. Dot-txt files contain plain text data for a single cell for profiling purposes. Post-processing utilties are available in the `HYCOM-tools `_ repository. - -.. _HYCOM_OutputFiles: - -.. list-table:: *The following table describes HYCOM output files.* - :widths: 10 10 - :header-rows: 1 - - * - Filename - - Description - * - archs.YYYY_DDD_HH.(a,b,txt) - - HYCOM surface archive data - * - archv.YYYY_DDD_HH.(a,b,txt) - - HYCOM archive data - * - restart_out.(a,b) - - HYCOM restart files - .. _cice-out: ------- From 7df8b77912dbf4e277d17027f877b907bb9017df Mon Sep 17 00:00:00 2001 From: Joshua Kublnick Date: Fri, 20 Mar 2026 14:45:51 -0400 Subject: [PATCH 2/4] Adding back in pertinent info --- doc/UsersGuide/source/InputsOutputs.rst | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/doc/UsersGuide/source/InputsOutputs.rst b/doc/UsersGuide/source/InputsOutputs.rst index cf4aa2a324..3c79367721 100644 --- a/doc/UsersGuide/source/InputsOutputs.rst +++ b/doc/UsersGuide/source/InputsOutputs.rst @@ -346,10 +346,18 @@ The input files containing grid information and the initial conditions for globa - land mask - 1.00, 0.50 - - * - basin_codes.nc + * - basin_codes.nc - ocean basin classification grid - 0.50 - + * - hycom1_25.nc + - vertical coordinate thickness defining 25 vertical levels + - 9.00, 5.00 + - + * - hycom1_75_800m.nc + - vertical coordinate level thickness + - 1.00, 0.50, 0.25 + - * - layer_coord.nc - vertical layer target potential density - 1.00, 0.50, 0.25 From 1c3daa866bd3956deb5a3d8174be0154538cf12f Mon Sep 17 00:00:00 2001 From: Joshua Kublnick <47824899+jdkublnick@users.noreply.github.com> Date: Fri, 20 Mar 2026 16:49:24 -0400 Subject: [PATCH 3/4] Update doc/UsersGuide/source/InputsOutputs.rst Co-authored-by: Gillian Petro <96886803+gspetro-NOAA@users.noreply.github.com> --- doc/UsersGuide/source/InputsOutputs.rst | 1 - 1 file changed, 1 deletion(-) diff --git a/doc/UsersGuide/source/InputsOutputs.rst b/doc/UsersGuide/source/InputsOutputs.rst index 3c79367721..221fdc6571 100644 --- a/doc/UsersGuide/source/InputsOutputs.rst +++ b/doc/UsersGuide/source/InputsOutputs.rst @@ -56,7 +56,6 @@ mediator). Currently, supported configurations include: * - HAFS - Coupled :term:`ATM` - :term:`CMEPS` * - HAFSW - - Coupled :term:`ATM` - :term:`WW3` - :term:`CMEPS` * - HAFS-MOM6W - Coupled :term:`ATM` - :term:`MOM6`- :term:`WW3` - :term:`CMEPS` * - HAFS-ALL From 16f092b33077254bb0abebd4a86d6e570e2acfe3 Mon Sep 17 00:00:00 2001 From: Joshua Kublnick <47824899+jdkublnick@users.noreply.github.com> Date: Fri, 20 Mar 2026 16:49:30 -0400 Subject: [PATCH 4/4] Update doc/UsersGuide/source/InputsOutputs.rst Co-authored-by: Gillian Petro <96886803+gspetro-NOAA@users.noreply.github.com> --- doc/UsersGuide/source/InputsOutputs.rst | 1 - 1 file changed, 1 deletion(-) diff --git a/doc/UsersGuide/source/InputsOutputs.rst b/doc/UsersGuide/source/InputsOutputs.rst index 221fdc6571..ee80b52f50 100644 --- a/doc/UsersGuide/source/InputsOutputs.rst +++ b/doc/UsersGuide/source/InputsOutputs.rst @@ -54,7 +54,6 @@ mediator). Currently, supported configurations include: * - LND-LM4 - Coupled :term:`CDEPS` - :term:`DATM` - :term:`LM4` * - HAFS - - Coupled :term:`ATM` - :term:`CMEPS` * - HAFSW * - HAFS-MOM6W - Coupled :term:`ATM` - :term:`MOM6`- :term:`WW3` - :term:`CMEPS`