Update documentation including namelist tables (#322)

* update documentation including namelist tables * update version
CICE-Consortium · Jun 5, 2020 · 2b27a78 · 2b27a78
1 parent fdc7479
commit 2b27a78
Show file tree

Hide file tree

Showing 6 changed files with 432 additions and 316 deletions.
diff --git a/columnphysics/version.txt b/columnphysics/version.txt
@@ -1 +1 @@
-ICEPACK 1.2.1
+ICEPACK 1.2.2
diff --git a/doc/source/conf.py b/doc/source/conf.py
@@ -62,9 +62,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'1.2.1' 
+version = u'1.2.2' 
 # The full version, including alpha/beta/rc tags.
-version = u'1.2.1' 
+version = u'1.2.2' 
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/doc/source/developer_guide/dg_other.rst b/doc/source/developer_guide/dg_other.rst
@@ -0,0 +1,28 @@
+:tocdepth: 3
+
+.. _adding:
+
+Other things
+=============
+
+
+.. _debugger:
+
+Running with a Debugger
+-------------------------
+
+Availability and usage of interactive debuggers varies across machines.  Contact your 
+system administrator for additional information about what’s available on your system.  
+To run with an interactive debugger, the following general steps should be taken.
+
+- Setup a case
+- Modify the env file and Macros file to add appropriate modules and compiler/ linker flags
+- Build the model
+- Get interactive hardware resources as needed
+- Open a csh shell
+- Source the env.${machine} file
+- Source cice.settings
+- Change directories to the run directory
+- Manually launch the executable thru the debugger
+
+
diff --git a/doc/source/developer_guide/index.rst b/doc/source/developer_guide/index.rst
@@ -16,3 +16,4 @@ Developer Guide
    dg_driver.rst
    dg_scripts.rst
    dg_adding_tracers.rst
+   dg_other.rst
diff --git a/doc/source/master_list.bib b/doc/source/master_list.bib
@@ -366,6 +366,15 @@ @Article{Taylor04
   issue = {C12},
   url = {http://dx.doi.org/10.1029/2004JC002361}
 }
+@Article{Lavoie05,
+  author = "D. Lavoie and K. Denman and C. Michel",
+  title = "{Modeling ice algal growth and decline in a seasonally ice- covered region of the Arctic (Resolute Passage, Canadian Archipelago)}",
+  journal = JGRO,
+  year = {2005},
+  volume = {110},
+  issue = {C11},
+  url = {http://dx.doi.org/10.1029/2005JC002922}
+}
 @Book{Notz05
   author = "D. Notz",
   title = "Thermodynamic and Fluid-Dynamical Processes in Sea Ice",
@@ -462,6 +471,15 @@ @Article{Hunke09
   issue = {CB},
   url = {http://dx.doi.org/10.1029/2008JC005186}
 }
+@Article{Tagliabue09,
+  author = "A. Tagliabue and L. Bopp and O. Aumont",
+  title = "{Evaluating the importance of atmospheric and sedimentary iron sources to Southern Ocean biogeochemistry}",
+  journal = GRL,
+  year = {2009},
+  volume = {36},
+  issue = {13},
+  url = {http://dx.doi.org/10.1029/2009GL038914}
+}
 @Article{Flocco10
   author = "D. Flocco and D.L. Feltham and A.K. Turner",
   title = "{Incorporation of a physically based melt pond scheme into the sea ice component of a climate model}",