Icepack doc odds and ends (#161)

* Documentation

* Adding PDF

doc/source/conf.py

@@ -62,9 +62,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'0.0'
+version = u'1.0.0'
 # The full version, including alpha/beta/rc tags.
-release = u'0.0.01'
+release = u'1.0.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/source/user_guide/ug_running.rst

@@ -312,9 +312,9 @@ surface potential temperature and specific humidity.
     (:math:`kg/m^2/s`). Icepack's boundary layer calculation is used to derive sensible and latent heat fluxes. 
     In the namelist, set ``atm_data_type = ISPOL`` to use ISPOL atmospheric forcing.
 
-    Oceanic forcing fields are available from :cite:`JH14` and consist of sea surface temperature (K), 
-    sea surface salinity (ppt), boundary layer depth (m), ocean velocity in the x and y direction (m/s), 
-    and deep ocean heat flux (:math:`W/m^2`). 
+    Oceanic forcing fields are available from :cite:`JH14` derived from a POP 1-degree (gx1v3 simulation). 
+    These consist of sea surface temperature (K), sea surface salinity (ppt), boundary layer depth (m), 
+    ocean velocity in the x and y direction (m/s), and deep ocean heat flux (:math:`W/m^2`). 
     In the namelist, set ``ocn_data_type = ISPOL`` to use ISPOL oceanic forcing.
 
     Biogeochemical forcing fields are available from the World Ocean Atlas :cite:`WOA13`. The biogeochemical fields provided
@@ -323,15 +323,13 @@ surface potential temperature and specific humidity.
 
    c) **Surface HEat Budget of the Arctic (SHEBA)**
 
-    The opening and closing rates as derived from the SHEBA data have been used in Cecilia Bitz's column model previously. 
-    For more information go here:
-
-    https://atmos.washington.edu/~bitz/column_model/
-
-    https://atmos.washington.edu/~bitz/column_model/notes_forcing_data
+    The ice opening and closing rates (1/s) are derived from the SHEBA data and have been used 
+    previously in Cecilia Bitz's column model. For additional information see the following websites:
 
-    This forcing data includes opening and closing rates which is all that is used currently.
+    - https://atmos.washington.edu/~bitz/column_model/
+    - https://atmos.washington.edu/~bitz/column_model/notes_forcing_data
 
+    At present, only the opening and closing rates (1/s) are used from the forcing data. 
     In the namelist, set ``ocn_data_type = SHEBA`` to use this forcing in Icepack.
 
 3) **Climatological** - Maykut and Untersteiner 1971 :cite:`MU71`

doc/source/user_guide/ug_testing.rst

@@ -475,8 +475,8 @@ wait for all runs to be complete, and run the results and report_results scripts
 Test Plotting
 ----------------
 
-The Icepack scripts include a script (``timeseries.csh``) that will generate a timeseries figure of 
-the area fraction, average ice thickness (m), and average snow depth (m) from the diagnostic output file.  
+The Icepack scripts include a script (``timeseries.csh``) that will generate a timeseries 
+figure from the diagnostic output file.  
 When running a test suite, the ``timeseries.csh`` script is automatically copied to the suite directory.  
 If the ``timeseries.csh`` script is to be used on a test / case that is not a part of a test suite, 
 users will need to run the ``timeseries.csh`` script from the tests directory 
@@ -501,3 +501,25 @@ Run the timeseries script on the desired case. ::
 $ ./timeseries.csh /p/work1/turner/ICEPACK_RUNS/conrad_intel_smoke_col_1x1_diag1_run1year.t00/ice_diag.full_ITD
 
 The output figures are placed in the directory where the ice_diag file is located.
+
+This plotting script can be used to plot the following variables:
+
+  - area fraction
+  - average ice thickness (m)
+  - average snow depth (m)
+  - air temperature (C)
+  - shortwave radiation (:math:`W/m^2`)
+  - longwave radiation (:math:`W/m^2`)
+  - snowfall
+  - average salinity (ppt)
+  - surface temperature (C)
+  - outward longwave flux (:math:`W/m^2`)
+  - sensible heat flux (:math:`W/m^2`)
+  - latent heat flux (:math:`W/m^2`)
+  - top melt (m)
+  - bottom melt (m)
+  - lateral melt (m)
+  - new ice (m)
+  - congelation (m)
+  - snow-ice (m)
+  - initial energy change (:math:`W/m^2`)

doc/source/user_guide/ug_troubleshooting.rst

@@ -112,10 +112,10 @@ albedos will still be zero in the dark, polar winter hemisphere.
 Interpretation of general results
 ---------------------------------
 
-Icepack releases are ``functional releases'' in the sense that the code runs, 
+Icepack releases are "functional releases" in the sense that the code runs, 
 does not crash, passes various tests, and requires further work to establish 
 its scientific validity.  In general, users are not encouraged to use any of the
-CICE Consortium's model configurations to obtain ``scientific'' results.  The
+CICE Consortium's model configurations to obtain "scientific" results.  The
 test configurations are useful for model development, but sea ice models must
 be evaluated from a physical standpoint in a couple system because simplified
 configurations do not necessarily represent what is actually happening in the