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removed links from shell scripts CLM
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hkershaw-brown committed Mar 29, 2021
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116 changes: 58 additions & 58 deletions models/clm/readme.rst
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Expand Up @@ -28,64 +28,64 @@ scripts are not intended to be a 'black box'; you will have to read and understa
purpose. They are heavily commented -- in keeping with their origins as a set of notes. If you would like to offer
suggestions on how to improve those notes - please send them to dart@ucar.edu - we'd love to hear them.

+-------------------------------------------------------------------+------------------------------------------------------------+
| Script | Description |
+===================================================================+============================================================+
| `CESM1_1_1_setup_pmo <shell_scripts/CESM1_1_1_setup_pmo>`__ || runs a single instance of CLM to harvest synthetic |
| || observations for an OSSE or "perfect model" experiment. |
| || It requires a single CLM state from a previous experiment |
| || and uses a specified DATM stream for forcing. This |
| || parallels an assimilation experiment in that in the |
| || multi-instance setting each CLM instance may use (should |
| || use?) a unique DATM forcing. This script has almost |
| || nothing to do with DART. There is one (trivial) section |
| || that records some configuration information in the DART |
| || setup script, but that's about it. This script should |
| || initially be run without DART to ensure a working CESM |
| || environment. |
| || As of (V7195) 3 October 2014, this script demonstrates |
| || how to create 'vector'-based CLM history files (which |
| || requires a bugfix) and has an option to use a bugfixed |
| || snow grain-size code. |
| || http://bugs.cgd.ucar.edu/show_bug.cgi?id=1730 |
| || http://bugs.cgd.ucar.edu/show_bug.cgi?id=1934 |
+-------------------------------------------------------------------+------------------------------------------------------------+
| `CESM1_2_1_setup_pmo <shell_scripts/CESM1_2_1_setup_pmo>`__ || Is functionally identical to ``CESM1_1_1_setup_pmo`` but |
| || is appropriate for the the CESM 1_2_1 release, which |
| || supports both CLM 4 and CLM 4.5. |
+-------------------------------------------------------------------+------------------------------------------------------------+
| `CESM1_1_1_setup_hybrid <shell_scripts/CESM1_1_1_setup_hybrid>`__ || runs a multi-instance CLM experiment and can be used to |
| || perform a free run or 'open loop' experiment. By default, |
| || each CLM instance uses a unique DATM forcing. This script |
| || also has almost nothing to do with DART. There is one |
| || (trivial) section that records some configuration |
| || information in the DART setup script, but that's about |
| || it. This script should initially be run without DART to |
| || ensure a working CESM. |
| || As of (V7195) 3 October 2014, this script demonstrates |
| || how to create 'vector'-based CLM history files (which |
| || requires a bugfix) and has an option to use a bugfixed |
| || snow grain-size code. |
| || http://bugs.cgd.ucar.edu/show_bug.cgi?id=1730 |
| || http://bugs.cgd.ucar.edu/show_bug.cgi?id=1934 |
+-------------------------------------------------------------------+------------------------------------------------------------+
| `CESM1_2_1_setup_hybrid <shell_scripts/CESM1_2_1_setup_hybrid>`__ || Is functionally identical to ``CESM1_1_1_setup_hybrid`` |
| || but is appropriate for the the CESM 1_2_1 release, which |
| || supports both CLM 4 and CLM 4.5. |
+-------------------------------------------------------------------+------------------------------------------------------------+
| `CESM_DART_config <shell_scripts/CESM_DART_config>`__ || augments a CESM case with the bits and pieces required to |
| || run DART. When either ``CESM1_?_1_setup_pmo`` or |
| || ``CESM1_?_1_setup_hybrid`` gets executed, |
| || ``CESM_DART_config`` gets copied to the CESM "caseroot" |
| || directory. It is designed such that you can execute it at |
| || any time during a CESM experiment. When you do execute |
| || it, it will build the DART executables and copy them into |
| || the CESM "bld" directory, stage the run-time configurable |
| || ``input.nml`` in the "caseroot" directory, etc. and also |
| || *modifies* the CESM ``case.run`` script to call the DART |
| || scripts for assimilation or to harvest synthetic |
| || observations. |
+-------------------------------------------------------------------+------------------------------------------------------------+
+------------------------------------------+------------------------------------------------------------+
| Script | Description |
+==========================================+============================================================+
| ``shell_scripts/CESM1_1_1_setup_pmo`` || runs a single instance of CLM to harvest synthetic |
| || observations for an OSSE or "perfect model" experiment. |
| || It requires a single CLM state from a previous experiment |
| || and uses a specified DATM stream for forcing. This |
| || parallels an assimilation experiment in that in the |
| || multi-instance setting each CLM instance may use (should |
| || use?) a unique DATM forcing. This script has almost |
| || nothing to do with DART. There is one (trivial) section |
| || that records some configuration information in the DART |
| || setup script, but that's about it. This script should |
| || initially be run without DART to ensure a working CESM |
| || environment. |
| || As of (V7195) 3 October 2014, this script demonstrates |
| || how to create 'vector'-based CLM history files (which |
| || requires a bugfix) and has an option to use a bugfixed |
| || snow grain-size code. |
| || http://bugs.cgd.ucar.edu/show_bug.cgi?id=1730 |
| || http://bugs.cgd.ucar.edu/show_bug.cgi?id=1934 |
+------------------------------------------+------------------------------------------------------------+
| ``shell_scripts/CESM1_2_1_setup_pmo`` || Is functionally identical to ``CESM1_1_1_setup_pmo`` but |
| || is appropriate for the the CESM 1_2_1 release, which |
| || supports both CLM 4 and CLM 4.5. |
+------------------------------------------+------------------------------------------------------------+
| ``shell_scripts/CESM1_1_1_setup_hybrid`` || runs a multi-instance CLM experiment and can be used to |
| || perform a free run or 'open loop' experiment. By default, |
| || each CLM instance uses a unique DATM forcing. This script |
| || also has almost nothing to do with DART. There is one |
| || (trivial) section that records some configuration |
| || information in the DART setup script, but that's about |
| || it. This script should initially be run without DART to |
| || ensure a working CESM. |
| || As of (V7195) 3 October 2014, this script demonstrates |
| || how to create 'vector'-based CLM history files (which |
| || requires a bugfix) and has an option to use a bugfixed |
| || snow grain-size code. |
| || http://bugs.cgd.ucar.edu/show_bug.cgi?id=1730 |
| || http://bugs.cgd.ucar.edu/show_bug.cgi?id=1934 |
+------------------------------------------+------------------------------------------------------------+
| ``shell_scripts/CESM1_2_1_setup_hybrid`` || Is functionally identical to ``CESM1_1_1_setup_hybrid`` |
| || but is appropriate for the the CESM 1_2_1 release, which |
| || supports both CLM 4 and CLM 4.5. |
+------------------------------------------+------------------------------------------------------------+
| ``shell_scripts/CESM_DART_config`` || augments a CESM case with the bits and pieces required to |
| || run DART. When either ``CESM1_?_1_setup_pmo`` or |
| || ``CESM1_?_1_setup_hybrid`` gets executed, |
| || ``CESM_DART_config`` gets copied to the CESM "caseroot" |
| || directory. It is designed such that you can execute it at |
| || any time during a CESM experiment. When you do execute |
| || it, it will build the DART executables and copy them into |
| || the CESM "bld" directory, stage the run-time configurable |
| || ``input.nml`` in the "caseroot" directory, etc. and also |
| || *modifies* the CESM ``case.run`` script to call the DART |
| || scripts for assimilation or to harvest synthetic |
| || observations. |
+------------------------------------------+------------------------------------------------------------+

In addition to the script above, there are a couple scripts that will either perform an assimilation
(``assimilate.csh``) or harvest observations for a perfect model experiment
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