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<div class="section" id="fix-saed-vtk-command">
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<span id="index-0"></span><h1>fix saed/vtk command<a class="headerlink" href="#fix-saed-vtk-command" title="Permalink to this headline">¶</a></h1>
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<div class="section" id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>fix ID group-ID saed/vtk Nevery Nrepeat Nfreak c_ID attribute args ... keyword args ...
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</pre></div>
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</div>
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<ul class="simple">
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<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><em>fix</em></a> command</li>
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<li>saed/vtk = style name of this fix command</li>
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<li>Nevery = use input values every this many timesteps</li>
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<li>Nrepeat = # of times to use input values for calculating averages</li>
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<li>Nfreq = calculate averages every this many timesteps</li>
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<li>c_ID = saed compute ID</li>
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</ul>
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<pre class="literal-block">
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keyword = <em>file</em> or <em>ave</em> or <em>start</em> or <em>file</em> or <em>overwrite</em>:l
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<em>ave</em> args = <em>one</em> or <em>running</em> or <em>window M</em>
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one = output a new average value every Nfreq steps
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running = output cumulative average of all previous Nfreq steps
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window M = output average of M most recent Nfreq steps
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<em>start</em> args = Nstart
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Nstart = start averaging on this timestep
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<em>file</em> arg = filename
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filename = name of file to output time averages to
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<em>overwrite</em> arg = none = overwrite output file with only latest output
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</pre>
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</div>
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<div class="section" id="examples">
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<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5
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compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo
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</pre></div>
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</div>
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<div class="highlight-python"><div class="highlight"><pre>fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed
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fix saed/vtk 1 1 1 c_2 file Ni_000.saed
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</pre></div>
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</div>
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</div>
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<div class="section" id="description">
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<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
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<p>Time average computed intensities from <a class="reference external" href="compute_saed.txt">compute_saed</a> and
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write output to a file in the 3rd generation vtk image data format for
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visualization directly in parallelized visualization software packages
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like ParaView and VisIt. Note that if no time averaging is done, this
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command can be used as a convenient way to simply output diffraction
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intensities at a single snapshot.</p>
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<p>To produce output in the image data vtk format ghost data is added
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outside the <em>Kmax</em> range assigned in the compute saed. The ghost data is
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assigned a value of -1 and can be removed setting a minimum isovolume
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of 0 within the vizualiziton software. SAED images can be created by
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visualizing a spherical slice of the data that is centered at
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R_Ewald*[h k l]/norm([h k l]), where R_Ewald=1/lambda.</p>
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<p>The group specified within this command is ignored. However, note that
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specified values may represent calculations performed by saed computes
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which store their own “group” definitions.</p>
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<p>Fix saed/vtk is designed to work only with <a class="reference external" href="compute_saed.txt">compute_saed</a>
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values, e.g.</p>
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<div class="highlight-python"><div class="highlight"><pre>compute 3 top saed 0.0251 Al O
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fix saed/vtk 1 1 1 c_3 file Al2O3_001.saed
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</pre></div>
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</div>
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<hr class="docutils" />
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<p>The <em>Nevery</em>, <em>Nrepeat</em>, and <em>Nfreq</em> arguments specify on what
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timesteps the input values will be used in order to contribute to the
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average. The final averaged quantities are generated on timesteps
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that are a multiple of <em>Nfreq</em>. The average is over <em>Nrepeat</em>
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quantities, computed in the preceding portion of the simulation every
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<em>Nevery</em> timesteps. <em>Nfreq</em> must be a multiple of <em>Nevery</em> and
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<em>Nevery</em> must be non-zero even if <em>Nrepeat</em> is 1.
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Also, the timesteps
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contributing to the average value cannot overlap,
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i.e. Nrepeat*Nevery can not exceed Nfreq.</p>
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<p>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
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timesteps 90,92,94,96,98,100 will be used to compute the final average
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on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on
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timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time
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averaging is done; values are simply generated on timesteps
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100,200,etc.</p>
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<hr class="docutils" />
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<p>The output for fix ave/time/saed is a file writen with the 3rd generation
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vtk image data formatting. The filename assigned by the <em>file</em> keyword is
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appended with _N.vtk where N is an index (0,1,2...) to account for multiple
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diffraction intensity outputs.</p>
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<p>By default the header contains the following information (with example data):</p>
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<div class="highlight-python"><div class="highlight"><pre># vtk DataFile Version 3.0 c_SAED
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Image data set
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ASCII
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DATASET STRUCTURED_POINTS
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DIMENSIONS 337 219 209
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ASPECT_RATIO 0.00507953 0.00785161 0.00821458
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ORIGIN -0.853361 -0.855826 -0.854316
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POINT_DATA 15424827
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SCALARS intensity float
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LOOKUP_TABLE default
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...data
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</pre></div>
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</div>
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<p>In this example, kspace is sampled across a 337 x 219 x 209 point mesh
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where the mesh spacing is approximately 0.005, 0.007, and 0.008
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inv(length) units in the k1, k2, and k3 directions, respectively.
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The data is shifted by -0.85, -0.85, -0.85 inv(length) units so that
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the origin will lie at 0, 0, 0. Here, 15,424,827 kspace points are
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sampled in total.</p>
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<hr class="docutils" />
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<p>Additional optional keywords also affect the operation of this fix.</p>
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<p>The <em>ave</em> keyword determines how the values produced every <em>Nfreq</em>
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steps are averaged with values produced on previous steps that were
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multiples of <em>Nfreq</em>, before they are accessed by another output
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command or written to a file.</p>
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<p>If the <em>ave</em> setting is <em>one</em>, then the values produced on timesteps
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that are multiples of <em>Nfreq</em> are independent of each other; they are
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output as-is without further averaging.</p>
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<p>If the <em>ave</em> setting is <em>running</em>, then the values produced on
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timesteps that are multiples of <em>Nfreq</em> are summed and averaged in a
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cumulative sense before being output. Each output value is thus the
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average of the value produced on that timestep with all preceding
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values. This running average begins when the fix is defined; it can
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only be restarted by deleting the fix via the <a class="reference internal" href="unfix.html"><em>unfix</em></a>
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command, or by re-defining the fix by re-specifying it.</p>
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<p>If the <em>ave</em> setting is <em>window</em>, then the values produced on
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timesteps that are multiples of <em>Nfreq</em> are summed and averaged within
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a moving “window” of time, so that the last M values are used to
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produce the output. E.g. if M = 3 and Nfreq = 1000, then the output
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on step 10000 will be the average of the individual values on steps
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8000,9000,10000. Outputs on early steps will average over less than M
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values if they are not available.</p>
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<p>The <em>start</em> keyword specifies what timestep averaging will begin on.
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The default is step 0. Often input values can be 0.0 at time 0, so
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setting <em>start</em> to a larger value can avoid including a 0.0 in a
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running or windowed average.</p>
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<p>The <em>file</em> keyword allows a filename to be specified. Every <em>Nfreq</em>
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steps, the vector of saed intensity data is written to a new file using
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the 3rd generation vtk format. The base of each file is assigned by
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the <em>file</em> keyword and this string is appended with _N.vtk where N is
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an index (0,1,2...) to account for situations with multiple diffraction
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intensity outputs.</p>
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<p>The <em>overwrite</em> keyword will continuously overwrite the output file
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with the latest output, so that it only contains one timestep worth of
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output. This option can only be used with the <em>ave running</em> setting.</p>
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</div>
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<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
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<h2>Restart, fix_modify, output, run start/stop, minimize info<a class="headerlink" href="#restart-fix-modify-output-run-start-stop-minimize-info" title="Permalink to this headline">¶</a></h2>
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<p>No information about this fix is written to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>. None of the <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> options
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are relevant to this fix.</p>
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<p>No parameter of this fix can be used with the <em>start/stop</em> keywords of
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the <a class="reference internal" href="run.html"><em>run</em></a> command. This fix is not invoked during <a class="reference internal" href="minimize.html"><em>energy minimization</em></a>.</p>
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</div>
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<div class="section" id="restrictions">
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<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
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<p>The attributes for fix_saed_vtk must match the values assigned in the
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associated <a class="reference internal" href="compute_saed.html"><em>compute_saed</em></a> command.</p>
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</div>
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<div class="section" id="related-commands">
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<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
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<p><a class="reference internal" href="compute_saed.html"><em>compute_saed</em></a></p>
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</div>
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<div class="section" id="default">
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<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
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<p>The option defaults are ave = one, start = 0, no file output.</p>
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<hr class="docutils" />
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<p id="coleman"><strong>(Coleman)</strong> Coleman, Spearot, Capolungo, MSMSE, 21, 055020
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(2013).</p>
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