Update latest directory structure, inputs/outputs tables

doc/UsersGuide/source/CodeOverview.rst

@@ -36,8 +36,6 @@ The ufs-weather-model repository supports the short- and medium-range UFS applic
     - https://github.com/NOAA-EMC/GFDL_atmos_cubed_sphere
   * - Stochastic physics pattern generator  
     - https://github.com/noaa-psd/stochastic_physics
-  * - WAVEWATCH 3 wave model 
-    - https://github.com/NOAA-EMC/WW3
 
 In the table, the left column contains a description of each repository, and the right column shows the component repositories which are pointing to (or will point to) the authoritative repositories. The ufs-weather-model currently uses git submodule to manage the sub-components. 
 
@@ -55,7 +53,6 @@ The umbrella repository for the UFS Weather Model is named ufs-weather-model.  U
    ├── NEMS                                    https://github.com/NCAR/NEMS
    │   └── tests/produtil/NCEPLIBS-pyprodutil  https://github.com/NOAA-EMC/NCEPLIBS-pyprodutil
    ├── stochastic_physics                      https://github.com/noaa-psd/stochastic_physics
-   └── WW3                                     https://github.com/NOAA-EMC/WW3
 
 ===================
 Directory Structure 
@@ -90,17 +87,16 @@ When the ufs-weather-model is cloned, the basic directory structure will be simi
    │   │   └── physics     --------- unused - IPD version of physics codes
    │   ├── io              --------- FV3 write grid comp code
    │   ├── ipd             --------- unused - IPD driver/interfaces
+   |   ├── stochastic_physics  ----- Cmakefile for stochastic physics code
    ├── log                 --------- log files from NEMS compset regression tests
-   ├── modulefile          --------- system module files for supported HPC systems
+   ├── modulefiles         --------- system module files for supported HPC systems
    ├── NEMS                --------- NOAA Earth Modeling System framework
    │   ├── exe
    │   ├── src
    │   └── test
    ├── parm                --------- regression test configurations
-   ├── release             --------- unused
    ├── stochastic_physics   -------- stochastic physics pattern generator
    ├── tests               --------- regression test scripts
-   └── WW3                 --------- WAVEWATCH III (wave component)
 
 The physics subdirectory in the *gfsphysics* directory  is not used or supported as part of this release (all physics is available through the :term:`CCPP`).
 

doc/UsersGuide/source/InputsOutputs.rst

@@ -417,12 +417,15 @@ several Fortran namelist records, some of which are always required, others of w
 physics options are chosen.
 
 The following link describes the various physics-related namelist records:
-https://dtcenter.org/GMTB/v3.0/sci_doc/GFSsuite_nml.html
+
+https://dtcenter.org/GMTB/UFS/sci_doc/CCPPsuite_nml_desp.html
 
 The following link describes the stochastic physics namelist records
+
 https://stochastic-physics.readthedocs.io/en/ufs_public_release/namelist_options.html
 
 The following link describes some of the other namelist records (dynamics, grid, etc):
+
 https://www.gfdl.noaa.gov/wp-content/uploads/2017/09/fv3_namelist_Feb2017.pdf
 
 The namelist section relating to the FMS diagnostic manager is described in the last section of this chapter.
@@ -476,10 +479,6 @@ shows the following parameters that can be set in *model_configure* at run-time.
      - start second of model integration
      - integer 
      - 0
-   * - fhrot
-     - forecast hour at restart for nems/earth grid component clock in coupled model
-     - integer
-     - 0
    * - nhours_fcst
      - total forecast length
      - integer
@@ -500,14 +499,6 @@ shows the following parameters that can be set in *model_configure* at run-time.
      - number of threads for atmosphere
      - integer
      - 4
-   * - use_hyper_thread
-     - flag to use hyper threads
-     - logical
-     - .false.
-   * - ncores_per_node
-     - number of cores per node 
-     - integer
-     - 24
    * - restart_interval
      - frequency to output restart file 
      - integer
@@ -597,7 +588,11 @@ are not usually changed.
    * - calendar
      - type of calendar year
      - character(*)
-     - 'julian'
+     - 'gregorian'
+   * - fhrot
+     - forecast hour at restart for nems/earth grid component clock in coupled model
+     - integer
+     - 0
    * - cpl
      - flag for coupling with MOM6/CICE5
      - logical
@@ -653,11 +648,11 @@ corresponding to the six tiles of the model grid):
 
 - *atmos_4xdaily.tile[1-6].nc*
 - *atmos_static.tile[1-6].nc*
-- *phyfHHH.tile[1-6].nc*
-- *dynfHHH.tile[1-6].nc*
+- *sfcfHHH.nc*
+- *atmfHHH.nc*
 - *grid_spec.tile[1-6].nc*
 
-The specifications of the output files (type, projection, etc) may be overridden in the *model_configure* input file.
+Note that the sfcf* and atmf* files are not output on the 6 tiles, but instead as a single global gaussian grid file.  The specifications of the output files (type, projection, etc) may be overridden in the *model_configure* input file.
 
 Standard output files are *logf???*, and out and err as specified by the job submission. ESMF may also produce log
 files (controlled by variable print_esmf in the *model_configure* file), called *PET???.ESMF_LogFile*.

doc/UsersGuide/source/Introduction.rst

@@ -14,7 +14,7 @@ development. More information about the UFS can be found in its portal at https:
 Key architectural elements of the UFS WM, along with links to external detailed documentation
 for those elements, are listed below:
 
-- The Finite-Volume Cubed-Sphere (FV3) dynamical core (https://noaa-emc.github.io/FV3_Dycore/html/index.html).
+- The Finite-Volume Cubed-Sphere (FV3) dynamical core (https://noaa-emc.github.io/FV3_Dycore_v1.0/html/index.html).
 
 - The Flexible Modeling System (:term:`FMS`), a software infrastructure used for functions such as
   parallelization (https://www.gfdl.noaa.gov/fms/).
@@ -30,7 +30,7 @@ for those elements, are listed below:
   (https://stochastic-physics.readthedocs.io/en/ufs_public_release/).
 
 - The NOAA Environmental Modeling System (:term:`NEMS`) model driver used to create the main program
-  (https://docs.google.com/document/d/1-kFhPBf7GBTUd5SaB5D_3OUGX_93pWKP21QgTh4y6ok/edit#heading=h.dah4y9bxn10l).
+  (https://noaa-emc.github.io/NEMS_doc/index.html).
 
 - The libraries needed to build the system, such as: 
     - National Centers for Environmental Prediction (NCEP) Libraries 
@@ -88,7 +88,7 @@ The next chapter:
 
 - :numref:`Chapter %s <ContributingDevelopment>` (Contributing development)
 
-go beyond the capabilities supported in the public release to cover code management for conducting
+goes beyond the capabilities supported in the public release to cover code management for conducting
 development and proposing contributions back to the authoritative code repositories. It should be noted that the regression tests described here are mandatory for committing code back to the ufs-weather-model authoritative code repository. These regressions tests differ from those distributed with the workflows for UFS applications, which are intended for application users and developers to assess the quality of their installations and the impact of their code changes. Finally,
 :numref:`Chapters %s <Acronyms>` and :numref:`%s <Glossary>` contain a list of acronyms and a glossary, respectively.
 

doc/UsersGuide/source/SDFandNamelistExamplePractices.rst

@@ -8,15 +8,15 @@ The public release of the medium-range weather app includes two supported physic
 GFSv15p2 and GFSv16beta. You will find the Suite Definition Files (SDFs) for these suites
 in
 
-https://github.com/NOAA-EMC/fv3atm/tree/ufs_public_release/ccpp/suites
+https://github.com/NOAA-EMC/fv3atm/tree/release/public-v1/ccpp/suites
 
 (no other SDFs are available with this release). You will find the namelists for the C96 configuration here:
 
-https://github.com/ufs-community/ufs-weather-model/blob/ufs_public_release/parm/ccpp_v15p2_c96.nml.IN
+https://github.com/ufs-community/ufs-weather-model/tree/release/public-v1/parm/ccpp_v15p2_c96.nml.IN
 
 and
 
-https://github.com/ufs-community/ufs-weather-model/blob/ufs_public_release/parm/ccpp_v16beta_c96.nml.IN
+https://github.com/ufs-community/ufs-weather-model/tree/release/public-v1/parm/ccpp_v16beta_c96.nml.IN
 
 The two CCPP suites for the medium-range weather app release are supported in four grid resolutions:
 C96, C192, C384, and C768, with 64 vertical levels.