misc updates

whannah1 · whannah1 · commit 97dcc399ff8b · 2024-06-14T15:56:42.000-06:00
diff --git a/docs/dev-guide/adding-grid-support/adding-grid-support-step-by-step-guide.md b/docs/dev-guide/adding-grid-support/adding-grid-support-step-by-step-guide.md
@@ -13,7 +13,7 @@ If you wish to add a new ocean and sea-ice mesh you will need to use the compass
 
 1. [Generate a new grid file                               ](adding-grid-support-step-by-step-guide/generate-new-grid-file.md)
 1. [Generate mapping files                                 ](adding-grid-support-step-by-step-guide/generate-mapping-files.md)
-1. [Generate domain files                                  ](/generate_domain_files/)
+1. [Generate domain files                                  ](../../generate_domain_files/index.md)
 1. [Generate a topography file                             ](adding-grid-support-step-by-step-guide/generate-topo-file.md)
 1. [Generate atmospheric initial condition                 ](adding-grid-support-step-by-step-guide/generate-atm-initial-condition.md)
 1. [Generate land input data (*fsurdat*)                   ](adding-grid-support-step-by-step-guide/generate-lnd-input-data.md)
diff --git a/docs/dev-guide/adding-grid-support/adding-grid-support-step-by-step-guide/generate-RRM-grid-file.md b/docs/dev-guide/adding-grid-support/adding-grid-support-step-by-step-guide/generate-RRM-grid-file.md
@@ -1,7 +1,5 @@
 # Generate a RRM Grid File with SQuadGen
 
-[Back to Adding Support for New Grids](../adding-grid-support-step-by-step-guide.md)
-
 <!-- disable linter checks for inline html to allow collapsable code sections -->
 <!-- markdownlint-disable MD033 --> <!-- no-inline-html -->
 
@@ -256,3 +254,5 @@ RRM "quality" can be measured with the “Max Dinv-based element distortion” m
 This metric measures how distorted the elements become in the mesh transition region.  It is the ratio of the two singular values of the 2x2 derivative matrix of the element map to the unit square, representing the ration of the largest length scale to the smallest length scale.  
 
 A grid of perfect quadrilaterals will have a value of 1.0.  The equal-angle cubed-sphere grid has a value of 1.7.   A high quality regionally refined grid will have a value less than 4.  With a high quality grid, usually one can run with the timesteps used in a uniform grid with matching fine resolution.  RRM grids with a value > 4 may require smaller timesteps for stability.   Very large values indicate a problem with the grid and it should be redesigned.
+
+Back to step-by-step guide for [Adding Support for New Grids](../adding-grid-support-step-by-step-guide.md)
diff --git a/docs/dev-guide/adding-grid-support/adding-grid-support-step-by-step-guide/generate-atm-initial-condition.md b/docs/dev-guide/adding-grid-support/adding-grid-support-step-by-step-guide/generate-atm-initial-condition.md
@@ -1,6 +1,6 @@
 # Generate Atmospheric Initial Condition
 
-[Back to Adding Support for New Grids](../adding-grid-support-step-by-step-guide.md)
-
 !!!WARNING
     This page is still under construction
+
+Back to step-by-step guide for [Adding Support for New Grids](../adding-grid-support-step-by-step-guide.md)
diff --git a/docs/dev-guide/adding-grid-support/adding-grid-support-step-by-step-guide/generate-lnd-initial-condition.md b/docs/dev-guide/adding-grid-support/adding-grid-support-step-by-step-guide/generate-lnd-initial-condition.md
@@ -1,6 +1,6 @@
 # Generate Land Initial Condition (*finidat*)
 
-[Back to Adding Support for New Grids](../adding-grid-support-step-by-step-guide.md)
-
 !!!WARNING
     This page is still under construction
+
+Back to step-by-step guide for [Adding Support for New Grids](../adding-grid-support-step-by-step-guide.md)
diff --git a/docs/dev-guide/adding-grid-support/adding-grid-support-step-by-step-guide/generate-lnd-input-data.md b/docs/dev-guide/adding-grid-support/adding-grid-support-step-by-step-guide/generate-lnd-input-data.md
@@ -1,6 +1,6 @@
 # Generate Land Input Data (*fsurdat*)
 
-[Back to Adding Support for New Grids](../adding-grid-support-step-by-step-guide.md)
-
 !!!WARNING
     This page is still under construction
+
+Back to step-by-step guide for [Adding Support for New Grids](../adding-grid-support-step-by-step-guide.md)
diff --git a/docs/dev-guide/adding-grid-support/adding-grid-support-step-by-step-guide/generate-mapping-files.md b/docs/dev-guide/adding-grid-support/adding-grid-support-step-by-step-guide/generate-mapping-files.md
@@ -1,7 +1,5 @@
 # Generate mapping files
 
-[Back to Adding Support for New Grids](../adding-grid-support-step-by-step-guide.md)
-
 In order to pass data between different components at runtime, a set of mapping files between each component is generated offline.
 
 See [Recommended Mapping Procedures for E3SM Atmosphere Grids](https://acme-climate.atlassian.net/wiki/spaces/DOC/pages/178848194/Recommended+Mapping+Procedures+for+E3SM+Atmosphere+Grids) for a discussion of different remap algorithms and when to use each.
@@ -45,7 +43,7 @@ Chrysalis (LCRC):
 
 ## Create Mapping Files
 
-ncremap provides a convient 
+ncremap provides a convient
 
 We can use ncremap to generate ALL the needed mapping files between two grids, in this example the ne4 atmosphere and the oQU240 ocean grid (for the moment, we will put the land on the same grid as the atmosphere):
 
@@ -54,3 +52,5 @@ atm_grid_file=ne4.g
 ocn_grid_file=/global/cfs/cdirs/e3sm/inputdata/cpl/gridmaps/oQU240/ocean.QU.240km.scrip.151209.nc
 cd ${output_root} && ncremap -P mwf -s $ocn_grid_file -g $atm_grid_file --nm_src=oQU240 --nm_dst=ne4np4 --dt_sng=20181114
 ```
+
+Back to step-by-step guide for [Adding Support for New Grids](../adding-grid-support-step-by-step-guide.md)
diff --git a/docs/dev-guide/adding-grid-support/adding-grid-support-step-by-step-guide/generate-new-grid-file.md b/docs/dev-guide/adding-grid-support/adding-grid-support-step-by-step-guide/generate-new-grid-file.md
@@ -1,7 +1,5 @@
 # Generate a new Grid File
 
-[Back to Adding Support for New Grids](../adding-grid-support-step-by-step-guide.md)
-
 In order to generate mapping files between a new atmosphere grid and the surface component grids, we need a file that describes the new grid. [TempestRemap](https://github.com/ClimateGlobalChange/tempestremap) is our preferred tool for grid file generation because it can handle the spectral element grids used by the atmosphere dycore. The initial grid file will be saved in an "exodus" file with a `.g` extension (see [Types of Grid Description Files](../adding-grid-support-grid-types.md) for more info). TempestRemap can be installed via conda.
 
 ## Generating a Standard Exodus Grid File
@@ -36,3 +34,5 @@ GenerateCSMesh --alt --res ${NE} --file ${GRID_FILE_PATH}/ne${NE}.g
 GenerateVolumetricMesh --in ${GRID_FILE_PATH}/ne${NE}.g --out ${GRID_FILE_PATH}/ne${NE}pg2.g --np 2 --uniform
 ConvertMeshToSCRIP --in ${GRID_FILE_PATH}/ne${NE}pg2.g --out ${GRID_FILE_PATH}/ne${NE}pg2_scrip.nc
 ```
+
+Back to step-by-step guide for [Adding Support for New Grids](../adding-grid-support-step-by-step-guide.md)
diff --git a/docs/dev-guide/adding-grid-support/adding-grid-support-step-by-step-guide/generate-topo-file.md b/docs/dev-guide/adding-grid-support/adding-grid-support-step-by-step-guide/generate-topo-file.md
@@ -1,11 +1,9 @@
+# Generate a Topography File
+
 <!-- disable certain linter checks here for more readable nested markdown  -->
 <!-- markdownlint-disable  MD007 --> <!-- ul-indent -->
 <!-- markdownlint-disable  MD033 --> <!-- no-inline-html -->
 
-# Generate a Topography File
-
-[Back to Adding Support for New Grids](../adding-grid-support-step-by-step-guide.md)
-
 Topography needs to be interpolated from a high resolution dataset, and then doctored a bit to allow the model to run stably with the new topography. More information can be found in the following paper:  
 
 [P.H. Lauritzen, J.T. Bacmeister, P.F. Callaghan, M. Taylor,  NCAR_Topo (v1.0): NCAR global model topography generation software for unstructured grids, Geosci. Model Dev., 8, 3975-3986, 2015.](https://www.geosci-model-dev.net/8/3975/2015/)
@@ -617,3 +615,5 @@ To submit the slurm batch job use `sbatch <script>`
     #---------------------------------------------------------------------------
     ```
 </details>
+
+Back to step-by-step guide for [Adding Support for New Grids](../adding-grid-support-step-by-step-guide.md)
diff --git a/docs/dev-guide/adding-grid-support/index.md b/docs/dev-guide/adding-grid-support/index.md
@@ -3,7 +3,6 @@
 <!-- disable certain linter checks here to allow vertical alignment of links -->
 <!-- markdownlint-disable MD039 --> <!-- no-space-in-links -->
 
-<!-- - [Atmosphere Grid Overview                 ](/EAM/atmosphere-grid-overview.md) -->
-- [Atmosphere Grid Overview                 ](/EAM/tech-guide/atmosphere-grid-overview)
+- [Atmosphere Grid Overview                 ](../../EAM/tech-guide/atmosphere-grid-overview.md)
 - [Grid Description File Overview           ](adding-grid-support-grid-types.md)
-- [Step-by-Step Guide to Support a new Grid ](adding-grid-support-step-by-step-guide.md)
+- [Step-by-Step Guide to Support a New Grid ](adding-grid-support-step-by-step-guide.md)
diff --git a/tools/generate_domain_files/docs/index.md b/tools/generate_domain_files/docs/index.md
@@ -45,3 +45,5 @@ NE=30
 MAP_FILE=${MAP_FILE_ROOT}/map_oEC60to30v3_to_ne${NE}pg2_traave.20240313.nc
 python generate_domain_files_E3SM.py -m ${MAP_FILE} -o oEC60to30v3 -l ne${NE}pg2 --date-stamp=9999 --output-root=${OUTPUT_ROOT}
 ```
+
+Back to step-by-step guide for [Adding Support for New Grids](../dev-guide/adding-grid-support/adding-grid-support-step-by-step-guide.md)
