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<title>User’s Guide for the E3SM Atmosphere Model (EAM) — E3SM Atmosphere Model (EAM) documentation</title>
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<h1>User’s Guide for the E3SM Atmosphere Model (EAM)<a class="headerlink" href="#user-s-guide-for-the-e3sm-atmosphere-model-eam" title="Permalink to this headline">¶</a></h1>
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<p>Compiled by Kai Zhang with input from the EAM development team.</p>
<p>Contact: Kai Zhang (Pacific Northwest National Laboratory, <a class="reference external" href="mailto:kai.zhang%40pnnl.gov">kai<span>.</span>zhang<span>@</span>pnnl<span>.</span>gov</a>)</p>
<p>Documentation last edited : Jul 31, 2018</p>
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<h2>Source code of this documentation<a class="headerlink" href="#source-code-of-this-documentation" title="Permalink to this headline">¶</a></h2>
<p><a class="reference external" href="https://github.com/kaizhangpnl/kaizhangpnl.github.io">https://github.com/kaizhangpnl/kaizhangpnl.github.io</a></p>
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<h2>Documentation outline<a class="headerlink" href="#documentation-outline" title="Permalink to this headline">¶</a></h2>
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<li class="toctree-l1"><a class="reference internal" href="intro.html">Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="refer.html">Important references</a><ul>
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<li class="toctree-l1"><a class="reference internal" href="start.html">Getting started</a><ul>
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<li class="toctree-l1"><a class="reference internal" href="flow.html">Technical overview of EAM</a><ul>
<li class="toctree-l2"><a class="reference internal" href="flow.html#cime-in-e3sm">CIME in E3SM</a></li>
<li class="toctree-l2"><a class="reference internal" href="flow.html#flow-chart">Flow chart</a></li>
<li class="toctree-l2"><a class="reference internal" href="flow.html#spatial-resolution">Spatial resolution</a></li>
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<li class="toctree-l2"><a class="reference internal" href="flow.html#list-of-advective-tracers">List of advective tracers</a></li>
<li class="toctree-l2"><a class="reference internal" href="flow.html#list-of-tuning-parameters">List of tuning parameters</a></li>
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<li class="toctree-l1"><a class="reference internal" href="run.html">Compiling and running the model</a><ul>
<li class="toctree-l2"><a class="reference internal" href="run.html#run-script">Run script</a></li>
<li class="toctree-l2"><a class="reference internal" href="run.html#creating-a-new-case">Creating a new case</a></li>
<li class="toctree-l2"><a class="reference internal" href="run.html#setting-compsets">Setting compsets</a></li>
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<li class="toctree-l2"><a class="reference internal" href="run.html#single-column-model-scm-simulations">Single column model (SCM) simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="run.html#output-data-in-specified-regions">Output data in specified regions</a></li>
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<li class="toctree-l2"><a class="reference internal" href="run.html#specific-setup-for-constance-pnnl">Specific setup for Constance (PNNL)</a></li>
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<li class="toctree-l2"><a class="reference internal" href="output.html#storage-needed-for-a-one-year-simulation">Storage needed for a one-year simulation</a></li>
<li class="toctree-l2"><a class="reference internal" href="output.html#variables-in-the-default-h0-file">Variables in the default h0 file</a></li>
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<li class="toctree-l2"><a class="reference internal" href="output.html#variables-lists-for-special-diagnostics">Variables lists for special diagnostics</a></li>
<li class="toctree-l2"><a class="reference internal" href="output.html#netcdf-header-from-deck-simulations">NetCDF header from DECK simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="output.html#aerosol-mass-concentration-output">Aerosol mass concentration output</a></li>
<li class="toctree-l2"><a class="reference internal" href="output.html#e3sm-data-conversion-for-cmip6">E3SM data conversion for CMIP6</a></li>
<li class="toctree-l2"><a class="reference internal" href="output.html#reference">Reference</a></li>
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<li class="toctree-l1"><a class="reference internal" href="post.html">Post-processing</a><ul>
<li class="toctree-l2"><a class="reference internal" href="post.html#nco">NCO</a></li>
<li class="toctree-l2"><a class="reference internal" href="post.html#regridding-from-se-grid-to-lat-lon-grid">Regridding from SE grid to lat-lon grid</a></li>
<li class="toctree-l2"><a class="reference internal" href="post.html#making-climo-files">Making <cite>climo</cite> files</a></li>
<li class="toctree-l2"><a class="reference internal" href="post.html#bit-grooming">Bit-Grooming</a></li>
<li class="toctree-l2"><a class="reference internal" href="post.html#ncl-resources">NCL resources</a></li>
<li class="toctree-l2"><a class="reference internal" href="post.html#cdo-resources">CDO resources</a></li>
<li class="toctree-l2"><a class="reference internal" href="post.html#zstash-for-archiving">Zstash for archiving</a></li>
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<li class="toctree-l1"><a class="reference internal" href="diag.html">Diagnostics packages</a><ul>
<li class="toctree-l2"><a class="reference internal" href="diag.html#amwg-diagnostics">AMWG diagnostics</a></li>
<li class="toctree-l2"><a class="reference internal" href="diag.html#e3sm-diagnostics">E3SM diagnostics</a></li>
<li class="toctree-l2"><a class="reference internal" href="diag.html#arm-diagnostics">ARM diagnostics</a></li>
<li class="toctree-l2"><a class="reference internal" href="diag.html#e3sm-a-prime-diagnostics">E3SM A-prime diagnostics</a></li>
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<li class="toctree-l1"><a class="reference internal" href="advanced.html">Advanced configurations of EAM/E3SM</a><ul>
<li class="toctree-l2"><a class="reference internal" href="advanced.html#switching-on-nudging">Switching on nudging</a></li>
<li class="toctree-l2"><a class="reference internal" href="advanced.html#creating-nudging-files-from-a-baseline-simulation">Creating nudging files from a baseline simulation</a></li>
<li class="toctree-l2"><a class="reference internal" href="advanced.html#switching-on-the-satellite-aircraft-sampler">Switching on the satellite/aircraft sampler</a></li>
<li class="toctree-l2"><a class="reference internal" href="advanced.html#switching-on-off-individual-parameterizations">Switching on/off individual parameterizations</a></li>
<li class="toctree-l2"><a class="reference internal" href="advanced.html#switching-on-aerosol-forcing-diagnostics">Switching on aerosol forcing diagnostics</a></li>
<li class="toctree-l2"><a class="reference internal" href="advanced.html#changing-external-forcings">Changing external forcings</a></li>
<li class="toctree-l2"><a class="reference internal" href="advanced.html#regionally-refinement-model-rrm-simulations">Regionally-Refinement Model (RRM) simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="advanced.html#creating-ensembles">Creating ensembles</a></li>
<li class="toctree-l2"><a class="reference internal" href="advanced.html#creating-a-new-compset">Creating a new compset</a></li>
<li class="toctree-l2"><a class="reference internal" href="advanced.html#adding-a-new-parameterization">Adding a new parameterization</a></li>
<li class="toctree-l2"><a class="reference internal" href="advanced.html#creating-new-initial-condition-files">Creating new initial condition files</a></li>
<li class="toctree-l2"><a class="reference internal" href="advanced.html#creating-new-emission-files">Creating new emission files</a></li>
<li class="toctree-l2"><a class="reference internal" href="advanced.html#configuration-files">Configuration files</a></li>
<li class="toctree-l2"><a class="reference internal" href="advanced.html#reference">Reference</a></li>
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<li class="toctree-l1"><a class="reference internal" href="bug.html">Reporting a bug</a><ul>
<li class="toctree-l2"><a class="reference internal" href="bug.html#list-of-bugs-in-eam">List of bugs in EAM</a></li>
<li class="toctree-l2"><a class="reference internal" href="bug.html#how-to-report-a-bug">How to report a bug</a></li>
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<li class="toctree-l1"><a class="reference internal" href="freq.html">Frequently asked questions</a></li>
<li class="toctree-l1"><a class="reference internal" href="other.html">Other stuff</a><ul>
<li class="toctree-l2"><a class="reference internal" href="other.html#input-data">Input data</a></li>
<li class="toctree-l2"><a class="reference internal" href="other.html#mapping-files">Mapping files</a></li>
<li class="toctree-l2"><a class="reference internal" href="other.html#grids">Grids</a></li>
<li class="toctree-l2"><a class="reference internal" href="other.html#observational-data-for-analysis">Observational data for analysis</a></li>
<li class="toctree-l2"><a class="reference internal" href="other.html#fortran-performance-best-practices">Fortran Performance Best Practices</a></li>
<li class="toctree-l2"><a class="reference internal" href="other.html#list-of-important-simulations">List of important simulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="other.html#doe-machines">DOE machines</a></li>
<li class="toctree-l2"><a class="reference internal" href="other.html#how-to-acknowledge-the-e3sm-project">How to acknowledge the E3SM project</a></li>
<li class="toctree-l2"><a class="reference internal" href="other.html#how-to-cite-the-model">How to cite the model</a></li>
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<li class="toctree-l1"><a class="reference internal" href="contrb.html">Contributors</a></li>
<li class="toctree-l1"><a class="reference internal" href="acknow.html">Acknowledgement</a></li>
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