<glossary>
<title> Glossary</title>

<glossentry>
<glossterm>Branch</glossterm>
<glossdef>
<para>One of the three ways to initialize CESM runs. CESM runs can be
started as startup, hybrid or branch. Branch runs use the BRANCH
$RUN_TYPE and the restart files from a previous run.  See <link linkend="use_case_branch"><command>setting up a branch run.</command></link>  </para>
</glossdef>
</glossentry>

<glossentry>
<glossterm>case</glossterm>
<glossdef>
<para>
The name of your job. This can be any string.
</para>
</glossdef>
</glossentry>

<glossentry>
<glossterm>$CASE</glossterm>
<glossdef>
<para>
The case name. But when running &create_newcase;, it doubles as the case
directory path name where build and run scripts are placed. $CASE is
defined when you execute the &create_newcase command;, and set in
<filename>env_case.xml</filename>. Please see <link linkend="how_to_create_case">create a new case.</link>
</para>
</glossdef>
</glossentry>

<glossentry>
<glossterm>$CASEROOT</glossterm>
<glossdef>
<para>
$CASEROOT - the full pathname of the root directory for case scripts
(e.g. /user/$CASE). You define $CASEROOT when you execute the
&create_newcase;, and is set in
&env_case.xml;. $CASEROOT must be unique.
</para>
</glossdef>
</glossentry>

<glossentry>
<glossterm>component</glossterm>
<glossdef>
<para>
component - Each model can be run with one of several
components. Examples of components include CAM, CICE, CLM, and
POP. Component names will always be in all caps.
</para>
</glossdef>
</glossentry>

<glossentry>
<glossterm>component set (compset)</glossterm>
<glossdef>
<para>
Preset configuration settings for a model run. These are
defined in 
<ulink url="../cesm1.1/cesm/modelnl/compsets.html">component
sets</ulink>.
</para>
</glossdef>
</glossentry>

<glossentry>
<glossterm>$CCSMROOT</glossterm>
<glossdef>
<para>
The full pathname of the root directory of the CESM source code.
$CCSMROOT is defined when you execute the &create_newcase; command.
</para>
</glossdef>
</glossentry>

<glossentry>
<glossterm>$EXEROOT</glossterm>
<glossdef>
<para>
The case executable directory root. $EXEROOT is defined when you
execute the <command>configure</command> command, and is set in
<filename>env_build.xml</filename>.
</para>
</glossdef>
</glossentry>

<glossentry>
<glossterm>hybrid run</glossterm>
<glossdef>
<para>
A type of run. Hybrid runs use the HYBRID $RUN_TYPE and are
initialized as an initial run, but use restart datasets from a
previous CESM case. Please see <link linkend="use_case_branch"><command>setting up a hybrid run.</command></link>
</para>
</glossdef>
</glossentry>

<glossentry>
<glossterm>$MACH</glossterm>
<glossdef>
<para>
The supported machine name, and is defined in &env_case.xml;
when you run the configure command. Please see 
<ulink url="../modelnl/machines.html">hardware platforms</ulink>
for the list of supported machines.
</para>
</glossdef>
</glossentry>

<glossentry>
<glossterm>model</glossterm>
<glossdef>
<para>
CESM is comprised of five models (atm, ice, glc, lnd, ocn) and
the coupler, cpl. The word model is loosely used to mean any one of
the models or the coupler.
</para>
</glossdef>
</glossentry>

<glossentry>
<glossterm>model input data</glossterm>
<glossdef>
<para>
Refers to static input data for the model. Input data are
provided as part of the release via an inputdata area or data from a
server.
</para>
</glossdef>
</glossentry>

<glossentry>
<glossterm>release</glossterm>
<glossdef>
<para>
A supported version of CESM.
</para>
</glossdef>
</glossentry>

<glossentry>
<glossterm>restart</glossterm>
<glossdef>
<para>
Refers to a set of data files and pointer files that the
model generates and uses to restart a case.
</para>
</glossdef>
</glossentry>

<glossentry>
<glossterm>$RUNDIR</glossterm>
<glossdef>
<para>
The directory where the model is run, output data files are
created, and log files are found when the job fails. This is usually
$EXEROOT/run, and is set in env_build.xml by the configure command.
</para>
</glossdef>
</glossentry>

<glossentry>
<glossterm>tag</glossterm>
<glossdef>
<para>
A version of CESM. Note: A tag may not be supported.
</para>
</glossdef>
</glossentry>

</glossary>

