[WIP] Fixing broken documentation links

doc/source/lilac/specific-atm-models/wrf.rst

@@ -171,7 +171,7 @@ skip to section :numref:`wrf-set-ctsm-runtime-options`.
 
 Get WPS from this website::
 
-    https://www2.mmm.ucar.edu/wrf/users/download/wrf-regist_or_download.php
+    https://www2.mmm.ucar.edu/wrf/users/download/get_source.html
 
 New users must complete a registration form in this step.
 

doc/source/tech_note/Ecosystem/CLM50_Tech_Note_Ecosystem.rst

@@ -294,7 +294,7 @@ The current state of the atmosphere (:numref:`Table Atmospheric input to land mo
 
 :sup:`4`\ The nitrogen deposition rate is required by the biogeochemistry model when active and represents the total deposition of mineral nitrogen onto the land surface, combining deposition of NO\ :sub:`y` and NH\ :sub:`x`. The rate is supplied either as a time-invariant spatially-varying annual mean rate or time-varying for a transient simulation. Nitrogen deposition rates were calculated from the same CAM chemistry simulation that generated the aerosol deposition rates.
 
-:sup:`5`\ Climatological 3-hourly lightning frequency at :math:`\sim`\ 1.8° resolution is provided, which was calculated via bilinear interpolation from 1995-2011 NASA LIS/OTD grid product v2.2 (http://ghrc.msfc.nasa.gov) 2-hourly, 2.5° lightning frequency data. In future versions of the model, lightning data may be obtained directly from the atmosphere model.
+:sup:`5`\ Climatological 3-hourly lightning frequency at :math:`\sim`\ 1.8° resolution is provided, which was calculated via bilinear interpolation from 1995-2011 NASA LIS/OTD grid product v2.2 (https://cmr.earthdata.nasa.gov/search/concepts/C1995863244-GHRC_DAAC.html) 2-hourly, 2.5° lightning frequency data. In future versions of the model, lightning data may be obtained directly from the atmosphere model.
 
 Density of air (:math:`\rho _{atm}` ) (kg m\ :sup:`-3`) is also required but is calculated directly from :math:`\rho _{atm} =\frac{P_{atm} -0.378e_{atm} }{R_{da} T_{atm} }` where :math:`P_{atm}` is atmospheric pressure (Pa), :math:`e_{atm}` is atmospheric vapor pressure (Pa), :math:`R_{da}` is the gas constant for dry air (J kg\ :sup:`-1` K\ :sup:`-1`) (:numref:`Table Physical constants`), and :math:`T_{atm}` is the atmospheric temperature (K). The atmospheric vapor pressure :math:`e_{atm}` is derived from atmospheric specific humidity :math:`q_{atm}` (kg kg\ :sup:`-1`) as :math:`e_{atm} =\frac{q_{atm} P_{atm} }{0.622+0.378q_{atm} }`.
 

doc/source/tech_note/References/CLM50_Tech_Note_References.rst

@@ -549,7 +549,7 @@ Huang, M., and Liang, X. 2006. On the assessment of the impact of reducing param
 
 .. _Hugeliusetal2012:
 
-Hugelius, G., C. Tarnocai, G. Broll, J.G. Canadell, P. Kuhry, adn D.K. Swanson, 2012. The Northern Circumpolar Soil Carbon Database: spatially distributed datasets of soil coverage and soil carbon storage in the northern permafrost regions. Earth Syst. Sci. Data Discuss., 5, 707-733 (available online at (http://dev1.geo.su.se/bbcc/dev/ncscd/).
+Hugelius, G., C. Tarnocai, G. Broll, J.G. Canadell, P. Kuhry, adn D.K. Swanson, 2012. The Northern Circumpolar Soil Carbon Database: spatially distributed datasets of soil coverage and soil carbon storage in the northern permafrost regions. Earth Syst. Sci. Data Discuss., 5, 707-733 (available online at (https://essd.copernicus.org/articles/5/3/2013/essd-5-3-2013.html).
 
 .. _Huntetal1988:
 
@@ -1482,7 +1482,7 @@ Vionnet, V., E. Brun, S. Morin, A. Boone, S. Faroux, P. Le Moigne, E. Martin, an
 
 .. _Viovy2011:
 
-Viovy, N. 2011. CRUNCEP dataset. [Description available at http://dods.extra.cea.fr/data/p529viov/cruncep/readme.htm. Data available at http://dods.extra.cea.fr/store/p529viov/cruncep/V4\_1901\_2011/].
+Viovy, N. 2011. CRUNCEP dataset. [Description available at https://rda.ucar.edu/datasets/d314003/ Data available at https://rda.ucar.edu/datasets/d314003/dataaccess/].
 
 .. _VitousekHowarth1991:
 

doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst

@@ -6,7 +6,7 @@
  Customizing CLM's Configuration
 ********************************
 
-The section of the |cesmrelease| Quickstart `CESM Create a Case <https://escomp.github.io/cesm/release-cesm2/quickstart.html#create-a-case>`_ gives instructions on creating a case. Also see a similar section in the CIME User's Guide `CIME Create a case <http://esmci.github.io/cime/users_guide/create-a-case.html>`_. What is of interest here is how to customize your use of CLM for the case that you created.
+The section of the |cesmrelease| Quickstart `CESM Create a Case <https://escomp.github.io/CESM/release-cesm2/quickstart.html#create-a-case>`_ gives instructions on creating a case. Also see a similar section in the CIME User's Guide `CIME Create a case <https://esmci.github.io/cime/versions/master/html/users_guide/create-a-case.html>`_. What is of interest here is how to customize your use of CLM for the case that you created.
 
 For CLM when ``preview_namelist``, ``case.build``, or ``case.run`` are called there are two steps that take place:
 
@@ -503,7 +503,7 @@ Like other datasets, if you want to use a given initial condition file to be use
 Other noteworthy configuration items
 ------------------------------------
 
-For running "I" cases there are several other noteworthy configuration items that you may want to work with. Most of these involve settings for the DATM, but one ``CCSM_CO2_PPMV`` applies to all models. The list of DATM settings is `here <http://esmci.github.io/cime/data_models/data-atm.html>`_. If you are running a B, E, or F case that doesn't use the DATM obviously the DATM_* settings will not be used. All of the settings below are in your ``env_build.xml`` and ``env_run.xml`` files
+For running "I" cases there are several other noteworthy configuration items that you may want to work with. Most of these involve settings for the DATM, but one ``CCSM_CO2_PPMV`` applies to all models. The list of DATM settings is (**link currently broken**). If you are running a B, E, or F case that doesn't use the DATM obviously the DATM_* settings will not be used. All of the settings below are in your ``env_build.xml`` and ``env_run.xml`` files
 ::
 
    CCSM_CO2_PPMV

doc/source/users_guide/setting-up-and-running-a-case/customizing-the-datm-namelist.rst

@@ -11,7 +11,7 @@ When running "I" compsets with CLM you use the DATM model to give atmospheric fo
 1. **DATM Main Namelist and Stream Namlist gorup** (``datm_in``)
 2. **DATM stream files**
 
-The `Data Model Documentation <http://esmci.github.io/cime/data_models/data-atm.html>`_ gives the details of all the options for the data models and for DATM specifically. It goes into detail on all namelist items both for DATM and for DATM streams. So here we won't list ALL of the DATM namelist options, nor go into great details about stream files. But, we will talk about a few of the different options that are relevant for running with CLM. All of the options for changing the namelists or stream files is done by editing the ``user_nl_datm`` file.
+The Data Model Documentation (**link currently broken**) gives the details of all the options for the data models and for DATM specifically. It goes into detail on all namelist items both for DATM and for DATM streams. So here we won't list ALL of the DATM namelist options, nor go into great details about stream files. But, we will talk about a few of the different options that are relevant for running with CLM. All of the options for changing the namelists or stream files is done by editing the ``user_nl_datm`` file.
 
 Because, they aren't useful for work with CLM we will NOT discuss any of the options for the main DATM namelist. Use the DATM Users Guide at the link above to find details of that. For the streams namelist we will discuss three items:
 
@@ -56,7 +56,7 @@ CLMCRUNCEPv7 mode and it's DATM settings
 
 In ``CLMCRUNCEPv7`` mode the CRUNCEP dataset is used and all of it's data is on a 6-hourly interval. Like ``CLM_QIAN`` the dataset is divided into those three data streams: solar, precipitation, and everything else (temperature, pressure, humidity and wind). The time-stamps of the data were also adjusted so that they are the beginning of the interval for solar, and the middle for the other two. Because, of this the ``offset`` is set to zero, and the ``tintalgo`` is: ``coszen``, ``nearest``, and ``linear`` for the solar, precipitation and other data respectively. ``taxmode`` is set to ``cycle`` and ``mapalgo`` is set to ``bilinear`` so that the data is spatially interpolated from the input exact half degree grid to the grid the atmosphere model is being run at (to run at this same model resolution use the 360x720cru_360x720cru resolution)... note:: The "everything else" data stream (of temperature, pressure, humidity and wind) also includes the data for longwave downward forcing as well. Our simulations showed sensitivity to this field, so we backed off in using it, and let DATM calculate longwave down from the other fields.
 
-For more information on CRUNCEP forcing see `http://dods.extra.cea.fr/data/p529viov/cruncep/ <http://dods.extra.cea.fr/data/p529viov/cruncep/>`_.
+For more information on CRUNCEP forcing see `https://rda.ucar.edu/datasets/d314003/ <https://rda.ucar.edu/datasets/d314003/>`_.
 
 .. _clmcruncep-and-its-datm:
 

doc/source/users_guide/testing/testing.rst

@@ -14,7 +14,7 @@ Technically, you could use the customization we gave in :ref:`customizing_sectio
 CIME Testing scripts
 ====================
 
-We first introduce the test scripts that work for all CESM components. The CIME script ``create_test`` runs a specific type of test, at a given resolution, for a given compset using a given machine. See `CIME Chapter on Testing <http://esmci.github.io/cime/users_guide/testing.html>`_ for how to use it to run single tests as well as lists of tests. The standard testname for CLM is "aux_clm" for cheyenne with intel and gnu compilers as well as the CGD machine hobart for intel, nag, and pgi compilers. There's also a shorter test list called "clm_short". Also see the `CTSM Wiki on Testing <https://github.com/ESCOMP/ctsm/wiki/System-Testing-Guide>`_.
+We first introduce the test scripts that work for all CESM components. The CIME script ``create_test`` runs a specific type of test, at a given resolution, for a given compset using a given machine. See `CIME Chapter on Testing <https://esmci.github.io/cime/versions/master/html/users_guide/testing.html>`_ for how to use it to run single tests as well as lists of tests. The standard testname for CLM is "aux_clm" for cheyenne with intel and gnu compilers as well as the CGD machine hobart for intel, nag, and pgi compilers. There's also a shorter test list called "clm_short". Also see the `CTSM Wiki on Testing <https://github.com/ESCOMP/ctsm/wiki/System-Testing-Guide>`_.
 
 CTSM Fortran Unit Tests
 =======================

doc/source/users_guide/using-clm-tools/building-the-clm-tools.rst

@@ -20,5 +20,5 @@ The only CLM FORTRAN tool is mksurfdata_esmf which has it's own build system tha
 
 ``cprnc`` and ``gen_domain`` both use the CIME configure/build system rather than the CLM specific version described above.
 
-See `CIME documentation on adding grids <http://esmci.github.io/cime/users_guide/grids.html?highlight=gen_domain#adding-grids>`_ for more information on adding grids, creating mapping files, and running ``gen_domain``. Also see the CIME file: ``$CTSMROOT/tools/mapping/gen_domain_files/INSTALL`` for how to build ``gen_domain``.
+See `CIME documentation on adding grids <https://esmci.github.io/cime/versions/master/html/users_guide/grids.html>`_ for more information on adding grids, creating mapping files, and running ``gen_domain``. Also see the CIME file: ``$CTSMROOT/tools/mapping/gen_domain_files/INSTALL`` for how to build ``gen_domain``.