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<span class="target" id="advanced"></span><div class="section" id="advanced-configurations-of-eam-e3sm">
<h1>Advanced configurations of EAM/E3SM<a class="headerlink" href="#advanced-configurations-of-eam-e3sm" title="Permalink to this headline">¶</a></h1>
<p><a class="reference external" href="https://github.com/kaizhangpnl/kaizhangpnl.github.io/blob/master/source/advanced.rst">Github</a>
<a class="reference external" href="https://kaizhangpnl.github.io/advanced.html">Spinx</a></p>
<div class="section" id="switching-on-nudging">
<h2>Switching on nudging<a class="headerlink" href="#switching-on-nudging" title="Permalink to this headline">¶</a></h2>
<p>An introduction of nudging can be found in
<a class="reference external" href="https://www.atmos-chem-phys.net/14/8631/2014/">Zhang et al. (2014)</a> and references therein.</p>
<p>The following variables need to be modified to activate nudging.
The example shown below switches on nudging for horizontal winds</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>cat <<EOF >> user_nl_cam
!.......................................................
! nudging
!.......................................................
Nudge_Model = .True.
Nudge_Path = '${INPUT_NUDGING}/ne30/'
Nudge_File_Template = 'ACME.cam.h2.%y-%m-%d-%s.nc'
Nudge_Times_Per_Day = 4 !! nudging input data frequency
Model_Times_Per_Day = 48 !! should not be larger than 48 if dtime = 1800s
Nudge_Uprof = 1
Nudge_Ucoef = 1.
Nudge_Vprof = 1
Nudge_Vcoef = 1.
Nudge_Tprof = 0
Nudge_Tcoef = 0.
Nudge_Qprof = 0
Nudge_Qcoef = 0.
Nudge_PSprof = 0
Nudge_PScoef = 0.
Nudge_Beg_Year = 0000
Nudge_Beg_Month = 1
Nudge_Beg_Day = 1
Nudge_End_Year = 9999
Nudge_End_Month = 1
Nudge_End_Day = 1
EOF
</pre></div>
</div>
<p>This setup will nudge the model towards a baseline simulation. The nudging data were
created from the baseline simulation by archiving the 6-hourly meteorological fields.
Only the horizontal winds are nudged, with a relaxation time scale of 6h. The
nudging is applied at every grid box.
More detailed information on how to setup a nudged simulation can be found in the
source code <a class="reference external" href="https://github.com/E3SM-Project/E3SM/blob/master/components/cam/src/physics/cam/nudging.F90">nudging.F90</a>.</p>
<p>Note that the resulted nudging file name should not be longer than 80 characters.</p>
</div>
<div class="section" id="creating-nudging-files-from-a-baseline-simulation">
<h2>Creating nudging files from a baseline simulation<a class="headerlink" href="#creating-nudging-files-from-a-baseline-simulation" title="Permalink to this headline">¶</a></h2>
<p>To nudge the model towards a baseline model simulation (e.g. E3SMv1), you will need to
run the reference model first and output U,V,T,Q,PS 6-hourly:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>cat <<EOF >> user_nl_cam
nhtfrq = 0,-6
mfilt = 1,1
fincl2 = ‘PS’,’U,’V’,’T’,’Q’,
avgflag_pertape(2) = 'I'
EOF
</pre></div>
</div>
</div>
<div class="section" id="switching-on-the-satellite-aircraft-sampler">
<h2>Switching on the satellite/aircraft sampler<a class="headerlink" href="#switching-on-the-satellite-aircraft-sampler" title="Permalink to this headline">¶</a></h2>
<p>The following example shows how to sample data satellite/aircraft tracks. It will sample
the column data at each time slice defined in the profile-input file:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">cat</span> <span class="o"><<</span><span class="n">EOF</span> <span class="o">>></span> <span class="n">user_nl_cam</span>
<span class="n">sathist_fincl</span> <span class="o">=</span> <span class="s1">'T'</span><span class="p">,</span> <span class="s1">'Q'</span><span class="p">,</span> <span class="s1">'LWC'</span>
<span class="n">sathist_track_infile</span> <span class="o">=</span> <span class="s2">"profile_mpace.nc'</span>
<span class="n">sathist_mfilt</span> <span class="o">=</span> <span class="mi">47398</span>
<span class="n">sathist_hfilename_spec</span> <span class="o">=</span> <span class="s1">'</span><span class="si">%c</span><span class="s1">.e3sm.sat.%y-%m-</span><span class="si">%d</span><span class="s1">-</span><span class="si">%s</span><span class="s1">.nc'</span>
<span class="n">EOF</span>
</pre></div>
</div>
<p>The profile-input file should have a data structure shown below:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="nb">int</span> <span class="n">time</span><span class="p">(</span><span class="n">profs</span><span class="p">)</span> <span class="p">;</span>
<span class="n">time</span><span class="p">:</span><span class="n">long_name</span> <span class="o">=</span> <span class="s2">"time of day"</span> <span class="p">;</span>
<span class="n">time</span><span class="p">:</span><span class="n">units</span> <span class="o">=</span> <span class="s2">"s"</span> <span class="p">;</span>
<span class="nb">int</span> <span class="n">date</span><span class="p">(</span><span class="n">profs</span><span class="p">)</span> <span class="p">;</span>
<span class="n">date</span><span class="p">:</span><span class="n">long_name</span> <span class="o">=</span> <span class="s2">"date[yyyymmdd]"</span> <span class="p">;</span>
<span class="n">date</span><span class="p">:</span><span class="n">units</span> <span class="o">=</span> <span class="s2">"yyyymmdd"</span> <span class="p">;</span>
<span class="nb">float</span> <span class="n">lat</span><span class="p">(</span><span class="n">profs</span><span class="p">)</span> <span class="p">;</span>
<span class="n">lat</span><span class="p">:</span><span class="n">long_name</span> <span class="o">=</span> <span class="s2">"latitude"</span> <span class="p">;</span>
<span class="n">lat</span><span class="p">:</span><span class="n">units</span> <span class="o">=</span> <span class="s2">"degrees"</span> <span class="p">;</span>
<span class="nb">float</span> <span class="n">lon</span><span class="p">(</span><span class="n">profs</span><span class="p">)</span> <span class="p">;</span>
<span class="n">lon</span><span class="p">:</span><span class="n">long_name</span> <span class="o">=</span> <span class="s2">"longitude"</span> <span class="p">;</span>
<span class="n">lon</span><span class="p">:</span><span class="n">units</span> <span class="o">=</span> <span class="s2">"degrees"</span> <span class="p">;</span>
</pre></div>
</div>
</div>
<div class="section" id="switching-on-off-individual-parameterizations">
<h2>Switching on/off individual parameterizations<a class="headerlink" href="#switching-on-off-individual-parameterizations" title="Permalink to this headline">¶</a></h2>
<p>There is a set of switches that can be used to turn on/off certain processes:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>l_tracer_aero = .true. !! aerosol related processes
l_vdiff = .true. !! vertical diffusion
l_rayleigh = .true. !! rayleigh friction
l_gw_drag = .true. !! gravitity wave drag
l_ac_energy_chk = .true. !! energy conservation check
l_bc_energy_fix = .true. !! energy conservation fix
l_dry_adj = .true. !! dry adjustment
l_st_mac = .true. !! marcophysics
l_st_mic = .true. !! microphysics
l_rad = .true. !! radiation
</pre></div>
</div>
<p>See comments in <a class="reference external" href="https://github.com/E3SM-Project/E3SM/blob/master/components/cam/src/physics/cam/physpkg.F90">physpkg.F90</a>.</p>
</div>
<div class="section" id="switching-on-aerosol-forcing-diagnostics">
<h2>Switching on aerosol forcing diagnostics<a class="headerlink" href="#switching-on-aerosol-forcing-diagnostics" title="Permalink to this headline">¶</a></h2>
<p>Namelist setup</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">cat</span> <span class="o"><<</span><span class="n">EOF</span> <span class="o">>></span> <span class="n">user_nl_cam</span>
<span class="n">rad_diag_1</span> <span class="o">=</span> <span class="s1">'A:Q:H2O'</span><span class="p">,</span> <span class="s1">'N:O2:O2'</span><span class="p">,</span> <span class="s1">'N:CO2:CO2'</span><span class="p">,</span> <span class="s1">'A:O3:O3'</span><span class="p">,</span> <span class="s1">'N:N2O:N2O'</span><span class="p">,</span> <span class="s1">'N:CH4:CH4'</span><span class="p">,</span> <span class="s1">'N:CFC11:CFC11'</span><span class="p">,</span> <span class="s1">'N:CFC12:CFC12'</span><span class="p">,</span>
<span class="n">EOF</span>
</pre></div>
</div>
<p>Then the radiative flux calculated without aerosols are diagnosed
(with “_d1” appended to the original radiative flux name, e.g. “FSNT_d1”).</p>
<p>The detailed diagnostic method can be found in <a class="reference external" href="https://www.atmos-chem-phys.net/13/9971/2013/">Ghan (2013)</a>.</p>
<p>Some information about the AeroCom “Indirect forcing experiment” can be found <a class="reference external" href="https://wiki.met.no/aerocom/indirect">here</a>.</p>
</div>
<div class="section" id="changing-external-forcings">
<h2>Changing external forcings<a class="headerlink" href="#changing-external-forcings" title="Permalink to this headline">¶</a></h2>
<p>The following changes need to be made after executing “create_newcase”.</p>
<ul>
<li><p class="first">Changing SST, e.g.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">./</span><span class="n">xmlchange</span> <span class="o">-</span><span class="n">file</span> <span class="n">env_run</span><span class="o">.</span><span class="n">xml</span> <span class="o">-</span><span class="nb">id</span> <span class="n">SSTICE_DATA_FILENAME</span> <span class="o">-</span><span class="n">val</span> <span class="s1">'$DIN_LOC_ROOT/atm/cam/sst/sst_HadOIBl_bc_1x1_clim_pi_c101029.nc'</span>
<span class="o">./</span><span class="n">xmlchange</span> <span class="o">-</span><span class="n">file</span> <span class="n">env_run</span><span class="o">.</span><span class="n">xml</span> <span class="o">-</span><span class="nb">id</span> <span class="n">SSTICE_DATA_FILENAME</span> <span class="o">-</span><span class="n">val</span> <span class="s1">'$DIN_LOC_ROOT/atm/cam/sst/sst_HadOIBl_bc_1x1_clim_pi_plus4K.nc'</span>
</pre></div>
</div>
</li>
<li><p class="first">Changing aerosol emissions, e.g.</p>
</li>
</ul>
</div>
<div class="section" id="regionally-refinement-model-rrm-simulations">
<h2>Regionally-Refinement Model (RRM) simulations<a class="headerlink" href="#regionally-refinement-model-rrm-simulations" title="Permalink to this headline">¶</a></h2>
<p>RRM can be configured by specifying the resolution (e.g. “conusx4v1_conusx4v1”)</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>./create_newcase -case $MYCASE -project $MYPROJECT -compset FC5AV1C-04P2 -res conusx4v1_conusx4v1 -mach $MYMACH
</pre></div>
</div>
<p>Some resources are available internally within E3SM:</p>
<ul class="simple">
<li><a class="reference external" href="https://acme-climate.atlassian.net/wiki/spaces/ATM/pages/11010268/How+to+run+the+regionally+refined+model+RRM">How to run RRM</a></li>
<li><a class="reference external" href="https://acme-climate.atlassian.net/wiki/spaces/ATM/pages/27951986/Regridding+RRM+simulations">Regridding RRM simulations</a></li>
<li><a class="reference external" href="https://acme-climate.atlassian.net/wiki/spaces/Docs/pages/20153276/How+to+perform+nudging+simulations+with+the+regional+refined+model+RRM">How to perform nudged simulations with RRM</a></li>
</ul>
</div>
<div class="section" id="creating-ensembles">
<h2>Creating ensembles<a class="headerlink" href="#creating-ensembles" title="Permalink to this headline">¶</a></h2>
<p>In E3SM/EAM, ensembles can be created by perturbing the temperature field in the initial condition
with a specified magnitude (e.g. <code class="docutils literal notranslate"><span class="pre">1.e-14</span></code> K). The implementation will call the random number
generator (L’Ecuyer, 1996) and create random samples for each grid point:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">cat</span> <span class="o"><<</span><span class="n">EOF</span> <span class="o">>></span> <span class="n">user_nl_cam</span>
<span class="n">pertlim</span> <span class="o">=</span> <span class="mf">1.e-14</span>
<span class="n">new_random</span> <span class="o">=</span> <span class="o">.</span><span class="n">true</span><span class="o">.</span>
<span class="n">seed_clock</span> <span class="o">=</span> <span class="o">.</span><span class="n">false</span><span class="o">.</span>
<span class="n">seed_custom</span> <span class="o">=</span> <span class="mi">1</span>
<span class="n">EOF</span>
</pre></div>
</div>
<p>The user can change <code class="docutils literal notranslate"><span class="pre">pertlim</span></code> to change the perturbation magnitude and <code class="docutils literal notranslate"><span class="pre">seed_custom</span></code>
to change the seed to the random number generator.</p>
</div>
<div class="section" id="creating-a-new-compset">
<h2>Creating a new compset<a class="headerlink" href="#creating-a-new-compset" title="Permalink to this headline">¶</a></h2>
<p>Following files need to be changed in order to create a new compset:</p>
<ul class="simple">
<li><a class="reference external" href="https://github.com/E3SM-Project/E3SM/blob/master/components/cam/cime_config/config_compsets.xml">components/cam/cime_config/config_compsets.xml</a></li>
<li><a class="reference external" href="https://github.com/E3SM-Project/E3SM/blob/master/components/cam/cime_config/config_component.xml">components/cam/cime_config/config_component.xml</a></li>
<li><a class="reference external" href="https://github.com/E3SM-Project/E3SM/blob/master/cime/src/drivers/mct/cime_config/config_component_e3sm.xml">cime/src/drivers/mct/cime_config/config_component_e3sm.xml</a></li>
<li><a class="reference external" href="https://github.com/E3SM-Project/E3SM/blob/master/cime/config/e3sm/allactive/config_compsets.xml">cime/config/e3sm/allactive/config_compsets.xml</a></li>
<li><a class="reference external" href="https://github.com/E3SM-Project/E3SM/blob/master/components/cam/bld/build-namelist">components/cam/bld/build-namelist</a></li>
</ul>
<p>The namelist configuration files need to be changed too, e.g. :</p>
<ul class="simple">
<li><a class="reference external" href="https://github.com/E3SM-Project/E3SM/blob/master/components/cam/bld/namelist_files/use_cases/1850_cam5_av1c-04p2.xml">components/cam/bld/namelist_files/use_cases/1850_cam5_av1c-04p2.xml</a></li>
<li><a class="reference external" href="https://github.com/E3SM-Project/E3SM/blob/master/components/cam/bld/namelist_files/namelist_defaults_cam.xml">components/cam/bld/namelist_files/namelist_defaults_cam.xml</a></li>
</ul>
<p>A detailed guide based on an older version of E3SM can be found
<a class="reference external" href="https://acme-climate.atlassian.net/wiki/spaces/ATM/pages/46891102/How+to+create+a+new+compset">here</a>.
Note that some information on that page is obsolete.</p>
</div>
<div class="section" id="adding-a-new-parameterization">
<h2>Adding a new parameterization<a class="headerlink" href="#adding-a-new-parameterization" title="Permalink to this headline">¶</a></h2>
<p>Under construction</p>
</div>
<div class="section" id="creating-new-initial-condition-files">
<h2>Creating new initial condition files<a class="headerlink" href="#creating-new-initial-condition-files" title="Permalink to this headline">¶</a></h2>
<p>Under construction</p>
</div>
<div class="section" id="creating-new-emission-files">
<h2>Creating new emission files<a class="headerlink" href="#creating-new-emission-files" title="Permalink to this headline">¶</a></h2>
<p>Under construction</p>
</div>
<div class="section" id="configuration-files">
<h2>Configuration files<a class="headerlink" href="#configuration-files" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
<li><a class="reference external" href="https://github.com/E3SM-Project/E3SM/blob/master/cime/config/e3sm/machines/config_batch.xml">cime/config/e3sm/machines/config_batch.xml</a></li>
<li><a class="reference external" href="https://github.com/E3SM-Project/E3SM/blob/master/cime/config/e3sm/machines/config_compilers.xml">cime/config/e3sm/machines/config_compilers.xml</a></li>
<li><a class="reference external" href="https://github.com/E3SM-Project/E3SM/blob/master/cime/config/e3sm/allactive/config_compsets.xml">cime/config/e3sm/allactive/config_compsets.xml</a></li>
<li><a class="reference external" href="https://github.com/E3SM-Project/E3SM/blob/master/components/cam/cime_config/config_compsets.xml">components/cam/cime_config/config_compsets.xml</a></li>
<li><a class="reference external" href="https://github.com/E3SM-Project/E3SM/blob/master/cime/config/e3sm/config_grids.xml">cime/config/e3sm/config_grids.xml</a></li>
<li><a class="reference external" href="https://github.com/E3SM-Project/E3SM/blob/master/cime/config/e3sm/machines/config_machines.xml">cime/config/e3sm/machines/config_machines.xml</a></li>
<li><a class="reference external" href="https://github.com/E3SM-Project/E3SM/blob/master/cime/config/e3sm/allactive/config_pesall.xml">cime/config/e3sm/allactive/config_pesall.xml</a></li>
<li><a class="reference external" href="https://github.com/E3SM-Project/E3SM/blob/master/cime/config/e3sm/machines/config_pio.xml">cime/config/e3sm/machines/config_pio.xml</a></li>
<li><a class="reference external" href="https://github.com/E3SM-Project/E3SM/blob/master/cime/config/e3sm/machines/template.case.run">cime/config/e3sm/machines/template.case.run</a></li>
</ul>
<p>To find out more, search those items in <a class="reference external" href="http://esmci.github.io/cime/index.html">http://esmci.github.io/cime/index.html</a></p>
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<div class="section" id="reference">
<h2>Reference<a class="headerlink" href="#reference" title="Permalink to this headline">¶</a></h2>
<p>Documentation from <a class="reference external" href="http://www.cesm.ucar.edu/models/cesm1.2/cam/docs/ug5_3/">CAM5.3</a>.</p>
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<ul>
<li><a class="reference internal" href="#">Advanced configurations of EAM/E3SM</a><ul>
<li><a class="reference internal" href="#switching-on-nudging">Switching on nudging</a></li>
<li><a class="reference internal" href="#creating-nudging-files-from-a-baseline-simulation">Creating nudging files from a baseline simulation</a></li>
<li><a class="reference internal" href="#switching-on-the-satellite-aircraft-sampler">Switching on the satellite/aircraft sampler</a></li>
<li><a class="reference internal" href="#switching-on-off-individual-parameterizations">Switching on/off individual parameterizations</a></li>
<li><a class="reference internal" href="#switching-on-aerosol-forcing-diagnostics">Switching on aerosol forcing diagnostics</a></li>
<li><a class="reference internal" href="#changing-external-forcings">Changing external forcings</a></li>
<li><a class="reference internal" href="#regionally-refinement-model-rrm-simulations">Regionally-Refinement Model (RRM) simulations</a></li>
<li><a class="reference internal" href="#creating-ensembles">Creating ensembles</a></li>
<li><a class="reference internal" href="#creating-a-new-compset">Creating a new compset</a></li>
<li><a class="reference internal" href="#adding-a-new-parameterization">Adding a new parameterization</a></li>
<li><a class="reference internal" href="#creating-new-initial-condition-files">Creating new initial condition files</a></li>
<li><a class="reference internal" href="#creating-new-emission-files">Creating new emission files</a></li>
<li><a class="reference internal" href="#configuration-files">Configuration files</a></li>
<li><a class="reference internal" href="#reference">Reference</a></li>
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